Starting phenix.real_space_refine on Sun Jun 22 10:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g71_29793/06_2025/8g71_29793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g71_29793/06_2025/8g71_29793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g71_29793/06_2025/8g71_29793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g71_29793/06_2025/8g71_29793.map" model { file = "/net/cci-nas-00/data/ceres_data/8g71_29793/06_2025/8g71_29793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g71_29793/06_2025/8g71_29793.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 114 5.16 5 C 16386 2.51 5 N 4239 2.21 5 O 5022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25761 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.30, per 1000 atoms: 0.67 Number of scatterers: 25761 At special positions: 0 Unit cell: (151.84, 161.33, 195.64, 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 114 16.00 O 5022 8.00 N 4239 7.00 C 16386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 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-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 234 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B1074 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN D 717 " " NAG L 1 " - " ASN D 801 " " NAG M 1 " - " ASN D1098 " " NAG N 1 " - " ASN D1134 " Time building additional restraints: 7.22 Conformation dependent library (CDL) restraints added in 3.5 seconds 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 25.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.143A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.035A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.071A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.650A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.775A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.144A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.169A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.809A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.115A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.649A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.616A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.625A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.581A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.638A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.818A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.994A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.727A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.893A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.045A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 370 removed outlier: 4.096A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 3.941A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.936A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 411 " --> pdb=" O ARG D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.605A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.782A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 919 removed outlier: 3.961A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.733A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.498A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.087A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.379A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.932A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 135 current: chain 'A' and resid 153 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.848A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 removed outlier: 7.190A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.741A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.214A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.691A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (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 715 removed outlier: 3.830A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.108A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.271A 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 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.224A 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: 7.865A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.989A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.639A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 through 135 current: chain 'B' and resid 154 through 157 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.227A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.678A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.481A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.032A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.080A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.920A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.259A 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: 4.331A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.278A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.970A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 68 through 70 removed outlier: 3.683A pdb=" N HIS D 69 " --> pdb=" O ARG D 78 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 85 current: chain 'D' and resid 116 through 121 removed outlier: 7.974A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.312A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AE3, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.925A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.188A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'D' and resid 718 through 728 removed outlier: 7.095A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 1094 through 1097 990 hydrogen bonds defined for protein. 2724 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: 12.20 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8200 1.34 - 1.46: 6462 1.46 - 1.59: 11549 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 26355 Sorted by residual: bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL B 401 " pdb=" CA VAL B 401 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.95e+00 bond pdb=" N VAL D 227 " pdb=" CA VAL D 227 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.22e-02 6.72e+03 8.17e+00 bond pdb=" N PHE B 400 " pdb=" CA PHE B 400 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.20e-02 6.94e+03 7.97e+00 bond pdb=" N SER B 399 " pdb=" CA SER B 399 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.23e-02 6.61e+03 7.68e+00 ... (remaining 26350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 35028 1.87 - 3.74: 775 3.74 - 5.61: 61 5.61 - 7.48: 13 7.48 - 9.35: 8 Bond angle restraints: 35885 Sorted by residual: angle pdb=" C ASN D 61 " pdb=" CA ASN D 61 " pdb=" CB ASN D 61 " ideal model delta sigma weight residual 109.75 116.56 -6.81 1.65e+00 3.67e-01 1.70e+01 angle pdb=" CA LYS A 187 " pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " pdb=" CD LYS A 187 " ideal model delta sigma weight residual 111.30 119.75 -8.45 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CA VAL D 382 " pdb=" C VAL D 382 " pdb=" O VAL D 382 " ideal model delta sigma weight residual 121.64 118.23 3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" CA GLU D 132 " pdb=" C GLU D 132 " pdb=" O GLU D 132 " ideal model delta sigma weight residual 122.36 118.23 4.13 1.21e+00 6.83e-01 1.17e+01 ... (remaining 35880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 14406 18.04 - 36.07: 1413 36.07 - 54.11: 343 54.11 - 72.15: 89 72.15 - 90.18: 40 Dihedral angle restraints: 16291 sinusoidal: 6934 harmonic: 9357 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 164.39 -71.39 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS D 336 " pdb=" SG CYS D 336 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -37.24 -48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -39.06 -46.94 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 16288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3925 0.098 - 0.196: 261 0.196 - 0.294: 2 0.294 - 0.391: 0 0.391 - 0.489: 1 Chirality restraints: 4189 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE D 128 " pdb=" N ILE D 128 " pdb=" C ILE D 128 " pdb=" CB ILE D 128 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 4186 not shown) Planarity restraints: 4637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 353 " -0.033 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 353 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 353 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 353 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 353 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 353 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 353 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 353 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 353 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 353 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 588 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 589 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 61 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASN D 61 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN D 61 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL D 62 " -0.012 2.00e-02 2.50e+03 ... (remaining 4634 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 203 2.62 - 3.19: 22188 3.19 - 3.76: 39503 3.76 - 4.33: 56006 4.33 - 4.90: 90094 Nonbonded interactions: 207994 Sorted by model distance: nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.055 3.040 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.073 3.040 nonbonded pdb=" OG SER D 735 " pdb=" OG1 THR D 859 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.183 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.186 3.040 ... (remaining 207989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1307)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1307)) } ncs_group { reference = chain 'C' 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' } 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: 6.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 64.370 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.003 0.042 26439 Z= 0.186 Angle : 0.658 13.929 36098 Z= 0.348 Chirality : 0.047 0.489 4189 Planarity : 0.004 0.071 4603 Dihedral : 15.865 90.184 10160 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.27 % Allowed : 18.88 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3187 helix: 1.49 (0.20), residues: 676 sheet: -0.58 (0.17), residues: 785 loop : -1.21 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 353 HIS 0.014 0.001 HIS B1064 PHE 0.023 0.001 PHE D 192 TYR 0.021 0.001 TYR D 453 ARG 0.005 0.000 ARG B 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 34) link_NAG-ASN : angle 2.80948 ( 102) link_BETA1-4 : bond 0.00526 ( 11) link_BETA1-4 : angle 1.49618 ( 33) hydrogen bonds : bond 0.11787 ( 990) hydrogen bonds : angle 7.16527 ( 2724) SS BOND : bond 0.00342 ( 39) SS BOND : angle 1.15014 ( 78) covalent geometry : bond 0.00345 (26355) covalent geometry : angle 0.63871 (35885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 150 time to evaluate : 2.644 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 254 SER cc_start: 0.0069 (OUTLIER) cc_final: -0.0931 (p) REVERT: A 438 SER cc_start: 0.5280 (OUTLIER) cc_final: 0.4775 (p) REVERT: A 573 THR cc_start: 0.7171 (OUTLIER) cc_final: 0.6962 (p) REVERT: A 902 MET cc_start: 0.9220 (tpp) cc_final: 0.8944 (tpp) outliers start: 64 outliers final: 45 residues processed: 212 average time/residue: 1.1137 time to fit residues: 283.7287 Evaluate side-chains 186 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A1002 GLN B 69 HIS B 207 HIS B 542 ASN B 764 ASN B 957 GLN B1002 GLN D 121 ASN D 196 ASN D 218 GLN D 321 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.236960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183675 restraints weight = 22657.607| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.65 r_work: 0.3398 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 26439 Z= 0.246 Angle : 0.746 13.774 36098 Z= 0.387 Chirality : 0.053 0.510 4189 Planarity : 0.005 0.067 4603 Dihedral : 7.346 66.645 4461 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.76 % Rotamer: Outliers : 3.87 % Allowed : 17.71 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3187 helix: 1.61 (0.20), residues: 673 sheet: -0.59 (0.18), residues: 742 loop : -1.26 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 152 HIS 0.009 0.002 HIS A1048 PHE 0.031 0.002 PHE A 898 TYR 0.025 0.002 TYR A1067 ARG 0.006 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 34) link_NAG-ASN : angle 3.15648 ( 102) link_BETA1-4 : bond 0.00442 ( 11) link_BETA1-4 : angle 1.73563 ( 33) hydrogen bonds : bond 0.06875 ( 990) hydrogen bonds : angle 6.30439 ( 2724) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.44008 ( 78) covalent geometry : bond 0.00552 (26355) covalent geometry : angle 0.72371 (35885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 139 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.7375 (m-80) cc_final: 0.6744 (m-10) REVERT: A 902 MET cc_start: 0.9263 (tpp) cc_final: 0.8954 (tpp) REVERT: B 153 MET cc_start: -0.0159 (OUTLIER) cc_final: -0.0535 (ttm) REVERT: B 227 VAL cc_start: 0.7157 (OUTLIER) cc_final: 0.6826 (m) REVERT: B 494 SER cc_start: 0.3173 (OUTLIER) cc_final: 0.2938 (p) REVERT: B 580 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.4901 (mm-40) REVERT: B 619 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: D 202 LYS cc_start: 0.7186 (mttt) cc_final: 0.6869 (mtmp) REVERT: D 571 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.4964 (p0) REVERT: D 957 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: D 1081 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8774 (mt) outliers start: 109 outliers final: 51 residues processed: 239 average time/residue: 1.0601 time to fit residues: 306.9721 Evaluate side-chains 196 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 34 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 295 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 137 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 188 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 913 GLN A1002 GLN B 218 GLN B 354 ASN B 506 GLN B 542 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN D1010 GLN D1011 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.240504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.201271 restraints weight = 22987.255| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.67 r_work: 0.3881 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 26439 Z= 0.127 Angle : 0.588 13.043 36098 Z= 0.304 Chirality : 0.046 0.425 4189 Planarity : 0.004 0.051 4603 Dihedral : 6.168 58.515 4428 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 3.09 % Allowed : 18.35 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3187 helix: 2.01 (0.20), residues: 677 sheet: -0.50 (0.18), residues: 732 loop : -1.18 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.008 0.001 HIS B1064 PHE 0.029 0.001 PHE B 400 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 34) link_NAG-ASN : angle 2.62454 ( 102) link_BETA1-4 : bond 0.00370 ( 11) link_BETA1-4 : angle 1.47456 ( 33) hydrogen bonds : bond 0.05055 ( 990) hydrogen bonds : angle 5.81043 ( 2724) SS BOND : bond 0.00466 ( 39) SS BOND : angle 1.37747 ( 78) covalent geometry : bond 0.00279 (26355) covalent geometry : angle 0.56708 (35885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 148 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0911 (OUTLIER) cc_final: 0.0575 (m) REVERT: A 131 CYS cc_start: 0.1809 (OUTLIER) cc_final: 0.1600 (p) REVERT: A 574 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6708 (p0) REVERT: A 902 MET cc_start: 0.9047 (tpp) cc_final: 0.8802 (tpp) REVERT: A 935 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6055 (mt0) REVERT: B 153 MET cc_start: 0.0635 (OUTLIER) cc_final: -0.0431 (ttm) REVERT: B 177 MET cc_start: 0.3215 (OUTLIER) cc_final: 0.2549 (mmt) REVERT: B 318 PHE cc_start: 0.8111 (t80) cc_final: 0.7772 (p90) outliers start: 87 outliers final: 33 residues processed: 226 average time/residue: 1.1486 time to fit residues: 314.9055 Evaluate side-chains 173 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 48 optimal weight: 20.0000 chunk 302 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 280 optimal weight: 0.3980 chunk 288 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 603 ASN A1002 GLN B 542 ASN B 580 GLN B 957 GLN B1002 GLN D 121 ASN D 196 ASN D1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.240341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.199078 restraints weight = 23110.610| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 1.74 r_work: 0.3927 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26439 Z= 0.124 Angle : 0.573 12.706 36098 Z= 0.296 Chirality : 0.045 0.432 4189 Planarity : 0.004 0.048 4603 Dihedral : 5.649 55.231 4413 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 3.05 % Allowed : 18.10 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3187 helix: 2.11 (0.20), residues: 677 sheet: -0.52 (0.18), residues: 750 loop : -1.10 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.004 0.001 HIS B1064 PHE 0.026 0.001 PHE B 400 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG D 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 34) link_NAG-ASN : angle 2.56539 ( 102) link_BETA1-4 : bond 0.00351 ( 11) link_BETA1-4 : angle 1.46728 ( 33) hydrogen bonds : bond 0.05053 ( 990) hydrogen bonds : angle 5.67830 ( 2724) SS BOND : bond 0.00388 ( 39) SS BOND : angle 1.41117 ( 78) covalent geometry : bond 0.00271 (26355) covalent geometry : angle 0.55293 (35885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 142 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0928 (OUTLIER) cc_final: 0.0673 (m) REVERT: A 212 LEU cc_start: 0.3015 (OUTLIER) cc_final: 0.2713 (mm) REVERT: A 574 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6602 (p0) REVERT: A 935 GLN cc_start: 0.6497 (OUTLIER) cc_final: 0.6044 (mt0) REVERT: A 1119 ASN cc_start: 0.7884 (m-40) cc_final: 0.7648 (m110) REVERT: B 153 MET cc_start: 0.0716 (OUTLIER) cc_final: -0.0370 (ttm) REVERT: B 177 MET cc_start: 0.3387 (OUTLIER) cc_final: 0.2622 (mpm) REVERT: B 318 PHE cc_start: 0.8081 (t80) cc_final: 0.7811 (p90) REVERT: B 340 GLU cc_start: 0.3419 (OUTLIER) cc_final: 0.3213 (tt0) REVERT: B 619 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: D 646 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7432 (mtp-110) REVERT: D 902 MET cc_start: 0.8962 (tpp) cc_final: 0.8654 (tpp) outliers start: 86 outliers final: 38 residues processed: 221 average time/residue: 1.2497 time to fit residues: 333.1222 Evaluate side-chains 179 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 264 optimal weight: 0.4980 chunk 315 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 289 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 580 GLN B 957 GLN B1002 GLN D 196 ASN D1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.240805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.199303 restraints weight = 23102.083| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 1.79 r_work: 0.3903 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 26439 Z= 0.115 Angle : 0.556 12.356 36098 Z= 0.286 Chirality : 0.045 0.423 4189 Planarity : 0.004 0.047 4603 Dihedral : 5.300 55.753 4406 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 2.87 % Allowed : 18.67 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3187 helix: 2.20 (0.20), residues: 672 sheet: -0.47 (0.18), residues: 745 loop : -1.05 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 64 HIS 0.005 0.001 HIS B1064 PHE 0.025 0.001 PHE B 400 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG D 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 34) link_NAG-ASN : angle 2.57712 ( 102) link_BETA1-4 : bond 0.00372 ( 11) link_BETA1-4 : angle 1.43381 ( 33) hydrogen bonds : bond 0.04804 ( 990) hydrogen bonds : angle 5.57781 ( 2724) SS BOND : bond 0.00373 ( 39) SS BOND : angle 1.34802 ( 78) covalent geometry : bond 0.00249 (26355) covalent geometry : angle 0.53466 (35885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 141 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0919 (OUTLIER) cc_final: 0.0603 (m) REVERT: A 574 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6619 (p0) REVERT: A 1119 ASN cc_start: 0.7883 (m-40) cc_final: 0.7621 (m110) REVERT: B 153 MET cc_start: 0.0689 (OUTLIER) cc_final: -0.0373 (ttm) REVERT: B 177 MET cc_start: 0.3331 (OUTLIER) cc_final: 0.2592 (mpm) REVERT: B 318 PHE cc_start: 0.8095 (t80) cc_final: 0.7842 (p90) REVERT: B 441 LEU cc_start: 0.1461 (OUTLIER) cc_final: 0.1249 (tp) REVERT: B 619 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: B 1029 MET cc_start: 0.9011 (tpp) cc_final: 0.8738 (tpp) REVERT: D 646 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7452 (mtp-110) REVERT: D 902 MET cc_start: 0.8984 (tpp) cc_final: 0.8645 (tpp) outliers start: 81 outliers final: 46 residues processed: 214 average time/residue: 1.0683 time to fit residues: 277.1807 Evaluate side-chains 185 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 239 optimal weight: 0.0770 chunk 188 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 955 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 607 GLN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 787 GLN ** D1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.236665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.193234 restraints weight = 22726.407| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.74 r_work: 0.3873 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 26439 Z= 0.221 Angle : 0.712 14.899 36098 Z= 0.365 Chirality : 0.052 0.579 4189 Planarity : 0.005 0.070 4603 Dihedral : 6.114 77.498 4403 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 3.62 % Allowed : 17.89 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3187 helix: 1.98 (0.20), residues: 655 sheet: -0.51 (0.18), residues: 747 loop : -1.11 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 64 HIS 0.007 0.002 HIS A1048 PHE 0.031 0.002 PHE A 898 TYR 0.023 0.002 TYR A1067 ARG 0.006 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 34) link_NAG-ASN : angle 3.44423 ( 102) link_BETA1-4 : bond 0.00430 ( 11) link_BETA1-4 : angle 1.81730 ( 33) hydrogen bonds : bond 0.06472 ( 990) hydrogen bonds : angle 5.95919 ( 2724) SS BOND : bond 0.00417 ( 39) SS BOND : angle 1.86983 ( 78) covalent geometry : bond 0.00496 (26355) covalent geometry : angle 0.68197 (35885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 137 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.1033 (OUTLIER) cc_final: 0.0719 (m) REVERT: A 71 SER cc_start: 0.2141 (OUTLIER) cc_final: 0.1935 (p) REVERT: A 131 CYS cc_start: 0.2149 (OUTLIER) cc_final: 0.1933 (p) REVERT: A 212 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2615 (tp) REVERT: A 452 LEU cc_start: 0.4638 (OUTLIER) cc_final: 0.3775 (tp) REVERT: A 574 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6657 (p0) REVERT: A 935 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6404 (mt0) REVERT: B 153 MET cc_start: 0.0888 (OUTLIER) cc_final: -0.0203 (ttm) REVERT: B 177 MET cc_start: 0.3426 (OUTLIER) cc_final: 0.2805 (mpm) REVERT: B 353 TRP cc_start: 0.1320 (OUTLIER) cc_final: -0.0060 (m-10) REVERT: B 619 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: D 571 ASP cc_start: 0.5794 (OUTLIER) cc_final: 0.5062 (p0) REVERT: D 646 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7425 (mtp-110) REVERT: D 902 MET cc_start: 0.9100 (tpp) cc_final: 0.8737 (tpp) REVERT: D 1081 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8531 (mt) outliers start: 102 outliers final: 55 residues processed: 227 average time/residue: 1.0359 time to fit residues: 289.1896 Evaluate side-chains 204 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 135 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 214 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 242 optimal weight: 0.8980 chunk 234 optimal weight: 0.0770 chunk 30 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.238368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.196853 restraints weight = 22868.514| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.70 r_work: 0.3896 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26439 Z= 0.177 Angle : 0.657 12.727 36098 Z= 0.336 Chirality : 0.049 0.437 4189 Planarity : 0.005 0.050 4603 Dihedral : 5.967 80.742 4403 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 3.37 % Allowed : 17.96 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3187 helix: 2.03 (0.20), residues: 660 sheet: -0.45 (0.18), residues: 725 loop : -1.15 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS D1064 PHE 0.026 0.002 PHE A 898 TYR 0.036 0.002 TYR A 453 ARG 0.004 0.001 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 34) link_NAG-ASN : angle 3.23475 ( 102) link_BETA1-4 : bond 0.00335 ( 11) link_BETA1-4 : angle 1.70671 ( 33) hydrogen bonds : bond 0.05876 ( 990) hydrogen bonds : angle 5.84452 ( 2724) SS BOND : bond 0.00397 ( 39) SS BOND : angle 1.66565 ( 78) covalent geometry : bond 0.00396 (26355) covalent geometry : angle 0.62880 (35885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 139 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0993 (OUTLIER) cc_final: 0.0686 (m) REVERT: A 131 CYS cc_start: 0.2144 (OUTLIER) cc_final: 0.1933 (p) REVERT: A 212 LEU cc_start: 0.3042 (OUTLIER) cc_final: 0.2591 (tp) REVERT: A 452 LEU cc_start: 0.4469 (OUTLIER) cc_final: 0.3765 (tp) REVERT: A 574 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6590 (p0) REVERT: A 935 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6339 (mt0) REVERT: B 153 MET cc_start: 0.0813 (OUTLIER) cc_final: -0.0257 (ttm) REVERT: B 177 MET cc_start: 0.3492 (OUTLIER) cc_final: 0.2912 (mpm) REVERT: B 353 TRP cc_start: 0.1381 (OUTLIER) cc_final: -0.0026 (m-10) REVERT: B 619 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: D 318 PHE cc_start: 0.8089 (p90) cc_final: 0.7845 (p90) REVERT: D 902 MET cc_start: 0.9033 (tpp) cc_final: 0.8699 (tpp) REVERT: D 1081 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8545 (mt) outliers start: 95 outliers final: 60 residues processed: 225 average time/residue: 1.0401 time to fit residues: 286.0460 Evaluate side-chains 203 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 132 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 86 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 0.0070 overall best weight: 3.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 603 ASN A 655 HIS A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 542 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.237198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.195592 restraints weight = 22823.743| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.72 r_work: 0.3878 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 26439 Z= 0.231 Angle : 0.731 12.981 36098 Z= 0.376 Chirality : 0.052 0.458 4189 Planarity : 0.005 0.062 4603 Dihedral : 6.336 76.985 4403 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 3.58 % Allowed : 17.89 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3187 helix: 1.85 (0.20), residues: 655 sheet: -0.48 (0.18), residues: 725 loop : -1.23 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.009 0.002 HIS A 207 PHE 0.031 0.002 PHE A 898 TYR 0.023 0.002 TYR A1067 ARG 0.005 0.001 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 34) link_NAG-ASN : angle 3.48163 ( 102) link_BETA1-4 : bond 0.00403 ( 11) link_BETA1-4 : angle 1.89333 ( 33) hydrogen bonds : bond 0.06574 ( 990) hydrogen bonds : angle 6.06798 ( 2724) SS BOND : bond 0.00455 ( 39) SS BOND : angle 2.03636 ( 78) covalent geometry : bond 0.00523 (26355) covalent geometry : angle 0.70050 (35885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 135 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.1074 (OUTLIER) cc_final: 0.0746 (m) REVERT: A 131 CYS cc_start: 0.2252 (OUTLIER) cc_final: 0.1978 (p) REVERT: A 153 MET cc_start: -0.0407 (mmm) cc_final: -0.0642 (tpt) REVERT: A 212 LEU cc_start: 0.3104 (OUTLIER) cc_final: 0.2567 (tp) REVERT: A 574 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6622 (p0) REVERT: A 935 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6448 (mt0) REVERT: B 153 MET cc_start: 0.0907 (OUTLIER) cc_final: -0.0209 (ttm) REVERT: B 177 MET cc_start: 0.3728 (OUTLIER) cc_final: 0.2893 (mmp) REVERT: B 353 TRP cc_start: 0.1455 (OUTLIER) cc_final: 0.0034 (m-10) REVERT: B 619 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: D 318 PHE cc_start: 0.8132 (p90) cc_final: 0.7850 (p90) REVERT: D 902 MET cc_start: 0.9066 (tpp) cc_final: 0.8686 (tpp) REVERT: D 1081 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8504 (mt) outliers start: 101 outliers final: 60 residues processed: 221 average time/residue: 1.0415 time to fit residues: 282.4485 Evaluate side-chains 201 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 131 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 8 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 166 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 0.0050 chunk 278 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 955 ASN B 957 GLN B1002 GLN D 121 ASN D 196 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.239927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.198244 restraints weight = 23170.862| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.69 r_work: 0.3877 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26439 Z= 0.118 Angle : 0.577 12.442 36098 Z= 0.294 Chirality : 0.045 0.426 4189 Planarity : 0.004 0.053 4603 Dihedral : 5.665 81.875 4403 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 2.34 % Allowed : 19.27 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3187 helix: 2.14 (0.20), residues: 671 sheet: -0.42 (0.18), residues: 721 loop : -1.13 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 64 HIS 0.008 0.001 HIS B1064 PHE 0.017 0.001 PHE B 400 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG D 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 34) link_NAG-ASN : angle 2.86043 ( 102) link_BETA1-4 : bond 0.00335 ( 11) link_BETA1-4 : angle 1.54913 ( 33) hydrogen bonds : bond 0.04849 ( 990) hydrogen bonds : angle 5.62610 ( 2724) SS BOND : bond 0.00358 ( 39) SS BOND : angle 1.37477 ( 78) covalent geometry : bond 0.00257 (26355) covalent geometry : angle 0.55299 (35885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0983 (OUTLIER) cc_final: 0.0599 (m) REVERT: A 153 MET cc_start: -0.0331 (mmm) cc_final: -0.0577 (tpt) REVERT: A 212 LEU cc_start: 0.2945 (OUTLIER) cc_final: 0.2492 (tp) REVERT: A 452 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.3953 (tp) REVERT: A 574 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6659 (p0) REVERT: A 935 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.6058 (mt0) REVERT: A 1119 ASN cc_start: 0.7925 (m-40) cc_final: 0.7669 (m110) REVERT: B 153 MET cc_start: 0.0715 (OUTLIER) cc_final: -0.0302 (ttm) REVERT: B 318 PHE cc_start: 0.8150 (t80) cc_final: 0.7782 (p90) REVERT: B 353 TRP cc_start: 0.1255 (OUTLIER) cc_final: -0.0024 (m-10) REVERT: B 619 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: D 318 PHE cc_start: 0.8030 (p90) cc_final: 0.7759 (p90) REVERT: D 902 MET cc_start: 0.8877 (tpp) cc_final: 0.8665 (tpp) REVERT: D 1081 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8514 (mt) outliers start: 66 outliers final: 43 residues processed: 206 average time/residue: 1.0118 time to fit residues: 254.6597 Evaluate side-chains 186 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 249 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 256 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 542 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 607 GLN ** D1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.238546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.197119 restraints weight = 22890.075| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 1.71 r_work: 0.3899 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26439 Z= 0.155 Angle : 0.625 12.647 36098 Z= 0.320 Chirality : 0.047 0.450 4189 Planarity : 0.004 0.055 4603 Dihedral : 5.774 76.490 4403 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 2.24 % Allowed : 19.45 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3187 helix: 2.07 (0.20), residues: 670 sheet: -0.45 (0.18), residues: 727 loop : -1.12 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.006 0.001 HIS A 207 PHE 0.023 0.002 PHE A 898 TYR 0.022 0.002 TYR A1067 ARG 0.004 0.000 ARG D 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 34) link_NAG-ASN : angle 3.02223 ( 102) link_BETA1-4 : bond 0.00328 ( 11) link_BETA1-4 : angle 1.62863 ( 33) hydrogen bonds : bond 0.05598 ( 990) hydrogen bonds : angle 5.74662 ( 2724) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.82081 ( 78) covalent geometry : bond 0.00345 (26355) covalent geometry : angle 0.59819 (35885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 135 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0885 (OUTLIER) cc_final: 0.0582 (m) REVERT: A 212 LEU cc_start: 0.2913 (OUTLIER) cc_final: 0.2494 (tp) REVERT: A 452 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.3859 (tp) REVERT: A 574 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6607 (p0) REVERT: A 935 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.6325 (mt0) REVERT: B 153 MET cc_start: 0.0784 (OUTLIER) cc_final: -0.0276 (ttm) REVERT: B 353 TRP cc_start: 0.1408 (OUTLIER) cc_final: 0.0054 (m-10) REVERT: B 619 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: D 318 PHE cc_start: 0.8039 (p90) cc_final: 0.7815 (p90) REVERT: D 902 MET cc_start: 0.8995 (tpp) cc_final: 0.8653 (tpp) REVERT: D 1081 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8524 (mt) outliers start: 63 outliers final: 43 residues processed: 192 average time/residue: 1.0939 time to fit residues: 254.8579 Evaluate side-chains 183 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 245 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 chunk 309 optimal weight: 0.0970 chunk 184 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 overall best weight: 0.9458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 501 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.239710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.198227 restraints weight = 23032.342| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.68 r_work: 0.3865 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26439 Z= 0.124 Angle : 0.587 12.827 36098 Z= 0.299 Chirality : 0.045 0.431 4189 Planarity : 0.004 0.058 4603 Dihedral : 5.570 78.288 4403 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 2.09 % Allowed : 19.55 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3187 helix: 2.12 (0.20), residues: 678 sheet: -0.31 (0.18), residues: 729 loop : -1.11 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 64 HIS 0.007 0.001 HIS B1064 PHE 0.016 0.001 PHE A 898 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG D 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 34) link_NAG-ASN : angle 2.80249 ( 102) link_BETA1-4 : bond 0.00330 ( 11) link_BETA1-4 : angle 1.50883 ( 33) hydrogen bonds : bond 0.04945 ( 990) hydrogen bonds : angle 5.58626 ( 2724) SS BOND : bond 0.00319 ( 39) SS BOND : angle 1.57275 ( 78) covalent geometry : bond 0.00271 (26355) covalent geometry : angle 0.56283 (35885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28716.04 seconds wall clock time: 492 minutes 57.57 seconds (29577.57 seconds total)