Starting phenix.real_space_refine on Sat Jul 4 22:12:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lyq_23599/07_2026/7lyq_23599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyq_23599/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7lyq_23599/07_2026/7lyq_23599.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lyq_23599/07_2026/7lyq_23599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyq_23599/07_2026/7lyq_23599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyq_23599/07_2026/7lyq_23599.map" model { file = "/net/cci-nas-00/data/ceres_data/7lyq_23599/07_2026/7lyq_23599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyq_23599/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 chiralities: 11 Time building chain proxies: 5.26, 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: 1.84 Conformation dependent library (CDL) restraints added in 954.4 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: 1.01 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: 6.06 Time building geometry restraints manager: 2.48 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: 13109 17.87 - 35.75: 757 35.75 - 53.62: 103 53.62 - 71.50: 48 71.50 - 89.37: 26 Dihedral angle restraints: 14043 sinusoidal: 5370 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 14040 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 23.260 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 12.830 89.369 8349 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/Z covalent geometry : bond 0.01329 / 0.76 (24160) covalent geometry : angle 1.74243 / 1.17 (32888) SS BOND : bond 0.01144 / 0.65 ( 38) SS BOND : angle 1.71045 / 1.14 ( 76) hydrogen bonds : bond 0.16019 / 10.42 ( 1014) hydrogen bonds : angle 8.60633 / 6.09 ( 2877) link_NAG-ASN : bond 0.01426 / 0.83 ( 38) link_NAG-ASN : angle 4.70156 / 3.23 ( 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 : 0.697 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: 0.1741 time to fit residues: 97.2250 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 : 0.955 ------------------------------------------------------------------------------- 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... A 856 ASN A1048 HIS B 354 ASN B 907 ASN B1119 ASN C 460 ASN C 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.156387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.111758 restraints weight = 37906.528| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.59 r_work: 0.3201 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24236 Z= 0.143 Angle : 0.666 11.595 33078 Z= 0.346 Chirality : 0.046 0.193 3888 Planarity : 0.004 0.053 4191 Dihedral : 5.921 48.507 3198 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 1.49 % Allowed : 5.88 % Favored : 92.63 % 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: 0.14 (0.15), residues: 2937 helix: 1.21 (0.20), residues: 689 sheet: 0.35 (0.19), residues: 648 loop : -0.48 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 646 TYR 0.025 0.002 TYR C 170 PHE 0.018 0.001 PHE A 497 TRP 0.019 0.002 TRP B 64 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (24160) covalent geometry : angle 0.63630 / 0.34 (32888) SS BOND : bond 0.00358 / 0.22 ( 38) SS BOND : angle 1.14327 / 0.65 ( 76) hydrogen bonds : bond 0.04812 / 3.18 ( 1014) hydrogen bonds : angle 6.28876 / 4.48 ( 2877) link_NAG-ASN : bond 0.00366 / 0.24 ( 38) link_NAG-ASN : angle 3.31161 / 2.31 ( 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 225 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.6828 (tttt) cc_final: 0.6113 (tppt) REVERT: A 211 ASN cc_start: 0.7081 (m-40) cc_final: 0.6415 (p0) REVERT: A 394 ASN cc_start: 0.7974 (m-40) cc_final: 0.7752 (m-40) REVERT: A 405 ASP cc_start: 0.7218 (m-30) cc_final: 0.6863 (p0) REVERT: A 421 TYR cc_start: 0.7511 (m-80) cc_final: 0.7235 (m-10) REVERT: A 820 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8361 (t0) REVERT: B 64 TRP cc_start: 0.8288 (t60) cc_final: 0.7992 (t-100) REVERT: B 102 ARG cc_start: 0.6317 (mmp-170) cc_final: 0.5636 (mmt180) REVERT: B 816 SER cc_start: 0.9306 (p) cc_final: 0.8935 (t) REVERT: B 820 ASP cc_start: 0.8527 (t70) cc_final: 0.8169 (t0) REVERT: C 190 ARG cc_start: 0.7376 (mtt-85) cc_final: 0.7143 (mtt90) REVERT: C 238 PHE cc_start: 0.7506 (p90) cc_final: 0.7280 (p90) REVERT: C 349 SER cc_start: 0.7729 (m) cc_final: 0.7464 (p) REVERT: C 403 ARG cc_start: 0.7267 (ptm160) cc_final: 0.6834 (ptm160) REVERT: C 421 TYR cc_start: 0.7701 (m-80) cc_final: 0.7400 (m-80) REVERT: C 468 ILE cc_start: 0.8420 (pt) cc_final: 0.8009 (mm) REVERT: C 597 VAL cc_start: 0.8986 (t) cc_final: 0.8700 (p) REVERT: C 1029 MET cc_start: 0.9116 (mmt) cc_final: 0.8748 (tpt) outliers start: 38 outliers final: 23 residues processed: 217 average time/residue: 0.1588 time to fit residues: 56.2600 Evaluate side-chains 168 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 295 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 289 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 197 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.154613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111020 restraints weight = 37867.678| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.62 r_work: 0.3178 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24236 Z= 0.167 Angle : 0.601 10.266 33078 Z= 0.308 Chirality : 0.045 0.219 3888 Planarity : 0.004 0.053 4191 Dihedral : 5.242 52.836 3194 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 1.84 % Allowed : 6.90 % Favored : 91.26 % 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: 0.30 (0.15), residues: 2937 helix: 1.72 (0.21), residues: 677 sheet: 0.25 (0.19), residues: 666 loop : -0.46 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.031 0.002 TYR A 369 PHE 0.013 0.002 PHE A 559 TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (24160) covalent geometry : angle 0.58084 / 0.30 (32888) SS BOND : bond 0.00388 / 0.24 ( 38) SS BOND : angle 0.96527 / 0.56 ( 76) hydrogen bonds : bond 0.04265 / 2.82 ( 1014) hydrogen bonds : angle 5.80278 / 4.13 ( 2877) link_NAG-ASN : bond 0.00377 / 0.26 ( 38) link_NAG-ASN : angle 2.61106 / 1.83 ( 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 224 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8295 (mttt) cc_final: 0.8070 (mmtt) REVERT: A 356 LYS cc_start: 0.8063 (tptt) cc_final: 0.7784 (tptm) REVERT: A 403 ARG cc_start: 0.6875 (ptm160) cc_final: 0.6624 (ptm160) REVERT: A 421 TYR cc_start: 0.7506 (m-80) cc_final: 0.7187 (m-10) REVERT: A 465 GLU cc_start: 0.8029 (tt0) cc_final: 0.7360 (tt0) REVERT: A 820 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8566 (t0) REVERT: A 1041 ASP cc_start: 0.8888 (t0) cc_final: 0.8662 (t0) REVERT: B 64 TRP cc_start: 0.8183 (t60) cc_final: 0.7755 (t60) REVERT: B 102 ARG cc_start: 0.6461 (mmp-170) cc_final: 0.5642 (mmt180) REVERT: B 572 THR cc_start: 0.8476 (m) cc_final: 0.8167 (p) REVERT: B 820 ASP cc_start: 0.8619 (t70) cc_final: 0.8203 (t0) REVERT: C 238 PHE cc_start: 0.7502 (p90) cc_final: 0.7261 (p90) REVERT: C 349 SER cc_start: 0.7633 (m) cc_final: 0.7392 (p) REVERT: C 403 ARG cc_start: 0.7341 (ptm160) cc_final: 0.6833 (ptm160) REVERT: C 421 TYR cc_start: 0.7640 (m-80) cc_final: 0.7323 (m-80) REVERT: C 436 TRP cc_start: 0.7734 (p90) cc_final: 0.7280 (p90) REVERT: C 489 TYR cc_start: 0.8158 (m-80) cc_final: 0.7893 (m-80) REVERT: C 569 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8492 (mt) REVERT: C 902 MET cc_start: 0.9295 (tpp) cc_final: 0.9004 (tpt) REVERT: C 1029 MET cc_start: 0.9195 (mmt) cc_final: 0.8928 (tpt) outliers start: 47 outliers final: 35 residues processed: 217 average time/residue: 0.1542 time to fit residues: 54.9762 Evaluate side-chains 188 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 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 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: 0.0670 chunk 179 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 165 optimal weight: 0.0470 chunk 250 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN B 907 ASN B1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.156585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106445 restraints weight = 38005.705| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.57 r_work: 0.3204 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24236 Z= 0.117 Angle : 0.545 14.701 33078 Z= 0.276 Chirality : 0.044 0.215 3888 Planarity : 0.003 0.046 4191 Dihedral : 4.880 54.298 3194 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.68 % Allowed : 8.11 % Favored : 90.20 % 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: 0.48 (0.15), residues: 2937 helix: 2.01 (0.21), residues: 673 sheet: 0.33 (0.19), residues: 655 loop : -0.39 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.021 0.001 TYR C1067 PHE 0.019 0.001 PHE B 329 TRP 0.011 0.001 TRP B 64 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (24160) covalent geometry : angle 0.52625 / 0.27 (32888) SS BOND : bond 0.00302 / 0.19 ( 38) SS BOND : angle 0.84272 / 0.51 ( 76) hydrogen bonds : bond 0.03706 / 2.45 ( 1014) hydrogen bonds : angle 5.52879 / 3.93 ( 2877) link_NAG-ASN : bond 0.00319 / 0.20 ( 38) link_NAG-ASN : angle 2.40311 / 1.68 ( 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 221 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8271 (mttt) cc_final: 0.8003 (mmtt) REVERT: A 356 LYS cc_start: 0.8116 (tptt) cc_final: 0.7811 (tptm) REVERT: A 421 TYR cc_start: 0.7488 (m-80) cc_final: 0.7104 (m-10) REVERT: A 564 GLN cc_start: 0.8301 (tp40) cc_final: 0.8098 (tp40) REVERT: A 988 GLU cc_start: 0.8196 (mp0) cc_final: 0.7937 (mp0) REVERT: A 1041 ASP cc_start: 0.8909 (t0) cc_final: 0.8653 (t0) REVERT: B 64 TRP cc_start: 0.8045 (t60) cc_final: 0.7605 (t60) REVERT: B 95 THR cc_start: 0.8060 (p) cc_final: 0.7615 (t) REVERT: B 102 ARG cc_start: 0.6430 (mmp-170) cc_final: 0.6005 (mmt180) REVERT: B 572 THR cc_start: 0.8546 (m) cc_final: 0.7223 (p) REVERT: B 574 ASP cc_start: 0.8619 (p0) cc_final: 0.7801 (m-30) REVERT: B 656 VAL cc_start: 0.8867 (t) cc_final: 0.8560 (m) REVERT: B 820 ASP cc_start: 0.8622 (t70) cc_final: 0.8185 (t0) REVERT: C 238 PHE cc_start: 0.7514 (p90) cc_final: 0.7257 (p90) REVERT: C 349 SER cc_start: 0.7522 (m) cc_final: 0.7228 (p) REVERT: C 403 ARG cc_start: 0.7435 (ptm160) cc_final: 0.7047 (ptm160) REVERT: C 421 TYR cc_start: 0.7632 (m-80) cc_final: 0.7371 (m-80) REVERT: C 436 TRP cc_start: 0.7736 (p90) cc_final: 0.7332 (p90) REVERT: C 489 TYR cc_start: 0.8181 (m-80) cc_final: 0.7688 (m-80) REVERT: C 490 PHE cc_start: 0.8056 (t80) cc_final: 0.7816 (t80) REVERT: C 569 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8477 (mt) REVERT: C 985 ASP cc_start: 0.7991 (t70) cc_final: 0.7487 (t70) outliers start: 43 outliers final: 32 residues processed: 214 average time/residue: 0.1518 time to fit residues: 54.0376 Evaluate side-chains 189 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 1045 LYS 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 907 ASN 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 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: 0.7980 chunk 173 optimal weight: 0.5980 chunk 280 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 0.0270 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 207 HIS B 675 GLN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.156306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104028 restraints weight = 37667.956| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.41 r_work: 0.3234 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24236 Z= 0.101 Angle : 0.521 13.090 33078 Z= 0.263 Chirality : 0.043 0.215 3888 Planarity : 0.003 0.039 4191 Dihedral : 4.445 32.548 3190 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.80 % Allowed : 9.01 % 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: 0.57 (0.15), residues: 2937 helix: 2.15 (0.21), residues: 668 sheet: 0.42 (0.19), residues: 660 loop : -0.38 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.026 0.001 TYR A 369 PHE 0.027 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/Z covalent geometry : bond 0.00220 / 0.10 (24160) covalent geometry : angle 0.50416 / 0.26 (32888) SS BOND : bond 0.00268 / 0.17 ( 38) SS BOND : angle 0.76371 / 0.47 ( 76) hydrogen bonds : bond 0.03506 / 2.32 ( 1014) hydrogen bonds : angle 5.38282 / 3.82 ( 2877) link_NAG-ASN : bond 0.00316 / 0.19 ( 38) link_NAG-ASN : angle 2.25520 / 1.58 ( 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 220 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8280 (mttt) cc_final: 0.8020 (mptt) REVERT: A 356 LYS cc_start: 0.8123 (tptt) cc_final: 0.7820 (tptm) REVERT: A 403 ARG cc_start: 0.6157 (ptm160) cc_final: 0.5894 (ttm-80) REVERT: A 421 TYR cc_start: 0.7481 (m-80) cc_final: 0.7114 (m-10) REVERT: A 988 GLU cc_start: 0.8099 (mp0) cc_final: 0.7781 (mp0) REVERT: A 1041 ASP cc_start: 0.8877 (t0) cc_final: 0.8625 (t0) REVERT: B 64 TRP cc_start: 0.7891 (t60) cc_final: 0.7444 (t60) REVERT: B 95 THR cc_start: 0.8057 (p) cc_final: 0.7622 (t) REVERT: B 102 ARG cc_start: 0.6583 (mmp-170) cc_final: 0.6104 (mmt180) REVERT: B 307 THR cc_start: 0.9079 (m) cc_final: 0.8823 (p) REVERT: B 572 THR cc_start: 0.8617 (m) cc_final: 0.7503 (p) REVERT: B 574 ASP cc_start: 0.8499 (p0) cc_final: 0.7726 (m-30) REVERT: B 656 VAL cc_start: 0.8819 (t) cc_final: 0.8535 (m) REVERT: B 740 MET cc_start: 0.8627 (ttt) cc_final: 0.8298 (ttt) REVERT: B 820 ASP cc_start: 0.8579 (t70) cc_final: 0.8140 (t0) REVERT: C 190 ARG cc_start: 0.7095 (mtt90) cc_final: 0.6619 (mpt90) REVERT: C 207 HIS cc_start: 0.7205 (m90) cc_final: 0.6520 (m170) REVERT: C 238 PHE cc_start: 0.7475 (p90) cc_final: 0.7204 (p90) REVERT: C 349 SER cc_start: 0.7426 (m) cc_final: 0.7130 (p) REVERT: C 403 ARG cc_start: 0.7244 (ptm160) cc_final: 0.6765 (ptm160) REVERT: C 421 TYR cc_start: 0.7629 (m-80) cc_final: 0.7398 (m-80) REVERT: C 436 TRP cc_start: 0.7779 (p90) cc_final: 0.7387 (p90) REVERT: C 489 TYR cc_start: 0.8006 (m-80) cc_final: 0.7730 (m-80) REVERT: C 490 PHE cc_start: 0.8107 (t80) cc_final: 0.7831 (t80) REVERT: C 985 ASP cc_start: 0.7923 (t70) cc_final: 0.7538 (t0) outliers start: 46 outliers final: 39 residues processed: 210 average time/residue: 0.1504 time to fit residues: 52.2404 Evaluate side-chains 196 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 868 GLU 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 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 912 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 188 ASN 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 590 CYS Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 827 THR 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: 2.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.153214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100209 restraints weight = 37862.517| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.42 r_work: 0.3187 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24236 Z= 0.177 Angle : 0.555 12.510 33078 Z= 0.281 Chirality : 0.044 0.237 3888 Planarity : 0.003 0.040 4191 Dihedral : 4.542 34.732 3190 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.12 % Allowed : 9.17 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 2937 helix: 1.99 (0.21), residues: 668 sheet: 0.31 (0.19), residues: 662 loop : -0.37 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 983 TYR 0.023 0.001 TYR B1138 PHE 0.024 0.001 PHE B 329 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (24160) covalent geometry : angle 0.53842 / 0.28 (32888) SS BOND : bond 0.00359 / 0.23 ( 38) SS BOND : angle 0.86473 / 0.53 ( 76) hydrogen bonds : bond 0.03915 / 2.60 ( 1014) hydrogen bonds : angle 5.46367 / 3.86 ( 2877) link_NAG-ASN : bond 0.00301 / 0.19 ( 38) link_NAG-ASN : angle 2.29874 / 1.61 ( 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 216 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8272 (mttt) cc_final: 0.8004 (mmtt) REVERT: A 198 ASP cc_start: 0.8923 (p0) cc_final: 0.8666 (p0) REVERT: A 356 LYS cc_start: 0.8151 (tptt) cc_final: 0.7848 (tptm) REVERT: A 383 SER cc_start: 0.8630 (t) cc_final: 0.8210 (p) REVERT: A 403 ARG cc_start: 0.6106 (ptm160) cc_final: 0.5847 (ttm-80) REVERT: A 421 TYR cc_start: 0.7471 (m-80) cc_final: 0.7126 (m-10) REVERT: A 779 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: B 95 THR cc_start: 0.8049 (p) cc_final: 0.7599 (t) REVERT: B 102 ARG cc_start: 0.6581 (mmp-170) cc_final: 0.6144 (mmt180) REVERT: B 572 THR cc_start: 0.8597 (m) cc_final: 0.7493 (p) REVERT: B 574 ASP cc_start: 0.8326 (p0) cc_final: 0.7798 (m-30) REVERT: B 820 ASP cc_start: 0.8702 (t70) cc_final: 0.8274 (t0) REVERT: C 190 ARG cc_start: 0.7141 (mtt90) cc_final: 0.6664 (mmt180) REVERT: C 207 HIS cc_start: 0.7116 (m90) cc_final: 0.6695 (m170) REVERT: C 238 PHE cc_start: 0.7457 (p90) cc_final: 0.7193 (p90) REVERT: C 349 SER cc_start: 0.7658 (m) cc_final: 0.7344 (p) REVERT: C 403 ARG cc_start: 0.7233 (ptm160) cc_final: 0.6850 (ptm160) REVERT: C 421 TYR cc_start: 0.7618 (m-80) cc_final: 0.7356 (m-80) REVERT: C 436 TRP cc_start: 0.7846 (p90) cc_final: 0.7508 (p90) REVERT: C 489 TYR cc_start: 0.7969 (m-80) cc_final: 0.7589 (m-80) REVERT: C 985 ASP cc_start: 0.8018 (t70) cc_final: 0.7649 (t0) outliers start: 54 outliers final: 50 residues processed: 202 average time/residue: 0.1499 time to fit residues: 50.0712 Evaluate side-chains 203 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 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 976 VAL 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 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 745 ASP 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 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 188 ASN 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 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE 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 651 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 827 THR 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: 0.8980 chunk 76 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 242 optimal weight: 0.4980 chunk 240 optimal weight: 10.0000 chunk 257 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.155947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113668 restraints weight = 37914.356| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.92 r_work: 0.3173 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24236 Z= 0.125 Angle : 0.516 12.146 33078 Z= 0.261 Chirality : 0.043 0.230 3888 Planarity : 0.003 0.040 4191 Dihedral : 4.357 33.568 3190 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.92 % Allowed : 9.68 % Favored : 88.40 % 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: 2.12 (0.21), residues: 666 sheet: 0.31 (0.19), residues: 671 loop : -0.36 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1019 TYR 0.022 0.001 TYR B1138 PHE 0.021 0.001 PHE B 329 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (24160) covalent geometry : angle 0.49982 / 0.26 (32888) SS BOND : bond 0.00286 / 0.19 ( 38) SS BOND : angle 0.76303 / 0.46 ( 76) hydrogen bonds : bond 0.03554 / 2.36 ( 1014) hydrogen bonds : angle 5.32126 / 3.76 ( 2877) link_NAG-ASN : bond 0.00289 / 0.17 ( 38) link_NAG-ASN : angle 2.15865 / 1.51 ( 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 211 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8268 (mttt) cc_final: 0.8000 (mmtt) REVERT: A 356 LYS cc_start: 0.8173 (tptt) cc_final: 0.7868 (tptm) REVERT: A 383 SER cc_start: 0.8696 (t) cc_final: 0.8288 (p) REVERT: A 403 ARG cc_start: 0.6051 (ptm160) cc_final: 0.5529 (ptp-110) REVERT: A 421 TYR cc_start: 0.7440 (m-80) cc_final: 0.7193 (m-80) REVERT: A 493 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7950 (tm-30) REVERT: A 779 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: A 868 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8414 (pt0) REVERT: A 1041 ASP cc_start: 0.8895 (t0) cc_final: 0.8673 (t0) REVERT: B 95 THR cc_start: 0.8037 (p) cc_final: 0.7538 (t) REVERT: B 102 ARG cc_start: 0.6706 (mmp-170) cc_final: 0.6303 (mmt180) REVERT: B 572 THR cc_start: 0.8620 (m) cc_final: 0.7405 (p) REVERT: B 574 ASP cc_start: 0.8376 (p0) cc_final: 0.7947 (m-30) REVERT: B 656 VAL cc_start: 0.8904 (t) cc_final: 0.8634 (m) REVERT: B 820 ASP cc_start: 0.8685 (t70) cc_final: 0.8226 (t0) REVERT: C 190 ARG cc_start: 0.7260 (mtt90) cc_final: 0.6778 (mpt90) REVERT: C 207 HIS cc_start: 0.7221 (m90) cc_final: 0.6451 (m170) REVERT: C 238 PHE cc_start: 0.7465 (p90) cc_final: 0.7189 (p90) REVERT: C 349 SER cc_start: 0.7574 (m) cc_final: 0.7265 (p) REVERT: C 403 ARG cc_start: 0.7309 (ptm160) cc_final: 0.6797 (ptm160) REVERT: C 421 TYR cc_start: 0.7641 (m-80) cc_final: 0.7425 (m-80) REVERT: C 436 TRP cc_start: 0.7816 (p90) cc_final: 0.7523 (p90) REVERT: C 489 TYR cc_start: 0.8011 (m-80) cc_final: 0.7588 (m-80) REVERT: C 490 PHE cc_start: 0.8202 (t80) cc_final: 0.7244 (t80) REVERT: C 902 MET cc_start: 0.9297 (tpp) cc_final: 0.9018 (tpt) REVERT: C 985 ASP cc_start: 0.8093 (t70) cc_final: 0.7783 (t0) outliers start: 49 outliers final: 42 residues processed: 197 average time/residue: 0.1510 time to fit residues: 49.1582 Evaluate side-chains 200 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 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 976 VAL 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 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 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 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 701 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1073 LYS 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: 1.9990 chunk 274 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 129 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.153463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105276 restraints weight = 37590.600| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.57 r_work: 0.3167 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24236 Z= 0.154 Angle : 0.533 11.984 33078 Z= 0.270 Chirality : 0.044 0.235 3888 Planarity : 0.003 0.040 4191 Dihedral : 4.355 33.839 3190 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.04 % Allowed : 9.91 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 2937 helix: 2.02 (0.21), residues: 670 sheet: 0.23 (0.19), residues: 679 loop : -0.36 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.021 0.001 TYR B1138 PHE 0.031 0.001 PHE A 168 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (24160) covalent geometry : angle 0.51739 / 0.27 (32888) SS BOND : bond 0.00321 / 0.21 ( 38) SS BOND : angle 0.81434 / 0.49 ( 76) hydrogen bonds : bond 0.03715 / 2.46 ( 1014) hydrogen bonds : angle 5.33326 / 3.76 ( 2877) link_NAG-ASN : bond 0.00278 / 0.17 ( 38) link_NAG-ASN : angle 2.17278 / 1.52 ( 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 212 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8276 (mttt) cc_final: 0.7970 (mptt) REVERT: A 338 PHE cc_start: 0.8066 (m-10) cc_final: 0.7851 (m-10) REVERT: A 356 LYS cc_start: 0.8169 (tptt) cc_final: 0.7868 (tptm) REVERT: A 360 ASN cc_start: 0.8590 (m-40) cc_final: 0.7851 (t0) REVERT: A 383 SER cc_start: 0.8614 (t) cc_final: 0.8225 (p) REVERT: A 403 ARG cc_start: 0.6001 (ptm160) cc_final: 0.5614 (ptp-110) REVERT: A 421 TYR cc_start: 0.7431 (m-80) cc_final: 0.7197 (m-80) REVERT: A 779 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: A 868 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: A 1041 ASP cc_start: 0.8874 (t0) cc_final: 0.8646 (t0) REVERT: B 95 THR cc_start: 0.7924 (p) cc_final: 0.7416 (t) REVERT: B 102 ARG cc_start: 0.6780 (mmp-170) cc_final: 0.6323 (mmt180) REVERT: B 572 THR cc_start: 0.8637 (m) cc_final: 0.7432 (p) REVERT: B 574 ASP cc_start: 0.8299 (p0) cc_final: 0.7983 (m-30) REVERT: B 656 VAL cc_start: 0.8930 (t) cc_final: 0.8659 (m) REVERT: B 820 ASP cc_start: 0.8758 (t70) cc_final: 0.8287 (t0) REVERT: C 190 ARG cc_start: 0.7249 (mtt90) cc_final: 0.6807 (mpt90) REVERT: C 207 HIS cc_start: 0.7218 (m90) cc_final: 0.6454 (m170) REVERT: C 349 SER cc_start: 0.7598 (m) cc_final: 0.7287 (p) REVERT: C 403 ARG cc_start: 0.7342 (ptm160) cc_final: 0.6811 (ptm160) REVERT: C 489 TYR cc_start: 0.8036 (m-80) cc_final: 0.7612 (m-80) REVERT: C 490 PHE cc_start: 0.8211 (t80) cc_final: 0.7311 (t80) REVERT: C 985 ASP cc_start: 0.8071 (t70) cc_final: 0.7737 (t0) outliers start: 52 outliers final: 42 residues processed: 197 average time/residue: 0.1463 time to fit residues: 47.6741 Evaluate side-chains 196 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 514 SER Chi-restraints excluded: chain A residue 525 CYS 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 976 VAL 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 588 THR 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 B residue 987 VAL 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 393 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 468 ILE 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 701 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 978 ASN B 207 HIS C 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.153718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103566 restraints weight = 38120.732| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.57 r_work: 0.3148 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24236 Z= 0.198 Angle : 0.572 11.734 33078 Z= 0.289 Chirality : 0.045 0.243 3888 Planarity : 0.003 0.040 4191 Dihedral : 4.476 34.128 3190 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.88 % Allowed : 10.34 % 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: 0.39 (0.15), residues: 2937 helix: 1.95 (0.21), residues: 662 sheet: 0.21 (0.19), residues: 675 loop : -0.42 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.020 0.001 TYR B1138 PHE 0.026 0.001 PHE A 168 TRP 0.015 0.001 TRP C 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (24160) covalent geometry : angle 0.55374 / 0.28 (32888) SS BOND : bond 0.00491 / 0.28 ( 38) SS BOND : angle 1.32556 / 0.72 ( 76) hydrogen bonds : bond 0.03925 / 2.61 ( 1014) hydrogen bonds : angle 5.40757 / 3.81 ( 2877) link_NAG-ASN : bond 0.00302 / 0.18 ( 38) link_NAG-ASN : angle 2.27063 / 1.59 ( 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 197 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8335 (mttt) cc_final: 0.8015 (mptt) REVERT: A 338 PHE cc_start: 0.8136 (m-10) cc_final: 0.7920 (m-10) REVERT: A 356 LYS cc_start: 0.8151 (tptt) cc_final: 0.7855 (tptm) REVERT: A 360 ASN cc_start: 0.8600 (m-40) cc_final: 0.7872 (t0) REVERT: A 383 SER cc_start: 0.8650 (t) cc_final: 0.8252 (p) REVERT: A 403 ARG cc_start: 0.6011 (ptm160) cc_final: 0.5631 (ptp-110) REVERT: A 779 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: A 868 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: B 95 THR cc_start: 0.7916 (p) cc_final: 0.7394 (t) REVERT: B 102 ARG cc_start: 0.6908 (mmp-170) cc_final: 0.6451 (mmt180) REVERT: B 572 THR cc_start: 0.8576 (m) cc_final: 0.7382 (p) REVERT: B 574 ASP cc_start: 0.8270 (p0) cc_final: 0.8041 (m-30) REVERT: B 656 VAL cc_start: 0.8948 (t) cc_final: 0.8680 (m) REVERT: B 820 ASP cc_start: 0.8748 (t70) cc_final: 0.8239 (t0) REVERT: C 188 ASN cc_start: 0.5807 (OUTLIER) cc_final: 0.5498 (t0) REVERT: C 190 ARG cc_start: 0.7242 (mtt90) cc_final: 0.6715 (mpt90) REVERT: C 207 HIS cc_start: 0.7160 (m90) cc_final: 0.6431 (m170) REVERT: C 238 PHE cc_start: 0.7458 (p90) cc_final: 0.7135 (p90) REVERT: C 349 SER cc_start: 0.7649 (m) cc_final: 0.7326 (p) REVERT: C 403 ARG cc_start: 0.7372 (ptm160) cc_final: 0.6831 (ptm160) REVERT: C 489 TYR cc_start: 0.8052 (m-80) cc_final: 0.7617 (m-80) REVERT: C 490 PHE cc_start: 0.8200 (t80) cc_final: 0.7306 (t80) REVERT: C 985 ASP cc_start: 0.8060 (t70) cc_final: 0.7727 (t0) outliers start: 48 outliers final: 45 residues processed: 184 average time/residue: 0.1439 time to fit residues: 43.8379 Evaluate side-chains 193 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 514 SER Chi-restraints excluded: chain A residue 525 CYS 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 976 VAL 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 281 GLU 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 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 188 ASN 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 393 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 468 ILE 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 701 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 215 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 262 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 chunk 235 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 255 optimal weight: 0.3980 chunk 176 optimal weight: 0.6980 chunk 127 optimal weight: 50.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.156541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113350 restraints weight = 37869.921| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.69 r_work: 0.3204 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3721 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= 0.100 Angle : 0.513 11.790 33078 Z= 0.260 Chirality : 0.043 0.224 3888 Planarity : 0.003 0.040 4191 Dihedral : 4.246 33.038 3190 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.49 % Allowed : 10.85 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 2937 helix: 2.27 (0.21), residues: 655 sheet: 0.20 (0.19), residues: 674 loop : -0.33 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.034 0.001 TYR C 421 PHE 0.025 0.001 PHE A 168 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (24160) covalent geometry : angle 0.49724 / 0.26 (32888) SS BOND : bond 0.00267 / 0.18 ( 38) SS BOND : angle 1.06834 / 0.58 ( 76) hydrogen bonds : bond 0.03360 / 2.23 ( 1014) hydrogen bonds : angle 5.20211 / 3.67 ( 2877) link_NAG-ASN : bond 0.00301 / 0.17 ( 38) link_NAG-ASN : angle 2.04946 / 1.43 ( 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 202 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8155 (tptt) cc_final: 0.7854 (tptm) REVERT: A 360 ASN cc_start: 0.8570 (m-40) cc_final: 0.7844 (t0) REVERT: A 383 SER cc_start: 0.8711 (t) cc_final: 0.8304 (p) REVERT: A 394 ASN cc_start: 0.7660 (m-40) cc_final: 0.7180 (m-40) REVERT: A 403 ARG cc_start: 0.5844 (ptm160) cc_final: 0.5524 (ptp-110) REVERT: A 779 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: A 900 MET cc_start: 0.9174 (mtp) cc_final: 0.8974 (mtp) REVERT: A 988 GLU cc_start: 0.8165 (mp0) cc_final: 0.7838 (mp0) REVERT: B 95 THR cc_start: 0.7978 (p) cc_final: 0.7414 (t) REVERT: B 102 ARG cc_start: 0.6752 (mmp-170) cc_final: 0.6310 (mmt180) REVERT: B 572 THR cc_start: 0.8686 (m) cc_final: 0.7659 (p) REVERT: B 656 VAL cc_start: 0.8883 (t) cc_final: 0.8670 (m) REVERT: B 820 ASP cc_start: 0.8688 (t70) cc_final: 0.8206 (t0) REVERT: C 190 ARG cc_start: 0.7258 (mtt90) cc_final: 0.6826 (mpt90) REVERT: C 207 HIS cc_start: 0.7161 (m90) cc_final: 0.6500 (m170) REVERT: C 238 PHE cc_start: 0.7532 (p90) cc_final: 0.7226 (p90) REVERT: C 349 SER cc_start: 0.7538 (m) cc_final: 0.7220 (p) REVERT: C 489 TYR cc_start: 0.8094 (m-80) cc_final: 0.7678 (m-80) REVERT: C 490 PHE cc_start: 0.8270 (t80) cc_final: 0.7368 (t80) REVERT: C 985 ASP cc_start: 0.7964 (t70) cc_final: 0.7681 (t0) outliers start: 38 outliers final: 33 residues processed: 191 average time/residue: 0.1380 time to fit residues: 44.3750 Evaluate side-chains 183 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS 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 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL 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 281 GLU 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 912 THR Chi-restraints excluded: chain B residue 987 VAL 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 1073 LYS 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: 8.9990 chunk 127 optimal weight: 30.0000 chunk 205 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 271 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 135 optimal weight: 40.0000 chunk 136 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.155204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112596 restraints weight = 37768.858| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.95 r_work: 0.3173 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.003 0.034 24236 Z= 0.142 Angle : 0.532 11.714 33078 Z= 0.269 Chirality : 0.044 0.232 3888 Planarity : 0.003 0.041 4191 Dihedral : 4.275 33.693 3190 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.49 % Allowed : 11.17 % Favored : 87.34 % 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: 0.49 (0.15), residues: 2937 helix: 2.19 (0.21), residues: 654 sheet: 0.16 (0.19), residues: 671 loop : -0.36 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.026 0.001 TYR C 421 PHE 0.028 0.001 PHE A 168 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (24160) covalent geometry : angle 0.51764 / 0.27 (32888) SS BOND : bond 0.00314 / 0.21 ( 38) SS BOND : angle 1.02094 / 0.57 ( 76) hydrogen bonds : bond 0.03567 / 2.36 ( 1014) hydrogen bonds : angle 5.22844 / 3.68 ( 2877) link_NAG-ASN : bond 0.00300 / 0.17 ( 38) link_NAG-ASN : angle 2.05853 / 1.45 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6740.03 seconds wall clock time: 116 minutes 0.01 seconds (6960.01 seconds total)