Starting phenix.real_space_refine on Sat Jun 21 08:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmd_37650/06_2025/8wmd_37650_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmd_37650/06_2025/8wmd_37650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wmd_37650/06_2025/8wmd_37650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmd_37650/06_2025/8wmd_37650.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmd_37650/06_2025/8wmd_37650_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmd_37650/06_2025/8wmd_37650_neut.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 108 5.16 5 C 15594 2.51 5 N 4029 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24429 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7989 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 54, 'TRANS': 966} Chain breaks: 7 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Restraints were copied for chains: C, B Time building chain proxies: 22.56, per 1000 atoms: 0.92 Number of scatterers: 24429 At special positions: 0 Unit cell: (133.665, 141.705, 166.83, 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 108 16.00 O 4698 8.00 N 4029 7.00 C 15594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " Time building additional restraints: 5.87 Conformation dependent library (CDL) restraints added in 2.9 seconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 42 sheets defined 24.1% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.779A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.046A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.430A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.709A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.883A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.543A 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 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.069A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.621A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.866A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.674A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.289A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.779A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.047A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.430A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.709A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.883A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.543A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.069A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.621A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.866A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.674A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.289A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.779A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.046A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.430A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.709A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.883A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.543A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.069A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.622A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.866A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.674A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.289A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.636A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.874A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.339A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.244A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.826A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=10, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.824A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.796A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.627A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=14, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=15, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.637A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.874A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=18, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.339A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'B' and resid 325 through 327 removed outlier: 4.244A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.825A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=23, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=24, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.824A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.796A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.627A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=28, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=29, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.636A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.874A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=32, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.339A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'C' and resid 325 through 327 removed outlier: 4.244A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.826A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=37, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=38, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.824A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.795A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.628A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=42, first strand: chain 'C' and resid 1094 through 1097 963 hydrogen bonds defined for protein. 2619 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: 10.20 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7725 1.34 - 1.46: 5643 1.46 - 1.58: 11487 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 24990 Sorted by residual: bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.73e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 ... (remaining 24985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 33036 1.34 - 2.68: 770 2.68 - 4.02: 172 4.02 - 5.36: 18 5.36 - 6.70: 9 Bond angle restraints: 34005 Sorted by residual: angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 119.04 -6.70 2.04e+00 2.40e-01 1.08e+01 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 119.03 -6.69 2.04e+00 2.40e-01 1.07e+01 angle pdb=" N GLY B 526 " pdb=" CA GLY B 526 " pdb=" C GLY B 526 " ideal model delta sigma weight residual 112.34 119.02 -6.68 2.04e+00 2.40e-01 1.07e+01 angle pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta sigma weight residual 110.95 106.84 4.11 1.44e+00 4.82e-01 8.14e+00 angle pdb=" N ASN B 282 " pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta sigma weight residual 110.95 106.86 4.09 1.44e+00 4.82e-01 8.07e+00 ... (remaining 34000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 14090 17.81 - 35.61: 1020 35.61 - 53.42: 190 53.42 - 71.23: 30 71.23 - 89.04: 12 Dihedral angle restraints: 15342 sinusoidal: 6417 harmonic: 8925 Sorted by residual: dihedral pdb=" CA GLU C 281 " pdb=" C GLU C 281 " pdb=" N ASN C 282 " pdb=" CA ASN C 282 " ideal model delta harmonic sigma weight residual -180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU B 281 " pdb=" C GLU B 281 " pdb=" N ASN B 282 " pdb=" CA ASN B 282 " ideal model delta harmonic sigma weight residual 180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU A 281 " pdb=" C GLU A 281 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 15339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 3954 0.188 - 0.375: 3 0.375 - 0.563: 0 0.563 - 0.750: 0 0.750 - 0.938: 3 Chirality restraints: 3960 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.19e+01 ... (remaining 3957 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " 0.041 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN A 282 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " 0.041 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN B 282 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 282 " 0.041 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN C 282 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN C 282 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 282 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.042 2.00e-02 2.50e+03 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2130 2.75 - 3.28: 23226 3.28 - 3.82: 38025 3.82 - 4.36: 44563 4.36 - 4.90: 79918 Nonbonded interactions: 187862 Sorted by model distance: nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.208 3.040 nonbonded pdb=" OG SER B 735 " pdb=" OG1 THR B 859 " model vdw 2.208 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP B 142 " pdb=" OG SER B 155 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP A 142 " pdb=" OG SER A 155 " model vdw 2.231 3.040 ... (remaining 187857 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 64.870 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25062 Z= 0.147 Angle : 0.562 11.534 34182 Z= 0.282 Chirality : 0.050 0.938 3960 Planarity : 0.003 0.043 4347 Dihedral : 12.395 89.036 9477 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.34 % Allowed : 9.28 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3015 helix: 2.30 (0.21), residues: 630 sheet: 0.76 (0.20), residues: 687 loop : -1.18 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.002 0.001 HIS B 52 PHE 0.008 0.001 PHE A 400 TYR 0.014 0.001 TYR B1067 ARG 0.004 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 33) link_NAG-ASN : angle 4.01309 ( 99) hydrogen bonds : bond 0.13255 ( 957) hydrogen bonds : angle 5.77389 ( 2619) SS BOND : bond 0.00227 ( 39) SS BOND : angle 0.70776 ( 78) covalent geometry : bond 0.00284 (24990) covalent geometry : angle 0.51917 (34005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 287 time to evaluate : 2.968 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6755 (p90) cc_final: 0.6522 (p90) REVERT: A 237 ARG cc_start: 0.7905 (mtm180) cc_final: 0.6906 (mtm110) REVERT: A 309 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7803 (mp0) REVERT: A 794 ILE cc_start: 0.8319 (tt) cc_final: 0.8079 (pp) REVERT: A 1050 MET cc_start: 0.9384 (ptm) cc_final: 0.9165 (ptm) REVERT: B 121 ASN cc_start: 0.8424 (m-40) cc_final: 0.8212 (t0) REVERT: B 140 PHE cc_start: 0.6859 (p90) cc_final: 0.6596 (p90) REVERT: B 237 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7010 (mtm110) REVERT: B 309 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8070 (mp0) REVERT: C 121 ASN cc_start: 0.8574 (m-40) cc_final: 0.8287 (t0) REVERT: C 140 PHE cc_start: 0.6543 (p90) cc_final: 0.6241 (p90) REVERT: C 160 TYR cc_start: 0.8170 (p90) cc_final: 0.7967 (p90) REVERT: C 220 PHE cc_start: 0.7363 (m-80) cc_final: 0.7042 (m-80) REVERT: C 237 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7046 (mtm110) REVERT: C 309 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7681 (mp0) REVERT: C 1038 LYS cc_start: 0.8974 (mttp) cc_final: 0.8709 (mmtp) outliers start: 9 outliers final: 8 residues processed: 296 average time/residue: 1.1257 time to fit residues: 398.1235 Evaluate side-chains 143 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.5980 chunk 231 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 0.0870 chunk 145 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 7.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN B 188 ASN B1002 GLN B1088 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.133948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078432 restraints weight = 45984.246| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.82 r_work: 0.2989 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25062 Z= 0.115 Angle : 0.578 12.949 34182 Z= 0.288 Chirality : 0.045 0.297 3960 Planarity : 0.004 0.071 4347 Dihedral : 6.425 59.590 3985 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.01 % Allowed : 11.93 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3015 helix: 2.54 (0.21), residues: 645 sheet: 0.99 (0.20), residues: 657 loop : -1.14 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS B1064 PHE 0.027 0.001 PHE C 133 TYR 0.016 0.001 TYR A1067 ARG 0.013 0.001 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 33) link_NAG-ASN : angle 2.99579 ( 99) hydrogen bonds : bond 0.04804 ( 957) hydrogen bonds : angle 4.94896 ( 2619) SS BOND : bond 0.00171 ( 39) SS BOND : angle 0.84045 ( 78) covalent geometry : bond 0.00249 (24990) covalent geometry : angle 0.55488 (34005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 3.036 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8731 (p) cc_final: 0.8402 (m) REVERT: A 237 ARG cc_start: 0.8140 (mtm180) cc_final: 0.7073 (mtm180) REVERT: A 309 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8027 (mp0) REVERT: A 357 ARG cc_start: 0.7460 (tpp-160) cc_final: 0.7166 (tpp80) REVERT: A 387 LEU cc_start: 0.9266 (mt) cc_final: 0.9019 (mt) REVERT: B 121 ASN cc_start: 0.8434 (m-40) cc_final: 0.8136 (t0) REVERT: B 205 SER cc_start: 0.8840 (p) cc_final: 0.8459 (m) REVERT: B 237 ARG cc_start: 0.8154 (mtm180) cc_final: 0.7467 (mtm110) REVERT: B 309 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8293 (mp0) REVERT: B 357 ARG cc_start: 0.7521 (tpp-160) cc_final: 0.7166 (tpp80) REVERT: C 121 ASN cc_start: 0.8468 (m-40) cc_final: 0.8191 (t0) REVERT: C 220 PHE cc_start: 0.7376 (m-80) cc_final: 0.6993 (m-80) REVERT: C 237 ARG cc_start: 0.8117 (mtm180) cc_final: 0.7408 (mtm110) REVERT: C 309 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7917 (mp0) REVERT: C 357 ARG cc_start: 0.7543 (tpp-160) cc_final: 0.7162 (tpp80) outliers start: 54 outliers final: 23 residues processed: 197 average time/residue: 1.0124 time to fit residues: 243.2086 Evaluate side-chains 154 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 243 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 277 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 394 ASN B 343 ASN B 394 ASN B 755 GLN B 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 394 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.130184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073433 restraints weight = 45325.380| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.80 r_work: 0.2891 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25062 Z= 0.205 Angle : 0.623 10.261 34182 Z= 0.319 Chirality : 0.047 0.217 3960 Planarity : 0.005 0.066 4347 Dihedral : 6.170 57.804 3975 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.05 % Allowed : 12.64 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3015 helix: 2.27 (0.20), residues: 645 sheet: 0.74 (0.21), residues: 621 loop : -1.11 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 PHE 0.018 0.002 PHE C 565 TYR 0.020 0.002 TYR A1067 ARG 0.009 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 33) link_NAG-ASN : angle 2.82437 ( 99) hydrogen bonds : bond 0.06822 ( 957) hydrogen bonds : angle 5.12191 ( 2619) SS BOND : bond 0.00197 ( 39) SS BOND : angle 1.02898 ( 78) covalent geometry : bond 0.00507 (24990) covalent geometry : angle 0.60338 (34005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 2.629 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8857 (p) cc_final: 0.8594 (m) REVERT: A 237 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7732 (mpp80) REVERT: A 357 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.7204 (tpp80) REVERT: A 394 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7487 (t0) REVERT: A 558 LYS cc_start: 0.9150 (mmpt) cc_final: 0.8768 (mmpt) REVERT: A 794 ILE cc_start: 0.8594 (tt) cc_final: 0.8357 (pp) REVERT: B 121 ASN cc_start: 0.8354 (m-40) cc_final: 0.7979 (t0) REVERT: B 205 SER cc_start: 0.8858 (p) cc_final: 0.8597 (m) REVERT: B 237 ARG cc_start: 0.8197 (mtm180) cc_final: 0.7779 (mpp80) REVERT: B 309 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8438 (mp0) REVERT: B 338 PHE cc_start: 0.8683 (m-80) cc_final: 0.8269 (m-80) REVERT: C 121 ASN cc_start: 0.8501 (m-40) cc_final: 0.8149 (t0) REVERT: C 220 PHE cc_start: 0.7758 (m-80) cc_final: 0.7302 (m-80) REVERT: C 237 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7145 (mtm-85) REVERT: C 309 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8026 (mp0) REVERT: C 357 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7318 (ttt180) outliers start: 55 outliers final: 23 residues processed: 199 average time/residue: 0.9947 time to fit residues: 241.6386 Evaluate side-chains 162 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 146 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 285 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 260 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS A 394 ASN B 394 ASN B 901 GLN B1002 GLN C 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.131370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075330 restraints weight = 45716.657| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.83 r_work: 0.2903 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25062 Z= 0.148 Angle : 0.576 9.824 34182 Z= 0.295 Chirality : 0.045 0.232 3960 Planarity : 0.004 0.054 4347 Dihedral : 6.016 57.745 3975 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.46 % Allowed : 12.75 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3015 helix: 2.30 (0.20), residues: 645 sheet: 0.84 (0.21), residues: 621 loop : -1.10 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 PHE 0.023 0.001 PHE B 133 TYR 0.017 0.001 TYR C1067 ARG 0.006 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 33) link_NAG-ASN : angle 2.64768 ( 99) hydrogen bonds : bond 0.05871 ( 957) hydrogen bonds : angle 5.00199 ( 2619) SS BOND : bond 0.00201 ( 39) SS BOND : angle 1.03497 ( 78) covalent geometry : bond 0.00352 (24990) covalent geometry : angle 0.55688 (34005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8801 (p) cc_final: 0.8502 (m) REVERT: A 237 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7729 (mpp80) REVERT: A 309 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8328 (mp0) REVERT: A 357 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.7281 (tpp80) REVERT: A 380 TYR cc_start: 0.8420 (m-80) cc_final: 0.7933 (m-80) REVERT: A 558 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8766 (mmpt) REVERT: A 794 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 121 ASN cc_start: 0.8306 (m-40) cc_final: 0.7906 (t0) REVERT: B 205 SER cc_start: 0.8891 (p) cc_final: 0.8496 (m) REVERT: B 237 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7726 (mpp80) REVERT: B 309 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8413 (mp0) REVERT: B 338 PHE cc_start: 0.8583 (m-80) cc_final: 0.8212 (m-80) REVERT: B 357 ARG cc_start: 0.7627 (tpp-160) cc_final: 0.7119 (ttt180) REVERT: C 176 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7993 (pt) REVERT: C 220 PHE cc_start: 0.7729 (m-80) cc_final: 0.7292 (m-80) REVERT: C 309 GLU cc_start: 0.8585 (mm-30) cc_final: 0.7937 (mp0) REVERT: C 558 LYS cc_start: 0.9039 (mmpt) cc_final: 0.8711 (mmpt) outliers start: 66 outliers final: 34 residues processed: 204 average time/residue: 1.3901 time to fit residues: 353.9289 Evaluate side-chains 171 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 123 optimal weight: 6.9990 chunk 166 optimal weight: 0.0770 chunk 107 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 240 optimal weight: 0.0670 chunk 19 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 207 HIS B 755 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.132664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077078 restraints weight = 45646.717| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.82 r_work: 0.2941 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25062 Z= 0.105 Angle : 0.542 9.293 34182 Z= 0.275 Chirality : 0.044 0.247 3960 Planarity : 0.004 0.041 4347 Dihedral : 5.801 56.916 3975 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.20 % Allowed : 13.01 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3015 helix: 2.42 (0.20), residues: 645 sheet: 1.03 (0.21), residues: 651 loop : -1.10 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.019 0.001 HIS A 207 PHE 0.018 0.001 PHE C 565 TYR 0.017 0.001 TYR B 160 ARG 0.003 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 33) link_NAG-ASN : angle 2.54062 ( 99) hydrogen bonds : bond 0.04889 ( 957) hydrogen bonds : angle 4.82923 ( 2619) SS BOND : bond 0.00212 ( 39) SS BOND : angle 0.82861 ( 78) covalent geometry : bond 0.00226 (24990) covalent geometry : angle 0.52445 (34005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 145 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7204 (mm) REVERT: A 205 SER cc_start: 0.8771 (p) cc_final: 0.8525 (m) REVERT: A 309 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8400 (mp0) REVERT: A 357 ARG cc_start: 0.7599 (ttp-170) cc_final: 0.7260 (tpp80) REVERT: A 425 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6546 (tt) REVERT: A 558 LYS cc_start: 0.9157 (mmpt) cc_final: 0.8793 (mmpt) REVERT: A 794 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8404 (pp) REVERT: A 902 MET cc_start: 0.9281 (tpp) cc_final: 0.9045 (tpp) REVERT: A 1045 LYS cc_start: 0.8797 (tttm) cc_final: 0.8498 (ttmm) REVERT: B 121 ASN cc_start: 0.8298 (m-40) cc_final: 0.7903 (t0) REVERT: B 205 SER cc_start: 0.8841 (p) cc_final: 0.8483 (m) REVERT: B 309 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8434 (mp0) REVERT: B 338 PHE cc_start: 0.8601 (m-80) cc_final: 0.8230 (m-80) REVERT: B 357 ARG cc_start: 0.7609 (tpp-160) cc_final: 0.7276 (tpt-90) REVERT: B 425 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6488 (tt) REVERT: B 1045 LYS cc_start: 0.8829 (tttm) cc_final: 0.8537 (ttmm) REVERT: C 176 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7961 (pt) REVERT: C 220 PHE cc_start: 0.7772 (m-80) cc_final: 0.7330 (m-80) REVERT: C 309 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7953 (mp0) REVERT: C 357 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7280 (ttt180) REVERT: C 425 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6490 (tt) REVERT: C 558 LYS cc_start: 0.9024 (mmpt) cc_final: 0.8711 (mmpt) outliers start: 59 outliers final: 32 residues processed: 196 average time/residue: 1.0859 time to fit residues: 261.7505 Evaluate side-chains 166 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 8 optimal weight: 10.0000 chunk 187 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.131109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075129 restraints weight = 45438.875| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.81 r_work: 0.2897 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25062 Z= 0.160 Angle : 0.576 8.542 34182 Z= 0.294 Chirality : 0.046 0.228 3960 Planarity : 0.004 0.047 4347 Dihedral : 5.853 57.526 3975 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.57 % Allowed : 12.86 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3015 helix: 2.38 (0.20), residues: 645 sheet: 0.72 (0.21), residues: 627 loop : -1.03 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.028 0.001 HIS B 207 PHE 0.024 0.001 PHE A 133 TYR 0.034 0.001 TYR A 380 ARG 0.007 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 33) link_NAG-ASN : angle 2.54749 ( 99) hydrogen bonds : bond 0.05851 ( 957) hydrogen bonds : angle 4.91783 ( 2619) SS BOND : bond 0.00215 ( 39) SS BOND : angle 0.93535 ( 78) covalent geometry : bond 0.00388 (24990) covalent geometry : angle 0.55893 (34005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 5.025 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8832 (p) cc_final: 0.8584 (m) REVERT: A 309 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8367 (mp0) REVERT: A 338 PHE cc_start: 0.8518 (m-80) cc_final: 0.8286 (m-80) REVERT: A 357 ARG cc_start: 0.7611 (ttp-170) cc_final: 0.7257 (tpp80) REVERT: A 425 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6528 (tt) REVERT: A 558 LYS cc_start: 0.9165 (mmpt) cc_final: 0.8792 (mmpt) REVERT: A 794 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 121 ASN cc_start: 0.8322 (m-40) cc_final: 0.7913 (t0) REVERT: B 205 SER cc_start: 0.8752 (p) cc_final: 0.8520 (m) REVERT: B 237 ARG cc_start: 0.8321 (mtm180) cc_final: 0.7853 (mpp80) REVERT: B 309 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8468 (mp0) REVERT: B 338 PHE cc_start: 0.8634 (m-80) cc_final: 0.8249 (m-80) REVERT: B 1045 LYS cc_start: 0.8851 (tttm) cc_final: 0.8561 (ttmm) REVERT: C 176 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7978 (pt) REVERT: C 220 PHE cc_start: 0.7815 (m-80) cc_final: 0.7614 (m-80) REVERT: C 237 ARG cc_start: 0.8315 (mtm180) cc_final: 0.7322 (mtm110) REVERT: C 309 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8050 (mp0) REVERT: C 357 ARG cc_start: 0.7790 (tpp-160) cc_final: 0.7340 (ttt180) REVERT: C 512 VAL cc_start: 0.7913 (t) cc_final: 0.7650 (p) REVERT: C 558 LYS cc_start: 0.9030 (mmpt) cc_final: 0.8720 (mmpt) outliers start: 69 outliers final: 34 residues processed: 196 average time/residue: 1.4059 time to fit residues: 348.4255 Evaluate side-chains 168 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 108 optimal weight: 0.0770 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 260 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 755 GLN B1002 GLN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.131535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.075657 restraints weight = 45672.252| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.80 r_work: 0.2927 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25062 Z= 0.113 Angle : 0.543 8.494 34182 Z= 0.276 Chirality : 0.045 0.245 3960 Planarity : 0.004 0.037 4347 Dihedral : 5.637 57.050 3972 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.24 % Allowed : 13.46 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3015 helix: 2.20 (0.21), residues: 663 sheet: 1.02 (0.21), residues: 654 loop : -1.14 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.010 0.001 HIS A 207 PHE 0.011 0.001 PHE C 140 TYR 0.017 0.001 TYR A 160 ARG 0.003 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 33) link_NAG-ASN : angle 2.48689 ( 99) hydrogen bonds : bond 0.04969 ( 957) hydrogen bonds : angle 4.77864 ( 2619) SS BOND : bond 0.00187 ( 39) SS BOND : angle 0.81052 ( 78) covalent geometry : bond 0.00256 (24990) covalent geometry : angle 0.52633 (34005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 8.084 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8799 (p) cc_final: 0.8537 (m) REVERT: A 237 ARG cc_start: 0.8329 (mtm180) cc_final: 0.7627 (mtm-85) REVERT: A 309 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8389 (mp0) REVERT: A 338 PHE cc_start: 0.8548 (m-80) cc_final: 0.8273 (m-80) REVERT: A 357 ARG cc_start: 0.7602 (ttp-170) cc_final: 0.7252 (tpp80) REVERT: A 380 TYR cc_start: 0.8485 (m-80) cc_final: 0.8135 (m-10) REVERT: A 425 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6401 (tt) REVERT: A 558 LYS cc_start: 0.9151 (mmpt) cc_final: 0.8767 (mmpt) REVERT: A 794 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8430 (pp) REVERT: A 1045 LYS cc_start: 0.8823 (tttm) cc_final: 0.8536 (ttmm) REVERT: B 176 LEU cc_start: 0.8351 (mm) cc_final: 0.7889 (pt) REVERT: B 205 SER cc_start: 0.8770 (p) cc_final: 0.8487 (m) REVERT: B 237 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7856 (mpp80) REVERT: B 309 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8451 (mp0) REVERT: B 425 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6453 (tt) REVERT: B 1045 LYS cc_start: 0.8839 (tttm) cc_final: 0.8557 (ttmm) REVERT: C 220 PHE cc_start: 0.7843 (m-80) cc_final: 0.7616 (m-80) REVERT: C 309 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7959 (mp0) REVERT: C 357 ARG cc_start: 0.7803 (tpp-160) cc_final: 0.7383 (ttt180) REVERT: C 425 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6499 (tt) REVERT: C 558 LYS cc_start: 0.9027 (mmpt) cc_final: 0.8708 (mmpt) outliers start: 60 outliers final: 34 residues processed: 195 average time/residue: 1.0595 time to fit residues: 262.0503 Evaluate side-chains 170 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 159 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 273 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.075207 restraints weight = 45564.174| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.80 r_work: 0.2919 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25062 Z= 0.122 Angle : 0.555 8.423 34182 Z= 0.283 Chirality : 0.045 0.240 3960 Planarity : 0.004 0.036 4347 Dihedral : 5.611 57.005 3972 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 13.98 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3015 helix: 2.21 (0.21), residues: 663 sheet: 1.02 (0.21), residues: 654 loop : -1.14 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.010 0.001 HIS A 207 PHE 0.025 0.001 PHE A 133 TYR 0.023 0.001 TYR C 453 ARG 0.003 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 33) link_NAG-ASN : angle 2.47650 ( 99) hydrogen bonds : bond 0.05174 ( 957) hydrogen bonds : angle 4.78874 ( 2619) SS BOND : bond 0.00187 ( 39) SS BOND : angle 0.81457 ( 78) covalent geometry : bond 0.00285 (24990) covalent geometry : angle 0.53871 (34005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8818 (p) cc_final: 0.8570 (m) REVERT: A 309 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8358 (mp0) REVERT: A 338 PHE cc_start: 0.8600 (m-80) cc_final: 0.8344 (m-80) REVERT: A 357 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.7208 (tpp80) REVERT: A 380 TYR cc_start: 0.8491 (m-80) cc_final: 0.8263 (m-10) REVERT: A 425 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6509 (tt) REVERT: A 558 LYS cc_start: 0.9152 (mmpt) cc_final: 0.8782 (mmpt) REVERT: A 794 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8450 (pp) REVERT: A 1045 LYS cc_start: 0.8852 (tttm) cc_final: 0.8567 (ttmm) REVERT: B 100 ILE cc_start: 0.9038 (mm) cc_final: 0.8770 (tp) REVERT: B 205 SER cc_start: 0.8735 (p) cc_final: 0.8530 (m) REVERT: B 237 ARG cc_start: 0.8351 (mtm180) cc_final: 0.7879 (mpp80) REVERT: B 309 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8441 (mp0) REVERT: B 425 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6358 (tt) REVERT: B 1045 LYS cc_start: 0.8837 (tttm) cc_final: 0.8553 (ttmm) REVERT: C 237 ARG cc_start: 0.8269 (mtm180) cc_final: 0.7272 (mtm110) REVERT: C 309 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8002 (mp0) REVERT: C 357 ARG cc_start: 0.7759 (tpp-160) cc_final: 0.7348 (ttt180) REVERT: C 425 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6514 (tt) REVERT: C 558 LYS cc_start: 0.9029 (mmpt) cc_final: 0.8714 (mmpt) outliers start: 49 outliers final: 34 residues processed: 177 average time/residue: 0.9361 time to fit residues: 204.9177 Evaluate side-chains 166 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 170 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 257 optimal weight: 0.0870 chunk 148 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B1002 GLN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.132019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076421 restraints weight = 45690.121| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.82 r_work: 0.2925 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25062 Z= 0.118 Angle : 0.555 10.099 34182 Z= 0.282 Chirality : 0.045 0.245 3960 Planarity : 0.004 0.036 4347 Dihedral : 5.536 56.956 3972 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.79 % Allowed : 14.09 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3015 helix: 2.22 (0.21), residues: 663 sheet: 1.04 (0.21), residues: 654 loop : -1.12 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.011 0.001 HIS A 207 PHE 0.011 0.001 PHE A1121 TYR 0.019 0.001 TYR C 380 ARG 0.003 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 33) link_NAG-ASN : angle 2.45199 ( 99) hydrogen bonds : bond 0.05048 ( 957) hydrogen bonds : angle 4.75470 ( 2619) SS BOND : bond 0.00178 ( 39) SS BOND : angle 0.80134 ( 78) covalent geometry : bond 0.00273 (24990) covalent geometry : angle 0.53872 (34005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 2.835 Fit side-chains REVERT: A 205 SER cc_start: 0.8827 (p) cc_final: 0.8577 (m) REVERT: A 237 ARG cc_start: 0.8349 (mtm180) cc_final: 0.7659 (mtm110) REVERT: A 309 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8395 (mp0) REVERT: A 338 PHE cc_start: 0.8651 (m-80) cc_final: 0.8381 (m-80) REVERT: A 357 ARG cc_start: 0.7462 (ttp-170) cc_final: 0.7106 (tpp80) REVERT: A 425 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6591 (tt) REVERT: A 558 LYS cc_start: 0.9154 (mmpt) cc_final: 0.8776 (mmpt) REVERT: A 794 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8448 (pp) REVERT: B 205 SER cc_start: 0.8741 (p) cc_final: 0.8531 (m) REVERT: B 237 ARG cc_start: 0.8360 (mtm180) cc_final: 0.7889 (mpp80) REVERT: B 309 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8453 (mp0) REVERT: B 425 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6362 (tt) REVERT: B 1029 MET cc_start: 0.9027 (tpp) cc_final: 0.8775 (tpp) REVERT: B 1045 LYS cc_start: 0.8831 (tttm) cc_final: 0.8560 (ttmm) REVERT: C 205 SER cc_start: 0.8871 (p) cc_final: 0.8627 (m) REVERT: C 237 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7294 (mtm110) REVERT: C 309 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8038 (mp0) REVERT: C 357 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.7227 (ttt180) REVERT: C 380 TYR cc_start: 0.8311 (m-80) cc_final: 0.8079 (m-80) REVERT: C 425 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6547 (tt) REVERT: C 505 HIS cc_start: 0.7987 (m-70) cc_final: 0.7311 (t-170) REVERT: C 558 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8724 (mmpt) outliers start: 48 outliers final: 35 residues processed: 184 average time/residue: 0.9279 time to fit residues: 210.0181 Evaluate side-chains 171 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 232 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.130477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073846 restraints weight = 45663.680| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.88 r_work: 0.2878 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25062 Z= 0.139 Angle : 0.571 8.537 34182 Z= 0.291 Chirality : 0.045 0.236 3960 Planarity : 0.004 0.036 4347 Dihedral : 5.592 57.299 3972 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.90 % Allowed : 14.28 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3015 helix: 2.20 (0.21), residues: 663 sheet: 0.79 (0.21), residues: 624 loop : -1.05 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.010 0.001 HIS A 207 PHE 0.022 0.001 PHE A 133 TYR 0.024 0.001 TYR C 453 ARG 0.003 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 33) link_NAG-ASN : angle 2.47447 ( 99) hydrogen bonds : bond 0.05512 ( 957) hydrogen bonds : angle 4.82801 ( 2619) SS BOND : bond 0.00182 ( 39) SS BOND : angle 0.86026 ( 78) covalent geometry : bond 0.00333 (24990) covalent geometry : angle 0.55550 (34005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 2.903 Fit side-chains REVERT: A 205 SER cc_start: 0.8773 (p) cc_final: 0.8501 (m) REVERT: A 237 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7546 (mtm110) REVERT: A 309 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8311 (mp0) REVERT: A 314 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: A 338 PHE cc_start: 0.8624 (m-80) cc_final: 0.8343 (m-80) REVERT: A 357 ARG cc_start: 0.7312 (ttp-170) cc_final: 0.7049 (tpp80) REVERT: A 380 TYR cc_start: 0.8268 (m-80) cc_final: 0.8058 (m-10) REVERT: A 425 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6472 (tt) REVERT: A 558 LYS cc_start: 0.9129 (mmpt) cc_final: 0.8672 (mmpt) REVERT: A 794 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8335 (pp) REVERT: B 100 ILE cc_start: 0.9067 (mm) cc_final: 0.8789 (tp) REVERT: B 205 SER cc_start: 0.8739 (p) cc_final: 0.8464 (m) REVERT: B 237 ARG cc_start: 0.8258 (mtm180) cc_final: 0.7317 (mtm-85) REVERT: B 309 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8339 (mp0) REVERT: B 425 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6269 (tt) REVERT: B 1045 LYS cc_start: 0.8790 (tttm) cc_final: 0.8444 (ttmm) REVERT: C 173 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7544 (tm130) REVERT: C 205 SER cc_start: 0.8836 (p) cc_final: 0.8523 (m) REVERT: C 237 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7171 (mtm110) REVERT: C 309 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7883 (mp0) REVERT: C 357 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7239 (ttt180) REVERT: C 425 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6454 (tt) REVERT: C 505 HIS cc_start: 0.8016 (m-70) cc_final: 0.7300 (t-170) REVERT: C 558 LYS cc_start: 0.8999 (mmpt) cc_final: 0.8664 (mmpt) outliers start: 51 outliers final: 37 residues processed: 180 average time/residue: 0.9397 time to fit residues: 209.3591 Evaluate side-chains 175 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 78 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 205 optimal weight: 0.8980 chunk 203 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 370 ASN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.131587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.075462 restraints weight = 45778.279| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.89 r_work: 0.2911 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25062 Z= 0.106 Angle : 0.553 9.708 34182 Z= 0.280 Chirality : 0.045 0.258 3960 Planarity : 0.004 0.036 4347 Dihedral : 5.460 56.753 3972 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.68 % Allowed : 14.50 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3015 helix: 2.26 (0.21), residues: 663 sheet: 1.05 (0.21), residues: 654 loop : -1.10 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.009 0.001 HIS A 207 PHE 0.011 0.001 PHE C 140 TYR 0.017 0.001 TYR B 380 ARG 0.003 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 33) link_NAG-ASN : angle 2.42769 ( 99) hydrogen bonds : bond 0.04716 ( 957) hydrogen bonds : angle 4.71866 ( 2619) SS BOND : bond 0.00164 ( 39) SS BOND : angle 0.76497 ( 78) covalent geometry : bond 0.00233 (24990) covalent geometry : angle 0.53734 (34005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24287.25 seconds wall clock time: 421 minutes 13.81 seconds (25273.81 seconds total)