Starting phenix.real_space_refine on Sun Jul 5 10:56:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hhx_34806/07_2026/8hhx_34806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhx_34806/07_2026/8hhx_34806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hhx_34806/07_2026/8hhx_34806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhx_34806/07_2026/8hhx_34806.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hhx_34806/07_2026/8hhx_34806.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hhx_34806/07_2026/8hhx_34806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhx_34806/07_2026/8hhx_34806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhx_34806/07_2026/8hhx_34806.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 120 5.16 5 C 17425 2.51 5 N 4532 2.21 5 O 5358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27435 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6373 Classifications: {'peptide': 822} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 39, 'TRANS': 782} Chain breaks: 7 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 7871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7871 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 958} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7646 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 931} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1682 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "G" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1614 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 831 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" 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 chiralities: 7 Time building chain proxies: 5.45, per 1000 atoms: 0.20 Number of scatterers: 27435 At special positions: 0 Unit cell: (161.85, 174.3, 185.92, 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 120 16.00 O 5358 8.00 N 4532 7.00 C 17425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 224 " - pdb=" SG CYS G 216 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 801 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG D 1 " - " ASN A1074 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG P 1 " - " ASN B 717 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6490 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 63 sheets defined 21.9% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.996A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.997A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.549A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.847A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.755A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.980A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.797A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.869A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.937A pdb=" N SER B 373 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.597A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.576A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.798A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.632A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.560A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.200A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.549A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.445A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.386A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.665A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.501A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.558A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.930A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.429A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.656A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.977A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.526A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.238A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.163A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 126 through 132 removed outlier: 3.530A pdb=" N GLU G 129 " --> pdb=" O SER G 126 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.989A pdb=" N ASN G 175 " --> pdb=" O GLN G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 193 removed outlier: 4.198A pdb=" N TRP G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS G 193 " --> pdb=" O GLN G 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.695A pdb=" N ASN I 33 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.652A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.646A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 279 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 122 removed outlier: 3.777A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 205 removed outlier: 6.358A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.641A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.641A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.518A pdb=" N VAL A 551 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.305A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.931A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 656 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.051A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.568A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.612A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 89 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.533A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.977A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 118 through 122 Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 317 removed outlier: 5.897A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.218A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.818A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 719 removed outlier: 6.818A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 725 through 727 removed outlier: 3.586A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.201A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD4, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.860A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.745A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.948A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.278A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 312 removed outlier: 4.278A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.662A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.748A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 394 through 396 removed outlier: 3.715A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.506A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 714 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 719 removed outlier: 7.104A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1053 through 1056 removed outlier: 3.653A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF4, first strand: chain 'C' and resid 1089 through 1090 removed outlier: 3.531A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'F' and resid 4 through 8 removed outlier: 4.077A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 92 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL F 93 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 39 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR F 95 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL F 37 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.671A pdb=" N VAL F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 92 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N CYS F 96 " --> pdb=" O TRP F 111 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP F 111 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN F 98 " --> pdb=" O ASP F 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 49 through 51 removed outlier: 3.512A pdb=" N VAL F 50 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 59 " --> pdb=" O VAL F 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 170 through 171 Processing sheet with id=AG2, first strand: chain 'G' and resid 21 through 23 removed outlier: 4.539A pdb=" N ALA G 75 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER G 74 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP G 69 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 76 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G 67 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.900A pdb=" N VAL G 49 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 38 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR G 91 " --> pdb=" O TYR G 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 93 through 96 Processing sheet with id=AG5, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AG6, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AG7, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.840A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR H 95 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.660A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'H' and resid 70 through 73 removed outlier: 3.608A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7410 1.33 - 1.46: 6924 1.46 - 1.58: 13562 1.58 - 1.71: 1 1.71 - 1.83: 154 Bond restraints: 28051 Sorted by residual: bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CB PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.79e+00 bond pdb=" N ILE B 850 " pdb=" CA ILE B 850 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N VAL A 143 " pdb=" CA VAL A 143 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.27e+00 ... (remaining 28046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 37882 2.88 - 5.77: 261 5.77 - 8.65: 22 8.65 - 11.53: 5 11.53 - 14.41: 1 Bond angle restraints: 38171 Sorted by residual: angle pdb=" CA PRO C 272 " pdb=" N PRO C 272 " pdb=" CD PRO C 272 " ideal model delta sigma weight residual 112.00 97.59 14.41 1.40e+00 5.10e-01 1.06e+02 angle pdb=" N PRO C 272 " pdb=" CD PRO C 272 " pdb=" CG PRO C 272 " ideal model delta sigma weight residual 103.20 95.22 7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C ASP A 737 " pdb=" CA ASP A 737 " pdb=" CB ASP A 737 " ideal model delta sigma weight residual 110.77 118.42 -7.65 1.67e+00 3.59e-01 2.10e+01 angle pdb=" N GLN C 954 " pdb=" CA GLN C 954 " pdb=" CB GLN C 954 " ideal model delta sigma weight residual 110.32 117.74 -7.42 1.70e+00 3.46e-01 1.90e+01 angle pdb=" N GLN A 774 " pdb=" CA GLN A 774 " pdb=" CB GLN A 774 " ideal model delta sigma weight residual 110.12 116.37 -6.25 1.47e+00 4.63e-01 1.81e+01 ... (remaining 38166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14961 17.94 - 35.88: 1198 35.88 - 53.82: 179 53.82 - 71.76: 37 71.76 - 89.70: 22 Dihedral angle restraints: 16397 sinusoidal: 6299 harmonic: 10098 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -169.48 83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -164.92 78.92 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -163.24 77.24 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 16394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4430 0.190 - 0.380: 4 0.380 - 0.570: 0 0.570 - 0.760: 1 0.760 - 0.950: 1 Chirality restraints: 4436 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4433 not shown) Planarity restraints: 4909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 271 " 0.098 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO B 272 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 271 " 0.091 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO C 272 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.049 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN A 616 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.051 2.00e-02 2.50e+03 ... (remaining 4906 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 557 2.67 - 3.23: 26207 3.23 - 3.79: 40161 3.79 - 4.34: 53517 4.34 - 4.90: 86634 Nonbonded interactions: 207076 Sorted by model distance: nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.114 3.040 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.144 3.040 nonbonded pdb=" O THR B 961 " pdb=" OE1 GLN B 965 " model vdw 2.151 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR B1067 " pdb=" O ASN B1108 " model vdw 2.197 3.040 ... (remaining 207071 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 'B' and (resid 25 through 146 or resid 164 through 165 or resid 186 throu \ gh 463 or resid 491 through 1307)) selection = (chain 'C' and (resid 25 through 69 or resid 81 through 146 or resid 148 through \ 149 or resid 186 through 243 or resid 264 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.450 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 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 : 0.004 0.156 28122 Z= 0.187 Angle : 0.664 18.597 38348 Z= 0.345 Chirality : 0.050 0.950 4436 Planarity : 0.005 0.146 4881 Dihedral : 13.160 89.696 9799 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % Rotamer: Outliers : 0.17 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3419 helix: 0.24 (0.21), residues: 624 sheet: -0.85 (0.23), residues: 535 loop : -1.13 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.021 0.001 TYR A 873 PHE 0.024 0.001 PHE C1103 TRP 0.025 0.001 TRP B 353 HIS 0.014 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (28051) covalent geometry : angle 0.63726 / 0.34 (38171) SS BOND : bond 0.00408 / 0.21 ( 36) SS BOND : angle 1.27540 / 0.87 ( 72) hydrogen bonds : bond 0.21112 / 14.63 ( 766) hydrogen bonds : angle 9.57611 / 6.58 ( 2085) link_BETA1-4 : bond 0.00557 / 0.34 ( 7) link_BETA1-4 : angle 1.47726 / 0.89 ( 21) link_NAG-ASN : bond 0.00658 / 0.39 ( 28) link_NAG-ASN : angle 3.82678 / 2.45 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 414 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 ASP cc_start: 0.5106 (t70) cc_final: 0.4795 (t70) outliers start: 5 outliers final: 2 residues processed: 418 average time/residue: 0.1738 time to fit residues: 118.8660 Evaluate side-chains 326 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0010 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 6.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 164 ASN B 540 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.250924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.215824 restraints weight = 43664.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.213339 restraints weight = 40301.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.215860 restraints weight = 35205.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.215849 restraints weight = 22166.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.216748 restraints weight = 20634.925| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28122 Z= 0.160 Angle : 0.630 10.481 38348 Z= 0.326 Chirality : 0.047 0.338 4436 Planarity : 0.005 0.106 4881 Dihedral : 4.458 41.247 3722 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 1.10 % Allowed : 7.05 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3419 helix: 0.30 (0.21), residues: 618 sheet: -0.67 (0.23), residues: 574 loop : -1.19 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.019 0.001 TYR C1110 PHE 0.018 0.001 PHE B 275 TRP 0.020 0.001 TRP B 353 HIS 0.012 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (28051) covalent geometry : angle 0.61453 / 0.32 (38171) SS BOND : bond 0.00313 / 0.19 ( 36) SS BOND : angle 1.16443 / 0.76 ( 72) hydrogen bonds : bond 0.05059 / 3.40 ( 766) hydrogen bonds : angle 7.38197 / 5.11 ( 2085) link_BETA1-4 : bond 0.00618 / 0.37 ( 7) link_BETA1-4 : angle 1.06952 / 0.63 ( 21) link_NAG-ASN : bond 0.00543 / 0.37 ( 28) link_NAG-ASN : angle 2.86961 / 1.79 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 374 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 57 ASN cc_start: 0.5809 (p0) cc_final: 0.5391 (p0) outliers start: 33 outliers final: 20 residues processed: 393 average time/residue: 0.1721 time to fit residues: 110.6923 Evaluate side-chains 356 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 336 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 328 optimal weight: 8.9990 chunk 318 optimal weight: 7.9990 chunk 240 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 66 HIS A 675 GLN A 764 ASN ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 30 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 710 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.237826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.195119 restraints weight = 43344.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.190291 restraints weight = 38547.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.190887 restraints weight = 35194.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.191956 restraints weight = 26991.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.193844 restraints weight = 20266.981| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 28122 Z= 0.282 Angle : 0.747 12.401 38348 Z= 0.385 Chirality : 0.050 0.392 4436 Planarity : 0.005 0.082 4881 Dihedral : 5.035 50.038 3720 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.39 % Favored : 91.58 % Rotamer: Outliers : 2.39 % Allowed : 11.70 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3419 helix: -0.21 (0.20), residues: 615 sheet: -1.08 (0.23), residues: 537 loop : -1.44 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 765 TYR 0.029 0.002 TYR A1067 PHE 0.030 0.002 PHE A 192 TRP 0.026 0.002 TRP B 353 HIS 0.014 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.28 (28051) covalent geometry : angle 0.73127 / 0.38 (38171) SS BOND : bond 0.00443 / 0.24 ( 36) SS BOND : angle 1.39585 / 0.91 ( 72) hydrogen bonds : bond 0.05768 / 3.89 ( 766) hydrogen bonds : angle 7.43585 / 5.13 ( 2085) link_BETA1-4 : bond 0.00474 / 0.30 ( 7) link_BETA1-4 : angle 1.38542 / 0.87 ( 21) link_NAG-ASN : bond 0.00665 / 0.45 ( 28) link_NAG-ASN : angle 3.05301 / 1.88 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 359 time to evaluate : 0.917 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 61 ASN cc_start: 0.5909 (t0) cc_final: 0.5654 (t0) REVERT: A 191 GLU cc_start: 0.4565 (OUTLIER) cc_final: 0.4268 (mp0) REVERT: A 906 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: B 347 PHE cc_start: 0.4516 (m-80) cc_final: 0.3961 (m-10) REVERT: B 900 MET cc_start: 0.6987 (mmt) cc_final: 0.6694 (mmt) REVERT: C 41 LYS cc_start: 0.6764 (mtpp) cc_final: 0.6462 (mtpp) REVERT: C 716 THR cc_start: 0.7375 (p) cc_final: 0.7025 (t) REVERT: F 57 ASN cc_start: 0.5925 (p0) cc_final: 0.5465 (p0) outliers start: 72 outliers final: 47 residues processed: 406 average time/residue: 0.1564 time to fit residues: 103.9533 Evaluate side-chains 378 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 329 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 330 optimal weight: 30.0000 chunk 232 optimal weight: 1.9990 chunk 326 optimal weight: 8.9990 chunk 338 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 66 HIS A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1023 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 370 ASN C 710 ASN C 762 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN G 39 GLN G 174 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.242899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.201142 restraints weight = 42912.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.197927 restraints weight = 41753.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.199427 restraints weight = 29150.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.200127 restraints weight = 24457.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.202126 restraints weight = 19081.605| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28122 Z= 0.141 Angle : 0.615 12.456 38348 Z= 0.314 Chirality : 0.047 0.367 4436 Planarity : 0.004 0.071 4881 Dihedral : 4.637 52.574 3720 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.09 % Allowed : 13.20 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3419 helix: 0.09 (0.20), residues: 625 sheet: -0.93 (0.22), residues: 578 loop : -1.34 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.019 0.001 TYR C1110 PHE 0.015 0.001 PHE B 192 TRP 0.027 0.001 TRP B 353 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (28051) covalent geometry : angle 0.60165 / 0.31 (38171) SS BOND : bond 0.00249 / 0.14 ( 36) SS BOND : angle 1.07338 / 0.73 ( 72) hydrogen bonds : bond 0.04719 / 3.21 ( 766) hydrogen bonds : angle 6.83570 / 4.70 ( 2085) link_BETA1-4 : bond 0.00476 / 0.30 ( 7) link_BETA1-4 : angle 1.14720 / 0.68 ( 21) link_NAG-ASN : bond 0.00594 / 0.38 ( 28) link_NAG-ASN : angle 2.61666 / 1.62 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 346 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.4150 (OUTLIER) cc_final: 0.3861 (mp0) REVERT: A 906 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7289 (m-10) REVERT: B 347 PHE cc_start: 0.4260 (m-80) cc_final: 0.3772 (m-10) REVERT: B 773 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5159 (tt0) REVERT: B 900 MET cc_start: 0.6966 (mmt) cc_final: 0.6543 (mmt) REVERT: C 702 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7727 (mp0) REVERT: C 710 ASN cc_start: 0.6954 (m110) cc_final: 0.6652 (m-40) REVERT: C 716 THR cc_start: 0.7306 (p) cc_final: 0.7050 (t) REVERT: C 721 SER cc_start: 0.8387 (t) cc_final: 0.8101 (m) REVERT: C 949 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6738 (tp-100) REVERT: C 1005 GLN cc_start: 0.7204 (tp40) cc_final: 0.6953 (tp-100) REVERT: C 1106 GLN cc_start: 0.7694 (pm20) cc_final: 0.6890 (pm20) REVERT: F 57 ASN cc_start: 0.6061 (p0) cc_final: 0.5600 (p0) outliers start: 63 outliers final: 37 residues processed: 393 average time/residue: 0.1658 time to fit residues: 107.6410 Evaluate side-chains 367 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 264 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 536 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.244766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.208972 restraints weight = 43137.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.209197 restraints weight = 42907.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.209632 restraints weight = 38932.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.209749 restraints weight = 23539.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.210675 restraints weight = 19514.706| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28122 Z= 0.200 Angle : 0.652 11.729 38348 Z= 0.334 Chirality : 0.048 0.356 4436 Planarity : 0.005 0.063 4881 Dihedral : 4.737 55.541 3720 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.79 % Allowed : 14.73 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3419 helix: 0.11 (0.20), residues: 613 sheet: -1.02 (0.22), residues: 569 loop : -1.39 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.019 0.002 TYR A1067 PHE 0.022 0.002 PHE A 192 TRP 0.028 0.001 TRP B 353 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (28051) covalent geometry : angle 0.63920 / 0.33 (38171) SS BOND : bond 0.00504 / 0.28 ( 36) SS BOND : angle 1.12726 / 0.76 ( 72) hydrogen bonds : bond 0.04972 / 3.36 ( 766) hydrogen bonds : angle 6.86793 / 4.73 ( 2085) link_BETA1-4 : bond 0.00479 / 0.30 ( 7) link_BETA1-4 : angle 1.18844 / 0.74 ( 21) link_NAG-ASN : bond 0.00609 / 0.40 ( 28) link_NAG-ASN : angle 2.66674 / 1.66 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 345 time to evaluate : 1.255 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 191 GLU cc_start: 0.4379 (OUTLIER) cc_final: 0.4047 (mp0) REVERT: A 906 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: B 347 PHE cc_start: 0.4311 (m-80) cc_final: 0.3879 (m-10) REVERT: B 773 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5291 (tt0) REVERT: B 900 MET cc_start: 0.6903 (mmt) cc_final: 0.6568 (mmt) REVERT: C 716 THR cc_start: 0.7258 (p) cc_final: 0.6999 (t) REVERT: C 721 SER cc_start: 0.8388 (t) cc_final: 0.8131 (m) REVERT: C 964 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7661 (mtmm) REVERT: F 57 ASN cc_start: 0.5878 (p0) cc_final: 0.5454 (p0) outliers start: 84 outliers final: 59 residues processed: 402 average time/residue: 0.1681 time to fit residues: 111.8197 Evaluate side-chains 385 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 323 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 215 optimal weight: 7.9990 chunk 134 optimal weight: 0.1980 chunk 155 optimal weight: 0.9980 chunk 326 optimal weight: 20.0000 chunk 172 optimal weight: 0.8980 chunk 209 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 chunk 327 optimal weight: 0.0570 chunk 29 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.248993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.214593 restraints weight = 43208.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.215369 restraints weight = 41311.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.216260 restraints weight = 34143.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.216745 restraints weight = 21236.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.217790 restraints weight = 18814.742| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28122 Z= 0.120 Angle : 0.595 13.886 38348 Z= 0.302 Chirality : 0.046 0.423 4436 Planarity : 0.004 0.061 4881 Dihedral : 4.480 58.707 3720 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.06 % Allowed : 16.02 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3419 helix: 0.25 (0.21), residues: 620 sheet: -0.89 (0.22), residues: 586 loop : -1.30 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.023 0.001 TYR B 170 PHE 0.016 0.001 PHE B 888 TRP 0.029 0.001 TRP B 353 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (28051) covalent geometry : angle 0.58274 / 0.30 (38171) SS BOND : bond 0.00300 / 0.17 ( 36) SS BOND : angle 1.01335 / 0.70 ( 72) hydrogen bonds : bond 0.04364 / 2.97 ( 766) hydrogen bonds : angle 6.45727 / 4.45 ( 2085) link_BETA1-4 : bond 0.00517 / 0.33 ( 7) link_BETA1-4 : angle 1.14543 / 0.68 ( 21) link_NAG-ASN : bond 0.00533 / 0.35 ( 28) link_NAG-ASN : angle 2.44392 / 1.53 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 360 time to evaluate : 0.953 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 191 GLU cc_start: 0.4179 (OUTLIER) cc_final: 0.3842 (mp0) REVERT: B 347 PHE cc_start: 0.4048 (m-80) cc_final: 0.3663 (m-10) REVERT: B 900 MET cc_start: 0.6853 (mmt) cc_final: 0.6568 (mmt) REVERT: B 1029 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4684 (ttm) REVERT: C 716 THR cc_start: 0.7314 (p) cc_final: 0.7064 (t) REVERT: C 721 SER cc_start: 0.8046 (t) cc_final: 0.7832 (m) REVERT: C 818 ILE cc_start: 0.7060 (mt) cc_final: 0.6691 (mt) REVERT: C 900 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6019 (mmm) REVERT: C 964 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7565 (mtmm) REVERT: C 1106 GLN cc_start: 0.7691 (pm20) cc_final: 0.6845 (pm20) REVERT: F 57 ASN cc_start: 0.5942 (p0) cc_final: 0.5517 (p0) outliers start: 62 outliers final: 43 residues processed: 406 average time/residue: 0.1740 time to fit residues: 115.8977 Evaluate side-chains 373 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 126 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 312 optimal weight: 20.0000 chunk 54 optimal weight: 0.0870 chunk 247 optimal weight: 0.0020 chunk 285 optimal weight: 10.0000 chunk 34 optimal weight: 0.0000 chunk 224 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 chunk 340 optimal weight: 8.9990 chunk 133 optimal weight: 0.3980 overall best weight: 0.8972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1005 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.249407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.215017 restraints weight = 43171.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.213969 restraints weight = 42818.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.215787 restraints weight = 34888.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.215976 restraints weight = 21604.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.217218 restraints weight = 19677.891| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28122 Z= 0.125 Angle : 0.601 13.888 38348 Z= 0.303 Chirality : 0.046 0.437 4436 Planarity : 0.004 0.062 4881 Dihedral : 4.401 58.536 3720 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.29 % Allowed : 16.32 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3419 helix: 0.25 (0.20), residues: 621 sheet: -0.84 (0.22), residues: 580 loop : -1.24 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 765 TYR 0.018 0.001 TYR B 170 PHE 0.013 0.001 PHE C 275 TRP 0.023 0.001 TRP B 353 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (28051) covalent geometry : angle 0.58815 / 0.30 (38171) SS BOND : bond 0.00258 / 0.15 ( 36) SS BOND : angle 0.99272 / 0.69 ( 72) hydrogen bonds : bond 0.04252 / 2.87 ( 766) hydrogen bonds : angle 6.29967 / 4.34 ( 2085) link_BETA1-4 : bond 0.00490 / 0.31 ( 7) link_BETA1-4 : angle 1.14569 / 0.70 ( 21) link_NAG-ASN : bond 0.00534 / 0.36 ( 28) link_NAG-ASN : angle 2.56472 / 1.62 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 348 time to evaluate : 1.024 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 660 TYR cc_start: 0.6747 (p90) cc_final: 0.6472 (p90) REVERT: B 900 MET cc_start: 0.6741 (mmt) cc_final: 0.6527 (mmt) REVERT: B 902 MET cc_start: 0.7920 (mmt) cc_final: 0.7516 (mmt) REVERT: B 1029 MET cc_start: 0.4817 (OUTLIER) cc_final: 0.4465 (ttm) REVERT: C 721 SER cc_start: 0.8032 (t) cc_final: 0.7723 (m) REVERT: C 818 ILE cc_start: 0.7077 (mt) cc_final: 0.6796 (mt) REVERT: C 900 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.6032 (mmm) REVERT: C 964 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7538 (mtmm) REVERT: F 57 ASN cc_start: 0.5990 (p0) cc_final: 0.5554 (p0) outliers start: 69 outliers final: 52 residues processed: 398 average time/residue: 0.1731 time to fit residues: 113.3429 Evaluate side-chains 383 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 329 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 317 optimal weight: 8.9990 chunk 6 optimal weight: 0.0040 chunk 187 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.247242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.212300 restraints weight = 43311.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.210150 restraints weight = 43485.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.211606 restraints weight = 40570.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.212135 restraints weight = 22679.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.213554 restraints weight = 19256.737| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28122 Z= 0.161 Angle : 0.624 13.913 38348 Z= 0.317 Chirality : 0.047 0.428 4436 Planarity : 0.004 0.063 4881 Dihedral : 4.467 57.028 3720 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.36 % Allowed : 16.76 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3419 helix: 0.22 (0.20), residues: 620 sheet: -0.91 (0.22), residues: 591 loop : -1.27 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.039 0.001 TYR A1007 PHE 0.017 0.001 PHE A 192 TRP 0.026 0.001 TRP B 353 HIS 0.023 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (28051) covalent geometry : angle 0.61184 / 0.31 (38171) SS BOND : bond 0.00321 / 0.18 ( 36) SS BOND : angle 1.03285 / 0.70 ( 72) hydrogen bonds : bond 0.04528 / 3.06 ( 766) hydrogen bonds : angle 6.39026 / 4.41 ( 2085) link_BETA1-4 : bond 0.00469 / 0.29 ( 7) link_BETA1-4 : angle 1.14619 / 0.71 ( 21) link_NAG-ASN : bond 0.00544 / 0.37 ( 28) link_NAG-ASN : angle 2.53995 / 1.57 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 344 time to evaluate : 0.992 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 660 TYR cc_start: 0.6866 (p90) cc_final: 0.6554 (p90) REVERT: B 347 PHE cc_start: 0.4211 (m-80) cc_final: 0.3810 (m-10) REVERT: B 900 MET cc_start: 0.6934 (mmt) cc_final: 0.6658 (mmt) REVERT: B 1029 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.4889 (ttm) REVERT: C 143 VAL cc_start: -0.0819 (OUTLIER) cc_final: -0.1134 (p) REVERT: C 716 THR cc_start: 0.7372 (p) cc_final: 0.7100 (t) REVERT: C 721 SER cc_start: 0.8176 (t) cc_final: 0.7849 (m) REVERT: C 818 ILE cc_start: 0.7230 (mt) cc_final: 0.6930 (mt) REVERT: C 900 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.6107 (mmm) REVERT: C 964 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7569 (mtmm) REVERT: F 57 ASN cc_start: 0.6026 (p0) cc_final: 0.5596 (p0) outliers start: 71 outliers final: 59 residues processed: 400 average time/residue: 0.1650 time to fit residues: 108.3968 Evaluate side-chains 391 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 329 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 1 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 230 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 329 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 895 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 710 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.247648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.212640 restraints weight = 43123.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.211784 restraints weight = 42848.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.213497 restraints weight = 35345.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.213731 restraints weight = 21449.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.215377 restraints weight = 19313.130| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28122 Z= 0.140 Angle : 0.621 14.350 38348 Z= 0.316 Chirality : 0.047 0.456 4436 Planarity : 0.004 0.067 4881 Dihedral : 4.410 52.440 3720 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.36 % Allowed : 16.95 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3419 helix: 0.20 (0.20), residues: 622 sheet: -0.88 (0.22), residues: 591 loop : -1.21 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 765 TYR 0.032 0.001 TYR A1007 PHE 0.013 0.001 PHE A 192 TRP 0.025 0.001 TRP B 353 HIS 0.018 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (28051) covalent geometry : angle 0.61006 / 0.31 (38171) SS BOND : bond 0.00297 / 0.16 ( 36) SS BOND : angle 1.12634 / 0.78 ( 72) hydrogen bonds : bond 0.04438 / 2.99 ( 766) hydrogen bonds : angle 6.31554 / 4.36 ( 2085) link_BETA1-4 : bond 0.00442 / 0.27 ( 7) link_BETA1-4 : angle 1.12426 / 0.68 ( 21) link_NAG-ASN : bond 0.00516 / 0.35 ( 28) link_NAG-ASN : angle 2.37942 / 1.50 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 343 time to evaluate : 1.128 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 660 TYR cc_start: 0.6896 (p90) cc_final: 0.6608 (p90) REVERT: B 347 PHE cc_start: 0.4192 (m-80) cc_final: 0.3811 (m-10) REVERT: B 900 MET cc_start: 0.6849 (mmt) cc_final: 0.6577 (mmt) REVERT: B 1029 MET cc_start: 0.4969 (OUTLIER) cc_final: 0.4757 (ttm) REVERT: C 143 VAL cc_start: -0.0809 (OUTLIER) cc_final: -0.1133 (p) REVERT: C 721 SER cc_start: 0.7946 (t) cc_final: 0.7668 (m) REVERT: C 818 ILE cc_start: 0.7107 (mt) cc_final: 0.6791 (mt) REVERT: C 900 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.6074 (mmm) REVERT: C 964 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7484 (mtmm) REVERT: F 57 ASN cc_start: 0.6042 (p0) cc_final: 0.5620 (p0) REVERT: G 183 LEU cc_start: 0.1303 (OUTLIER) cc_final: 0.1087 (pt) outliers start: 71 outliers final: 56 residues processed: 392 average time/residue: 0.1574 time to fit residues: 102.2812 Evaluate side-chains 395 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 116 optimal weight: 0.0770 chunk 172 optimal weight: 0.9980 chunk 193 optimal weight: 0.1980 chunk 283 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.247558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.212255 restraints weight = 43147.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.212342 restraints weight = 41758.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.213102 restraints weight = 37484.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.213541 restraints weight = 21336.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.214784 restraints weight = 18305.939| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 28122 Z= 0.204 Angle : 0.927 59.199 38348 Z= 0.521 Chirality : 0.048 0.472 4436 Planarity : 0.005 0.079 4881 Dihedral : 4.405 52.402 3720 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.36 % Allowed : 17.25 % Favored : 80.39 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3419 helix: 0.20 (0.20), residues: 622 sheet: -0.87 (0.22), residues: 591 loop : -1.21 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.026 0.001 TYR A1007 PHE 0.027 0.001 PHE B1075 TRP 0.024 0.001 TRP B 353 HIS 0.015 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (28051) covalent geometry : angle 0.92039 / 0.52 (38171) SS BOND : bond 0.00295 / 0.17 ( 36) SS BOND : angle 1.10219 / 0.76 ( 72) hydrogen bonds : bond 0.04460 / 3.00 ( 766) hydrogen bonds : angle 6.33131 / 4.37 ( 2085) link_BETA1-4 : bond 0.00501 / 0.30 ( 7) link_BETA1-4 : angle 1.23725 / 0.77 ( 21) link_NAG-ASN : bond 0.00514 / 0.35 ( 28) link_NAG-ASN : angle 2.37586 / 1.50 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6838 Ramachandran restraints generated. 3419 Oldfield, 0 Emsley, 3419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 340 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 TYR cc_start: 0.6898 (p90) cc_final: 0.6603 (p90) REVERT: B 347 PHE cc_start: 0.4213 (m-80) cc_final: 0.3823 (m-10) REVERT: B 900 MET cc_start: 0.6851 (mmt) cc_final: 0.6566 (mmt) REVERT: B 1029 MET cc_start: 0.5029 (OUTLIER) cc_final: 0.4810 (ttm) REVERT: C 143 VAL cc_start: -0.0803 (OUTLIER) cc_final: -0.1137 (p) REVERT: C 721 SER cc_start: 0.7939 (t) cc_final: 0.7677 (m) REVERT: C 900 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.6053 (mmm) REVERT: C 964 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7556 (mtmm) REVERT: C 1106 GLN cc_start: 0.7409 (mp10) cc_final: 0.6921 (mp10) REVERT: F 57 ASN cc_start: 0.6046 (p0) cc_final: 0.5623 (p0) REVERT: G 183 LEU cc_start: 0.1253 (OUTLIER) cc_final: 0.1037 (pt) outliers start: 71 outliers final: 62 residues processed: 387 average time/residue: 0.1568 time to fit residues: 100.3081 Evaluate side-chains 400 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 334 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 280 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 293 optimal weight: 0.5980 chunk 180 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 304 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.248084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.213921 restraints weight = 43090.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.214820 restraints weight = 45427.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.215730 restraints weight = 35316.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.216076 restraints weight = 21828.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.217224 restraints weight = 19648.022| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 28122 Z= 0.204 Angle : 0.927 59.199 38348 Z= 0.521 Chirality : 0.048 0.472 4436 Planarity : 0.005 0.079 4881 Dihedral : 4.405 52.402 3720 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.19 % Allowed : 17.35 % Favored : 80.45 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3419 helix: 0.20 (0.20), residues: 622 sheet: -0.87 (0.22), residues: 591 loop : -1.21 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.026 0.001 TYR A1007 PHE 0.027 0.001 PHE B1075 TRP 0.024 0.001 TRP B 353 HIS 0.015 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (28051) covalent geometry : angle 0.92040 / 0.52 (38171) SS BOND : bond 0.00295 / 0.17 ( 36) SS BOND : angle 1.10219 / 0.76 ( 72) hydrogen bonds : bond 0.04460 / 3.00 ( 766) hydrogen bonds : angle 6.33131 / 4.37 ( 2085) link_BETA1-4 : bond 0.00501 / 0.30 ( 7) link_BETA1-4 : angle 1.23725 / 0.77 ( 21) link_NAG-ASN : bond 0.00514 / 0.35 ( 28) link_NAG-ASN : angle 2.37586 / 1.50 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4504.34 seconds wall clock time: 79 minutes 9.02 seconds (4749.02 seconds total)