Starting phenix.real_space_refine on Thu Mar 5 16:34:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lyq_23599/03_2026/7lyq_23599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyq_23599/03_2026/7lyq_23599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lyq_23599/03_2026/7lyq_23599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyq_23599/03_2026/7lyq_23599.map" model { file = "/net/cci-nas-00/data/ceres_data/7lyq_23599/03_2026/7lyq_23599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyq_23599/03_2026/7lyq_23599.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.064 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 103 5.16 5 C 15097 2.51 5 N 3887 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23641 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7713 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7712 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7684 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 47, 'TRANS': 945} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.14, per 1000 atoms: 0.22 Number of scatterers: 23641 At special positions: 0 Unit cell: (129.349, 134.694, 194.558, 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 103 16.00 O 4554 8.00 N 3887 7.00 C 15097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B1098 " " NAG B1314 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 873.1 milliseconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 46 sheets defined 27.0% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.749A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.867A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.906A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.837A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.929A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.577A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.023A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.679A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.304A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.639A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.474A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.981A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.897A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.613A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.602A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.117A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.535A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.661A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.804A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.747A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.696A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.778A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.789A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.522A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.726A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.740A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.632A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.644A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.516A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.670A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.680A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.378A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.658A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.590A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.732A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.628A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.369A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.053A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.510A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.510A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.784A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.089A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.407A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.197A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.695A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.658A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.794A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.873A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.313A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.886A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.587A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.955A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.060A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.546A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LYS C 790 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.914A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.914A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.510A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.258A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.608A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.847A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.515A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.899A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.669A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.431A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.431A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.849A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1043 hydrogen bonds defined for protein. 2877 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: 5.52 Time building geometry restraints manager: 2.46 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: 6023 1.33 - 1.46: 4721 1.46 - 1.58: 13289 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24160 Sorted by residual: bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C5 NAG B1314 " pdb=" O5 NAG B1314 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 24155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 27713 2.48 - 4.95: 4993 4.95 - 7.43: 175 7.43 - 9.90: 4 9.90 - 12.38: 3 Bond angle restraints: 32888 Sorted by residual: angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 133.92 -12.38 1.91e+00 2.74e-01 4.20e+01 angle pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " pdb=" CG PHE C 565 " ideal model delta sigma weight residual 113.80 119.71 -5.91 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N ASN B 137 " pdb=" CA ASN B 137 " pdb=" C ASN B 137 " ideal model delta sigma weight residual 111.36 117.70 -6.34 1.09e+00 8.42e-01 3.39e+01 angle pdb=" CA ASP B 568 " pdb=" CB ASP B 568 " pdb=" CG ASP B 568 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.01e+01 angle pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sigma weight residual 113.80 119.29 -5.49 1.00e+00 1.00e+00 3.01e+01 ... (remaining 32883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13844 17.87 - 35.75: 798 35.75 - 53.62: 124 53.62 - 71.50: 49 71.50 - 89.37: 26 Dihedral angle restraints: 14841 sinusoidal: 6168 harmonic: 8673 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -171.19 85.19 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -156.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CA PRO A 479 " pdb=" C PRO A 479 " pdb=" N CYS A 480 " pdb=" CA CYS A 480 " ideal model delta harmonic sigma weight residual 180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 3871 0.276 - 0.552: 15 0.552 - 0.828: 0 0.828 - 1.104: 0 1.104 - 1.380: 2 Chirality restraints: 3888 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.76e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.75e+01 chirality pdb=" CA ASP C 198 " pdb=" N ASP C 198 " pdb=" C ASP C 198 " pdb=" CB ASP C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.33e+00 ... (remaining 3885 not shown) Planarity restraints: 4229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.131 2.00e-02 2.50e+03 1.44e-01 2.58e+02 pdb=" CG ASN B 122 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " 0.228 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.130 2.00e-02 2.50e+03 1.43e-01 2.54e+02 pdb=" CG ASN A 122 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " -0.126 2.00e-02 2.50e+03 1.39e-01 2.40e+02 pdb=" CG ASN C 709 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " 0.219 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.166 2.00e-02 2.50e+03 ... (remaining 4226 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11790 3.00 - 3.47: 22714 3.47 - 3.95: 38864 3.95 - 4.42: 42677 4.42 - 4.90: 72907 Nonbonded interactions: 188952 Sorted by model distance: nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.521 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.526 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.541 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.548 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.550 3.040 ... (remaining 188947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 and (name N or name CA or name C or name O or name C \ B )) or resid 215 through 217 or (resid 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 through 238 or (resid 239 and (name N or name \ CA or name C or name O or name CB )) or resid 240 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 9 through 810 or (resid 811 and (name N or name CA or name C or name O or name C \ B )) or resid 812 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 1 \ 141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) or r \ esid 1143 through 1144 or (resid 1145 through 1146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1147 through 1311)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 130 or (resid 131 through 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 through 134 or (resid 1 \ 35 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (nam \ e N or name CA or name C or name O or name CB )) or resid 192 through 195 or (re \ sid 196 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 241 or (resid 242 through 264 and (name N or name CA or name C \ or name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or n \ ame CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 \ and (name N or name CA or name C or name O or name CB )) or resid 569 through 58 \ 2 or (resid 583 and (name N or name CA or name C or name O or name CB )) or resi \ d 584 through 585 or (resid 586 and (name N or name CA or name C or name O or na \ me CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name C \ or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or (r \ esid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 t \ hrough 747 or (resid 748 and (name N or name CA or name C or name O or name CB ) \ ) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or nam \ e O or name CB )) or resid 812 through 813 or (resid 814 and (name N or name CA \ or name C or name O or name CB )) or resid 815 through 827 or resid 855 through \ 866 or (resid 867 through 868 and (name N or name CA or name C or name O or name \ CB )) or resid 869 through 1091 or (resid 1092 and (name N or name CA or name C \ or name O or name CB )) or resid 1093 through 1143 or (resid 1144 through 1146 \ and (name N or name CA or name C or name O or name CB )) or resid 1147 through 1 \ 311)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 130 or (resid 131 through 132 and (name N or name CA or name C o \ r name O or name CB )) or resid 133 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 143 or ( \ resid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 195 or (resid 196 through 197 and (name N or name CA or name C or name O \ or name CB )) or resid 198 through 213 or (resid 214 and (name N or name CA or \ name C or name O or name CB )) or resid 215 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 238 or (resi \ d 239 and (name N or name CA or name C or name O or name CB )) or resid 240 thro \ ugh 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) o \ r resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O \ or name CB )) or resid 529 through 567 or (resid 568 and (name N or name CA or \ name C or name O or name CB )) or resid 569 through 582 or (resid 583 and (name \ N or name CA or name C or name O or name CB )) or resid 584 through 585 or (resi \ d 586 and (name N or name CA or name C or name O or name CB )) or resid 587 thro \ ugh 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) o \ r resid 620 through 813 or (resid 814 and (name N or name CA or name C or name O \ or name CB )) or resid 815 through 1091 or (resid 1092 and (name N or name CA o \ r name C or name O or name CB )) or resid 1093 through 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 or (resid 1144 \ through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 through 1311)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.590 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.013 0.077 24236 Z= 0.763 Angle : 1.761 12.378 33078 Z= 1.171 Chirality : 0.099 1.380 3888 Planarity : 0.013 0.139 4191 Dihedral : 12.672 89.369 9147 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.21 % Favored : 94.35 % Rotamer: Outliers : 0.43 % Allowed : 1.80 % Favored : 97.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 2937 helix: -0.86 (0.17), residues: 698 sheet: 0.60 (0.22), residues: 495 loop : -0.73 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 273 TYR 0.168 0.019 TYR B 707 PHE 0.087 0.011 PHE A 718 TRP 0.156 0.024 TRP A 64 HIS 0.010 0.003 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.01329 (24160) covalent geometry : angle 1.74243 (32888) SS BOND : bond 0.01144 ( 38) SS BOND : angle 1.71045 ( 76) hydrogen bonds : bond 0.16019 ( 1014) hydrogen bonds : angle 8.60633 ( 2877) link_NAG-ASN : bond 0.01426 ( 38) link_NAG-ASN : angle 4.70156 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 349 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.6667 (tttt) cc_final: 0.6122 (tppt) REVERT: A 403 ARG cc_start: 0.6662 (ptm160) cc_final: 0.6455 (ptm160) REVERT: A 820 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7628 (t0) REVERT: A 902 MET cc_start: 0.8997 (mmm) cc_final: 0.8748 (mmm) REVERT: B 100 ILE cc_start: 0.8254 (mt) cc_final: 0.7878 (mm) REVERT: B 102 ARG cc_start: 0.6127 (mmp-170) cc_final: 0.5790 (mmp-170) REVERT: B 572 THR cc_start: 0.8026 (m) cc_final: 0.6899 (m) REVERT: B 574 ASP cc_start: 0.8205 (p0) cc_final: 0.7122 (m-30) REVERT: B 587 ILE cc_start: 0.8181 (mt) cc_final: 0.7654 (pt) REVERT: B 816 SER cc_start: 0.9200 (p) cc_final: 0.8779 (t) REVERT: B 820 ASP cc_start: 0.7822 (t70) cc_final: 0.7574 (t0) REVERT: B 988 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7094 (mt-10) REVERT: C 190 ARG cc_start: 0.6921 (mtt-85) cc_final: 0.6547 (mmm160) REVERT: C 403 ARG cc_start: 0.6733 (ptm160) cc_final: 0.6376 (ptm160) REVERT: C 417 ASN cc_start: 0.6641 (m110) cc_final: 0.6419 (m110) REVERT: C 421 TYR cc_start: 0.7580 (m-80) cc_final: 0.7212 (m-80) REVERT: C 490 PHE cc_start: 0.7671 (t80) cc_final: 0.7004 (t80) REVERT: C 816 SER cc_start: 0.9218 (p) cc_final: 0.8984 (t) outliers start: 11 outliers final: 4 residues processed: 359 average time/residue: 0.1635 time to fit residues: 90.8780 Evaluate side-chains 163 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 955 ASN A1048 HIS B 354 ASN B 907 ASN B1119 ASN C 460 ASN C 506 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.156405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111953 restraints weight = 37892.114| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.64 r_work: 0.3201 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24236 Z= 0.140 Angle : 0.656 11.625 33078 Z= 0.341 Chirality : 0.046 0.195 3888 Planarity : 0.004 0.051 4191 Dihedral : 6.992 57.135 3996 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 1.45 % Allowed : 5.88 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 2937 helix: 1.26 (0.20), residues: 689 sheet: 0.35 (0.19), residues: 648 loop : -0.46 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 646 TYR 0.024 0.002 TYR C 170 PHE 0.019 0.001 PHE A 497 TRP 0.019 0.001 TRP B 64 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00310 (24160) covalent geometry : angle 0.62394 (32888) SS BOND : bond 0.00368 ( 38) SS BOND : angle 1.26627 ( 76) hydrogen bonds : bond 0.04769 ( 1014) hydrogen bonds : angle 6.26266 ( 2877) link_NAG-ASN : bond 0.00334 ( 38) link_NAG-ASN : angle 3.36961 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.779 Fit side-chains REVERT: A 187 LYS cc_start: 0.6837 (tttt) cc_final: 0.6100 (tppt) REVERT: A 211 ASN cc_start: 0.7099 (m-40) cc_final: 0.6435 (p0) REVERT: A 405 ASP cc_start: 0.7224 (m-30) cc_final: 0.6859 (p0) REVERT: A 421 TYR cc_start: 0.7671 (m-80) cc_final: 0.7390 (m-10) REVERT: A 493 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7749 (tm-30) REVERT: A 820 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8353 (t0) REVERT: A 995 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7687 (mtp85) REVERT: B 64 TRP cc_start: 0.8303 (t60) cc_final: 0.8000 (t-100) REVERT: B 102 ARG cc_start: 0.6340 (mmp-170) cc_final: 0.5671 (mmt180) REVERT: B 816 SER cc_start: 0.9307 (p) cc_final: 0.8937 (t) REVERT: B 820 ASP cc_start: 0.8538 (t70) cc_final: 0.8175 (t0) REVERT: C 190 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.7132 (mtt90) REVERT: C 238 PHE cc_start: 0.7515 (p90) cc_final: 0.7277 (p90) REVERT: C 349 SER cc_start: 0.7713 (m) cc_final: 0.7456 (p) REVERT: C 403 ARG cc_start: 0.7253 (ptm160) cc_final: 0.6821 (ptm160) REVERT: C 421 TYR cc_start: 0.7706 (m-80) cc_final: 0.7401 (m-80) REVERT: C 597 VAL cc_start: 0.8992 (t) cc_final: 0.8700 (p) REVERT: C 1029 MET cc_start: 0.9109 (mmt) cc_final: 0.8731 (tpt) outliers start: 37 outliers final: 23 residues processed: 219 average time/residue: 0.1507 time to fit residues: 53.6831 Evaluate side-chains 169 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 119 optimal weight: 0.5980 chunk 295 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 197 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 955 ASN B 207 HIS B 907 ASN B1048 HIS B1135 ASN C 613 GLN C 901 GLN C 935 GLN C1048 HIS C1083 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.154824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111583 restraints weight = 37794.893| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.68 r_work: 0.3181 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24236 Z= 0.155 Angle : 0.593 10.296 33078 Z= 0.305 Chirality : 0.045 0.205 3888 Planarity : 0.004 0.050 4191 Dihedral : 6.416 57.003 3992 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 1.65 % Allowed : 6.94 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 2937 helix: 1.77 (0.21), residues: 677 sheet: 0.23 (0.19), residues: 669 loop : -0.42 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.035 0.001 TYR A 369 PHE 0.013 0.001 PHE C 135 TRP 0.012 0.001 TRP B 64 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00362 (24160) covalent geometry : angle 0.56933 (32888) SS BOND : bond 0.00574 ( 38) SS BOND : angle 1.08100 ( 76) hydrogen bonds : bond 0.04240 ( 1014) hydrogen bonds : angle 5.81728 ( 2877) link_NAG-ASN : bond 0.00413 ( 38) link_NAG-ASN : angle 2.79804 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8285 (mttt) cc_final: 0.8030 (mmtt) REVERT: A 356 LYS cc_start: 0.8107 (tptt) cc_final: 0.7819 (tptm) REVERT: A 403 ARG cc_start: 0.6877 (ptm160) cc_final: 0.6533 (ptm160) REVERT: A 421 TYR cc_start: 0.7516 (m-80) cc_final: 0.7201 (m-10) REVERT: A 465 GLU cc_start: 0.7997 (tt0) cc_final: 0.7407 (tt0) REVERT: A 820 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8504 (t0) REVERT: A 995 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7583 (mtp85) REVERT: B 64 TRP cc_start: 0.8236 (t60) cc_final: 0.7852 (t60) REVERT: B 102 ARG cc_start: 0.6459 (mmp-170) cc_final: 0.5659 (mmt180) REVERT: B 572 THR cc_start: 0.8407 (m) cc_final: 0.8062 (p) REVERT: B 816 SER cc_start: 0.9339 (p) cc_final: 0.9137 (p) REVERT: B 820 ASP cc_start: 0.8631 (t70) cc_final: 0.8211 (t0) REVERT: B 1051 SER cc_start: 0.9095 (p) cc_final: 0.8886 (m) REVERT: C 238 PHE cc_start: 0.7511 (p90) cc_final: 0.7294 (p90) REVERT: C 349 SER cc_start: 0.7587 (m) cc_final: 0.7348 (p) REVERT: C 403 ARG cc_start: 0.7317 (ptm160) cc_final: 0.6789 (ptm160) REVERT: C 421 TYR cc_start: 0.7635 (m-80) cc_final: 0.7318 (m-80) REVERT: C 436 TRP cc_start: 0.7729 (p90) cc_final: 0.7254 (p90) REVERT: C 569 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8489 (mt) REVERT: C 902 MET cc_start: 0.9335 (tpp) cc_final: 0.9047 (tpt) REVERT: C 1029 MET cc_start: 0.9188 (mmt) cc_final: 0.8865 (tpt) outliers start: 42 outliers final: 33 residues processed: 196 average time/residue: 0.1517 time to fit residues: 48.4619 Evaluate side-chains 184 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 250 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 207 HIS B 907 ASN B1119 ASN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113670 restraints weight = 37963.224| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.86 r_work: 0.3180 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24236 Z= 0.134 Angle : 0.552 14.807 33078 Z= 0.280 Chirality : 0.044 0.217 3888 Planarity : 0.004 0.046 4191 Dihedral : 6.117 56.027 3992 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 1.96 % Allowed : 7.80 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 2937 helix: 1.96 (0.21), residues: 671 sheet: 0.27 (0.19), residues: 659 loop : -0.40 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.021 0.001 TYR C1067 PHE 0.022 0.001 PHE B 329 TRP 0.010 0.001 TRP B 64 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00310 (24160) covalent geometry : angle 0.53037 (32888) SS BOND : bond 0.00333 ( 38) SS BOND : angle 0.91311 ( 76) hydrogen bonds : bond 0.03831 ( 1014) hydrogen bonds : angle 5.59473 ( 2877) link_NAG-ASN : bond 0.00338 ( 38) link_NAG-ASN : angle 2.57487 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8277 (mttt) cc_final: 0.8007 (mmtt) REVERT: A 356 LYS cc_start: 0.8113 (tptt) cc_final: 0.7816 (tptm) REVERT: A 421 TYR cc_start: 0.7453 (m-80) cc_final: 0.7072 (m-10) REVERT: A 988 GLU cc_start: 0.8195 (mp0) cc_final: 0.7903 (mp0) REVERT: A 995 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7620 (mtp85) REVERT: A 1041 ASP cc_start: 0.8887 (t0) cc_final: 0.8649 (t0) REVERT: B 64 TRP cc_start: 0.8072 (t60) cc_final: 0.7687 (t60) REVERT: B 95 THR cc_start: 0.8146 (p) cc_final: 0.7748 (t) REVERT: B 102 ARG cc_start: 0.6554 (mmp-170) cc_final: 0.6045 (mmt180) REVERT: B 572 THR cc_start: 0.8517 (m) cc_final: 0.8240 (p) REVERT: B 816 SER cc_start: 0.9319 (p) cc_final: 0.9105 (p) REVERT: B 820 ASP cc_start: 0.8640 (t70) cc_final: 0.8214 (t0) REVERT: B 1051 SER cc_start: 0.9111 (p) cc_final: 0.8815 (m) REVERT: C 190 ARG cc_start: 0.7537 (mtt90) cc_final: 0.7119 (mmt90) REVERT: C 207 HIS cc_start: 0.6898 (t-170) cc_final: 0.5806 (t-170) REVERT: C 238 PHE cc_start: 0.7528 (p90) cc_final: 0.7293 (p90) REVERT: C 349 SER cc_start: 0.7537 (m) cc_final: 0.7258 (p) REVERT: C 403 ARG cc_start: 0.7394 (ptm160) cc_final: 0.7018 (ptm160) REVERT: C 421 TYR cc_start: 0.7629 (m-80) cc_final: 0.7346 (m-80) REVERT: C 436 TRP cc_start: 0.7711 (p90) cc_final: 0.7292 (p90) REVERT: C 468 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7960 (mm) REVERT: C 489 TYR cc_start: 0.8175 (m-80) cc_final: 0.7680 (m-80) REVERT: C 490 PHE cc_start: 0.8051 (t80) cc_final: 0.7814 (t80) REVERT: C 569 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8486 (mt) outliers start: 50 outliers final: 36 residues processed: 222 average time/residue: 0.1408 time to fit residues: 51.8008 Evaluate side-chains 203 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.0970 chunk 173 optimal weight: 0.7980 chunk 280 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 856 ASN B 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.155661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105383 restraints weight = 37833.060| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.70 r_work: 0.3168 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24236 Z= 0.142 Angle : 0.547 13.036 33078 Z= 0.277 Chirality : 0.044 0.226 3888 Planarity : 0.003 0.041 4191 Dihedral : 5.860 55.910 3988 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.92 % Allowed : 8.89 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 2937 helix: 1.98 (0.21), residues: 672 sheet: 0.28 (0.19), residues: 662 loop : -0.42 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.026 0.001 TYR A 369 PHE 0.026 0.001 PHE B 329 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00331 (24160) covalent geometry : angle 0.52743 (32888) SS BOND : bond 0.00320 ( 38) SS BOND : angle 0.85599 ( 76) hydrogen bonds : bond 0.03790 ( 1014) hydrogen bonds : angle 5.49281 ( 2877) link_NAG-ASN : bond 0.00308 ( 38) link_NAG-ASN : angle 2.46797 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8281 (mttt) cc_final: 0.8030 (mmtt) REVERT: A 356 LYS cc_start: 0.8151 (tptt) cc_final: 0.7852 (tptm) REVERT: A 394 ASN cc_start: 0.7886 (m-40) cc_final: 0.7440 (m-40) REVERT: A 421 TYR cc_start: 0.7514 (m-80) cc_final: 0.7174 (m-10) REVERT: A 493 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7992 (tm-30) REVERT: A 988 GLU cc_start: 0.8237 (mp0) cc_final: 0.7867 (mp0) REVERT: A 995 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7745 (mtp85) REVERT: A 1041 ASP cc_start: 0.8898 (t0) cc_final: 0.8622 (t0) REVERT: B 64 TRP cc_start: 0.8099 (t60) cc_final: 0.7632 (t60) REVERT: B 95 THR cc_start: 0.8162 (p) cc_final: 0.7722 (t) REVERT: B 102 ARG cc_start: 0.6594 (mmp-170) cc_final: 0.6098 (mmt180) REVERT: B 307 THR cc_start: 0.9085 (m) cc_final: 0.8802 (p) REVERT: B 572 THR cc_start: 0.8577 (m) cc_final: 0.7430 (p) REVERT: B 574 ASP cc_start: 0.8562 (p0) cc_final: 0.7791 (m-30) REVERT: B 656 VAL cc_start: 0.8900 (t) cc_final: 0.8590 (m) REVERT: B 820 ASP cc_start: 0.8664 (t70) cc_final: 0.8256 (t0) REVERT: C 190 ARG cc_start: 0.7458 (mtt90) cc_final: 0.7014 (mmt90) REVERT: C 207 HIS cc_start: 0.6781 (t-170) cc_final: 0.4453 (t-170) REVERT: C 238 PHE cc_start: 0.7490 (p90) cc_final: 0.7245 (p90) REVERT: C 349 SER cc_start: 0.7495 (m) cc_final: 0.7201 (p) REVERT: C 403 ARG cc_start: 0.7369 (ptm160) cc_final: 0.6830 (ptm160) REVERT: C 418 ILE cc_start: 0.7890 (mt) cc_final: 0.7673 (tp) REVERT: C 421 TYR cc_start: 0.7616 (m-80) cc_final: 0.7389 (m-80) REVERT: C 436 TRP cc_start: 0.7797 (p90) cc_final: 0.7404 (p90) REVERT: C 489 TYR cc_start: 0.8055 (m-80) cc_final: 0.7763 (m-80) REVERT: C 902 MET cc_start: 0.9312 (tpp) cc_final: 0.9017 (tpt) REVERT: C 985 ASP cc_start: 0.8237 (t0) cc_final: 0.7718 (t70) outliers start: 49 outliers final: 40 residues processed: 213 average time/residue: 0.1503 time to fit residues: 51.4435 Evaluate side-chains 195 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 207 HIS B 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.156455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106337 restraints weight = 38116.989| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.58 r_work: 0.3197 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24236 Z= 0.111 Angle : 0.519 12.680 33078 Z= 0.263 Chirality : 0.043 0.222 3888 Planarity : 0.003 0.040 4191 Dihedral : 5.654 55.546 3988 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.84 % Allowed : 9.37 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 2937 helix: 2.16 (0.21), residues: 669 sheet: 0.29 (0.19), residues: 677 loop : -0.38 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.023 0.001 TYR B1138 PHE 0.024 0.001 PHE B 329 TRP 0.009 0.001 TRP B 104 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00252 (24160) covalent geometry : angle 0.50142 (32888) SS BOND : bond 0.00271 ( 38) SS BOND : angle 0.76485 ( 76) hydrogen bonds : bond 0.03520 ( 1014) hydrogen bonds : angle 5.35503 ( 2877) link_NAG-ASN : bond 0.00305 ( 38) link_NAG-ASN : angle 2.28528 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8283 (mttt) cc_final: 0.8012 (mmtt) REVERT: A 356 LYS cc_start: 0.8149 (tptt) cc_final: 0.7858 (tptm) REVERT: A 394 ASN cc_start: 0.7801 (m-40) cc_final: 0.7353 (m-40) REVERT: A 403 ARG cc_start: 0.6196 (ptm160) cc_final: 0.5649 (ptp-110) REVERT: A 421 TYR cc_start: 0.7491 (m-80) cc_final: 0.7150 (m-10) REVERT: A 493 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8056 (tm-30) REVERT: A 779 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: A 868 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: A 988 GLU cc_start: 0.8195 (mp0) cc_final: 0.7975 (mp0) REVERT: A 995 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7759 (mtp85) REVERT: A 1041 ASP cc_start: 0.8911 (t0) cc_final: 0.8643 (t0) REVERT: B 64 TRP cc_start: 0.7953 (t60) cc_final: 0.7456 (t60) REVERT: B 95 THR cc_start: 0.8109 (p) cc_final: 0.7640 (t) REVERT: B 102 ARG cc_start: 0.6592 (mmp-170) cc_final: 0.6147 (mmt180) REVERT: B 307 THR cc_start: 0.9059 (m) cc_final: 0.8850 (p) REVERT: B 572 THR cc_start: 0.8573 (m) cc_final: 0.7377 (p) REVERT: B 574 ASP cc_start: 0.8445 (p0) cc_final: 0.7855 (m-30) REVERT: B 656 VAL cc_start: 0.8861 (t) cc_final: 0.8585 (m) REVERT: B 820 ASP cc_start: 0.8646 (t70) cc_final: 0.8181 (t0) REVERT: C 238 PHE cc_start: 0.7455 (p90) cc_final: 0.7180 (p90) REVERT: C 349 SER cc_start: 0.7416 (m) cc_final: 0.7117 (p) REVERT: C 403 ARG cc_start: 0.7281 (ptm160) cc_final: 0.6874 (ptm160) REVERT: C 418 ILE cc_start: 0.7861 (mt) cc_final: 0.7628 (tp) REVERT: C 436 TRP cc_start: 0.7808 (p90) cc_final: 0.7496 (p90) REVERT: C 489 TYR cc_start: 0.7929 (m-80) cc_final: 0.7568 (m-80) REVERT: C 490 PHE cc_start: 0.8066 (t80) cc_final: 0.7771 (t80) REVERT: C 902 MET cc_start: 0.9266 (tpp) cc_final: 0.9000 (tpt) REVERT: C 985 ASP cc_start: 0.8158 (t0) cc_final: 0.7784 (t70) outliers start: 47 outliers final: 39 residues processed: 203 average time/residue: 0.1442 time to fit residues: 48.1459 Evaluate side-chains 194 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 158 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 253 optimal weight: 0.0010 chunk 41 optimal weight: 6.9990 chunk 296 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 240 optimal weight: 0.0370 chunk 257 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 overall best weight: 0.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.157176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113232 restraints weight = 37641.586| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.59 r_work: 0.3242 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24236 Z= 0.086 Angle : 0.493 12.172 33078 Z= 0.250 Chirality : 0.043 0.209 3888 Planarity : 0.003 0.038 4191 Dihedral : 5.402 55.820 3988 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.57 % Allowed : 9.84 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.16), residues: 2937 helix: 2.44 (0.21), residues: 657 sheet: 0.35 (0.19), residues: 670 loop : -0.31 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 983 TYR 0.022 0.001 TYR B1138 PHE 0.021 0.001 PHE B 329 TRP 0.010 0.001 TRP B 104 HIS 0.003 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00178 (24160) covalent geometry : angle 0.47753 (32888) SS BOND : bond 0.00233 ( 38) SS BOND : angle 0.65617 ( 76) hydrogen bonds : bond 0.03175 ( 1014) hydrogen bonds : angle 5.16744 ( 2877) link_NAG-ASN : bond 0.00333 ( 38) link_NAG-ASN : angle 2.08168 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8281 (mttt) cc_final: 0.8005 (mptt) REVERT: A 356 LYS cc_start: 0.8173 (tptt) cc_final: 0.7883 (tptm) REVERT: A 383 SER cc_start: 0.8741 (t) cc_final: 0.8285 (p) REVERT: A 394 ASN cc_start: 0.7606 (m-40) cc_final: 0.7187 (m-40) REVERT: A 403 ARG cc_start: 0.6187 (ptm160) cc_final: 0.5576 (ptp-110) REVERT: A 421 TYR cc_start: 0.7457 (m-80) cc_final: 0.7216 (m-80) REVERT: A 465 GLU cc_start: 0.7739 (tt0) cc_final: 0.7176 (tt0) REVERT: A 493 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8140 (tm-30) REVERT: A 868 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: A 988 GLU cc_start: 0.8290 (mp0) cc_final: 0.7903 (mp0) REVERT: B 64 TRP cc_start: 0.7864 (t60) cc_final: 0.7448 (t60) REVERT: B 95 THR cc_start: 0.7901 (p) cc_final: 0.7476 (t) REVERT: B 102 ARG cc_start: 0.6639 (mmp-170) cc_final: 0.6270 (mmt180) REVERT: B 233 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7877 (tp) REVERT: B 307 THR cc_start: 0.9041 (m) cc_final: 0.8831 (p) REVERT: B 572 THR cc_start: 0.8690 (m) cc_final: 0.7544 (p) REVERT: B 574 ASP cc_start: 0.8419 (p0) cc_final: 0.7915 (m-30) REVERT: B 656 VAL cc_start: 0.8838 (t) cc_final: 0.8604 (m) REVERT: B 820 ASP cc_start: 0.8628 (t70) cc_final: 0.8170 (t0) REVERT: C 190 ARG cc_start: 0.7539 (mtt90) cc_final: 0.6965 (mtp85) REVERT: C 349 SER cc_start: 0.7404 (m) cc_final: 0.7127 (p) REVERT: C 403 ARG cc_start: 0.7306 (ptm160) cc_final: 0.6936 (ptm160) REVERT: C 436 TRP cc_start: 0.7791 (p90) cc_final: 0.7532 (p90) REVERT: C 489 TYR cc_start: 0.7995 (m-80) cc_final: 0.7591 (m-80) REVERT: C 490 PHE cc_start: 0.8196 (t80) cc_final: 0.7225 (t80) REVERT: C 985 ASP cc_start: 0.7983 (t0) cc_final: 0.7720 (t0) outliers start: 40 outliers final: 28 residues processed: 210 average time/residue: 0.1417 time to fit residues: 49.1835 Evaluate side-chains 189 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 267 optimal weight: 3.9990 chunk 137 optimal weight: 40.0000 chunk 274 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 229 optimal weight: 0.4980 chunk 113 optimal weight: 0.1980 chunk 196 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.157413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113613 restraints weight = 37865.742| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.64 r_work: 0.3214 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24236 Z= 0.110 Angle : 0.502 12.082 33078 Z= 0.254 Chirality : 0.043 0.218 3888 Planarity : 0.003 0.039 4191 Dihedral : 5.369 55.558 3988 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.61 % Allowed : 10.15 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2937 helix: 2.36 (0.21), residues: 658 sheet: 0.31 (0.19), residues: 679 loop : -0.28 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 995 TYR 0.028 0.001 TYR C 421 PHE 0.022 0.001 PHE B 329 TRP 0.009 0.001 TRP B 104 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00252 (24160) covalent geometry : angle 0.48702 (32888) SS BOND : bond 0.00277 ( 38) SS BOND : angle 0.70488 ( 76) hydrogen bonds : bond 0.03341 ( 1014) hydrogen bonds : angle 5.16672 ( 2877) link_NAG-ASN : bond 0.00278 ( 38) link_NAG-ASN : angle 2.05976 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8264 (mttt) cc_final: 0.7978 (mptt) REVERT: A 356 LYS cc_start: 0.8189 (tptt) cc_final: 0.7898 (tptm) REVERT: A 383 SER cc_start: 0.8765 (t) cc_final: 0.8316 (p) REVERT: A 394 ASN cc_start: 0.7675 (m-40) cc_final: 0.7258 (m-40) REVERT: A 403 ARG cc_start: 0.6053 (ptm160) cc_final: 0.5612 (ptp-110) REVERT: A 421 TYR cc_start: 0.7415 (m-80) cc_final: 0.7174 (m-80) REVERT: A 988 GLU cc_start: 0.8246 (mp0) cc_final: 0.7877 (mp0) REVERT: B 64 TRP cc_start: 0.7902 (t60) cc_final: 0.7601 (t60) REVERT: B 95 THR cc_start: 0.7894 (p) cc_final: 0.7463 (t) REVERT: B 102 ARG cc_start: 0.6637 (mmp-170) cc_final: 0.6290 (mmt180) REVERT: B 307 THR cc_start: 0.9004 (m) cc_final: 0.8779 (p) REVERT: B 572 THR cc_start: 0.8727 (m) cc_final: 0.7638 (p) REVERT: B 574 ASP cc_start: 0.8385 (p0) cc_final: 0.8029 (m-30) REVERT: B 656 VAL cc_start: 0.8855 (t) cc_final: 0.8589 (m) REVERT: B 820 ASP cc_start: 0.8641 (t70) cc_final: 0.8202 (t0) REVERT: C 190 ARG cc_start: 0.7514 (mtt90) cc_final: 0.6920 (mtp85) REVERT: C 349 SER cc_start: 0.7532 (m) cc_final: 0.7233 (p) REVERT: C 403 ARG cc_start: 0.7326 (ptm160) cc_final: 0.6964 (ptm160) REVERT: C 436 TRP cc_start: 0.7799 (p90) cc_final: 0.7584 (p90) REVERT: C 489 TYR cc_start: 0.8083 (m-80) cc_final: 0.7618 (m-80) REVERT: C 490 PHE cc_start: 0.8209 (t80) cc_final: 0.7260 (t80) REVERT: C 985 ASP cc_start: 0.8012 (t0) cc_final: 0.7746 (t0) outliers start: 41 outliers final: 35 residues processed: 197 average time/residue: 0.1410 time to fit residues: 46.3549 Evaluate side-chains 192 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 207 HIS B1119 ASN C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.156011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105782 restraints weight = 38076.597| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.58 r_work: 0.3186 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24236 Z= 0.142 Angle : 0.523 11.777 33078 Z= 0.265 Chirality : 0.043 0.227 3888 Planarity : 0.003 0.040 4191 Dihedral : 5.459 55.891 3988 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.49 % Allowed : 10.50 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2937 helix: 2.27 (0.21), residues: 655 sheet: 0.25 (0.19), residues: 683 loop : -0.32 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 995 TYR 0.027 0.001 TYR C 421 PHE 0.021 0.001 PHE B 329 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00334 (24160) covalent geometry : angle 0.50692 (32888) SS BOND : bond 0.00322 ( 38) SS BOND : angle 1.00786 ( 76) hydrogen bonds : bond 0.03551 ( 1014) hydrogen bonds : angle 5.23389 ( 2877) link_NAG-ASN : bond 0.00321 ( 38) link_NAG-ASN : angle 2.12004 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8265 (mttt) cc_final: 0.7984 (mmtt) REVERT: A 356 LYS cc_start: 0.8174 (tptt) cc_final: 0.7881 (tptm) REVERT: A 383 SER cc_start: 0.8684 (t) cc_final: 0.8265 (p) REVERT: A 394 ASN cc_start: 0.7795 (m-40) cc_final: 0.7371 (m-40) REVERT: A 403 ARG cc_start: 0.6005 (ptm160) cc_final: 0.5577 (ptp-110) REVERT: A 421 TYR cc_start: 0.7433 (m-80) cc_final: 0.7207 (m-80) REVERT: A 988 GLU cc_start: 0.8228 (mp0) cc_final: 0.7739 (mp0) REVERT: B 95 THR cc_start: 0.7958 (p) cc_final: 0.7480 (t) REVERT: B 102 ARG cc_start: 0.6692 (mmp-170) cc_final: 0.6281 (mmt180) REVERT: B 307 THR cc_start: 0.8987 (m) cc_final: 0.8731 (p) REVERT: B 572 THR cc_start: 0.8683 (m) cc_final: 0.7613 (p) REVERT: B 574 ASP cc_start: 0.8268 (p0) cc_final: 0.8009 (m-30) REVERT: B 656 VAL cc_start: 0.8857 (t) cc_final: 0.8580 (m) REVERT: B 820 ASP cc_start: 0.8757 (t70) cc_final: 0.8278 (t0) REVERT: C 190 ARG cc_start: 0.7449 (mtt90) cc_final: 0.6835 (mtp85) REVERT: C 238 PHE cc_start: 0.7463 (p90) cc_final: 0.7141 (p90) REVERT: C 349 SER cc_start: 0.7558 (m) cc_final: 0.7251 (p) REVERT: C 403 ARG cc_start: 0.7332 (ptm160) cc_final: 0.6965 (ptm160) REVERT: C 489 TYR cc_start: 0.8058 (m-80) cc_final: 0.7590 (m-80) REVERT: C 490 PHE cc_start: 0.8111 (t80) cc_final: 0.7270 (t80) REVERT: C 985 ASP cc_start: 0.8087 (t70) cc_final: 0.7827 (t0) outliers start: 38 outliers final: 34 residues processed: 190 average time/residue: 0.1366 time to fit residues: 43.3671 Evaluate side-chains 189 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 215 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 262 optimal weight: 0.8980 chunk 167 optimal weight: 0.4980 chunk 235 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 127 optimal weight: 50.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN C 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.155772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108933 restraints weight = 37588.286| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.78 r_work: 0.3191 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24236 Z= 0.105 Angle : 0.506 11.643 33078 Z= 0.256 Chirality : 0.043 0.218 3888 Planarity : 0.003 0.039 4191 Dihedral : 5.357 55.486 3988 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.33 % Allowed : 10.74 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 2937 helix: 2.33 (0.21), residues: 658 sheet: 0.24 (0.19), residues: 685 loop : -0.29 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.027 0.001 TYR C 421 PHE 0.021 0.001 PHE B 329 TRP 0.015 0.001 TRP C 436 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00237 (24160) covalent geometry : angle 0.49030 (32888) SS BOND : bond 0.00281 ( 38) SS BOND : angle 1.08201 ( 76) hydrogen bonds : bond 0.03296 ( 1014) hydrogen bonds : angle 5.12960 ( 2877) link_NAG-ASN : bond 0.00284 ( 38) link_NAG-ASN : angle 2.05424 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8367 (mttt) cc_final: 0.8098 (mmtt) REVERT: A 356 LYS cc_start: 0.8188 (tptt) cc_final: 0.7895 (tptm) REVERT: A 383 SER cc_start: 0.8723 (t) cc_final: 0.8399 (p) REVERT: A 394 ASN cc_start: 0.7719 (m-40) cc_final: 0.7309 (m-40) REVERT: A 403 ARG cc_start: 0.6012 (ptm160) cc_final: 0.5572 (ptp-110) REVERT: A 988 GLU cc_start: 0.8245 (mp0) cc_final: 0.7819 (mp0) REVERT: B 95 THR cc_start: 0.8043 (p) cc_final: 0.7544 (t) REVERT: B 102 ARG cc_start: 0.6709 (mmp-170) cc_final: 0.6298 (mmt180) REVERT: B 307 THR cc_start: 0.8979 (m) cc_final: 0.8702 (p) REVERT: B 572 THR cc_start: 0.8756 (m) cc_final: 0.7681 (p) REVERT: B 656 VAL cc_start: 0.8860 (t) cc_final: 0.8605 (m) REVERT: B 820 ASP cc_start: 0.8792 (t70) cc_final: 0.8342 (t0) REVERT: B 934 ILE cc_start: 0.9148 (mm) cc_final: 0.8893 (tt) REVERT: B 988 GLU cc_start: 0.8670 (tp30) cc_final: 0.8238 (mt-10) REVERT: C 190 ARG cc_start: 0.7538 (mtt90) cc_final: 0.6916 (mtp85) REVERT: C 238 PHE cc_start: 0.7466 (p90) cc_final: 0.7146 (p90) REVERT: C 349 SER cc_start: 0.7516 (m) cc_final: 0.7202 (p) REVERT: C 403 ARG cc_start: 0.7255 (ptm160) cc_final: 0.6715 (ptm160) REVERT: C 489 TYR cc_start: 0.8011 (m-80) cc_final: 0.7567 (m-80) REVERT: C 490 PHE cc_start: 0.8209 (t80) cc_final: 0.7303 (t80) REVERT: C 985 ASP cc_start: 0.8096 (t70) cc_final: 0.7875 (t0) outliers start: 34 outliers final: 31 residues processed: 189 average time/residue: 0.1388 time to fit residues: 43.8590 Evaluate side-chains 189 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 279 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 205 optimal weight: 0.0570 chunk 257 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 chunk 152 optimal weight: 0.0980 chunk 135 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.155105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105632 restraints weight = 37423.404| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.60 r_work: 0.3207 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24236 Z= 0.120 Angle : 0.510 11.623 33078 Z= 0.258 Chirality : 0.043 0.221 3888 Planarity : 0.003 0.039 4191 Dihedral : 5.362 55.603 3988 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.37 % Allowed : 10.85 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.15), residues: 2937 helix: 2.29 (0.21), residues: 658 sheet: 0.22 (0.19), residues: 686 loop : -0.27 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.026 0.001 TYR C 421 PHE 0.020 0.001 PHE B 329 TRP 0.017 0.001 TRP C 436 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00277 (24160) covalent geometry : angle 0.49592 (32888) SS BOND : bond 0.00309 ( 38) SS BOND : angle 1.00694 ( 76) hydrogen bonds : bond 0.03383 ( 1014) hydrogen bonds : angle 5.14322 ( 2877) link_NAG-ASN : bond 0.00281 ( 38) link_NAG-ASN : angle 1.99440 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6861.55 seconds wall clock time: 117 minutes 36.81 seconds (7056.81 seconds total)