Starting phenix.real_space_refine on Fri May 23 21:06:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmd_37650/05_2025/8wmd_37650_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmd_37650/05_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_37650/05_2025/8wmd_37650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmd_37650/05_2025/8wmd_37650.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmd_37650/05_2025/8wmd_37650_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmd_37650/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 20.96, per 1000 atoms: 0.86 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: 6.22 Conformation dependent library (CDL) restraints added in 3.2 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: 3.32 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: 9.91 Time building geometry restraints manager: 7.20 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: 0.15 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: 4.070 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: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 61.390 Find NCS groups from input model: 0.430 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.850 ------------------------------------------------------------------------------- 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 : 2.521 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: 1.1076 time to fit residues: 389.5180 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 : 2.570 ------------------------------------------------------------------------------- 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 = 64)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078423 restraints weight = 45984.268| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.82 r_work: 0.2989 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- 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 2.99585 ( 99) hydrogen bonds : bond 0.04804 ( 957) hydrogen bonds : angle 4.94898 ( 2619) SS BOND : bond 0.00171 ( 39) SS BOND : angle 0.84051 ( 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 : 2.562 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8732 (p) cc_final: 0.8402 (m) REVERT: A 237 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7073 (mtm180) REVERT: A 309 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8026 (mp0) REVERT: A 357 ARG cc_start: 0.7458 (tpp-160) cc_final: 0.7163 (tpp80) REVERT: A 387 LEU cc_start: 0.9265 (mt) cc_final: 0.9018 (mt) REVERT: B 121 ASN cc_start: 0.8431 (m-40) cc_final: 0.8135 (t0) REVERT: B 205 SER cc_start: 0.8841 (p) cc_final: 0.8459 (m) REVERT: B 237 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7466 (mtm110) REVERT: B 309 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8294 (mp0) REVERT: B 357 ARG cc_start: 0.7519 (tpp-160) cc_final: 0.7164 (tpp80) REVERT: C 121 ASN cc_start: 0.8467 (m-40) cc_final: 0.8189 (t0) REVERT: C 220 PHE cc_start: 0.7375 (m-80) cc_final: 0.6993 (m-80) REVERT: C 237 ARG cc_start: 0.8114 (mtm180) cc_final: 0.7407 (mtm110) REVERT: C 309 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7918 (mp0) REVERT: C 357 ARG cc_start: 0.7543 (tpp-160) cc_final: 0.7161 (tpp80) outliers start: 54 outliers final: 23 residues processed: 197 average time/residue: 0.9718 time to fit residues: 232.4911 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 : 2.683 ------------------------------------------------------------------------------- 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: 10.0000 chunk 294 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 277 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.130572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073869 restraints weight = 45316.572| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.81 r_work: 0.2902 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25062 Z= 0.193 Angle : 0.611 10.317 34182 Z= 0.313 Chirality : 0.046 0.221 3960 Planarity : 0.005 0.060 4347 Dihedral : 6.126 57.538 3975 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.94 % Allowed : 12.75 % 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: 0.13 (0.15), residues: 3015 helix: 2.33 (0.21), residues: 645 sheet: 0.76 (0.21), residues: 621 loop : -1.09 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.007 0.001 HIS B1064 PHE 0.019 0.002 PHE C 565 TYR 0.019 0.002 TYR A1067 ARG 0.008 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 33) link_NAG-ASN : angle 2.79565 ( 99) hydrogen bonds : bond 0.06534 ( 957) hydrogen bonds : angle 5.06733 ( 2619) SS BOND : bond 0.00187 ( 39) SS BOND : angle 1.01022 ( 78) covalent geometry : bond 0.00475 (24990) covalent geometry : angle 0.59154 (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 208 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 2.752 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8820 (p) cc_final: 0.8565 (m) REVERT: A 237 ARG cc_start: 0.8235 (mtm180) cc_final: 0.7722 (mpp80) REVERT: A 357 ARG cc_start: 0.7569 (tpp-160) cc_final: 0.7272 (tpp80) REVERT: A 558 LYS cc_start: 0.9153 (mmpt) cc_final: 0.8796 (mmpt) REVERT: A 794 ILE cc_start: 0.8577 (tt) cc_final: 0.8348 (pp) REVERT: B 121 ASN cc_start: 0.8349 (m-40) cc_final: 0.7982 (t0) REVERT: B 205 SER cc_start: 0.8850 (p) cc_final: 0.8582 (m) REVERT: B 237 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7776 (mpp80) REVERT: B 309 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8427 (mp0) REVERT: B 338 PHE cc_start: 0.8676 (m-80) cc_final: 0.8267 (m-80) REVERT: C 121 ASN cc_start: 0.8500 (m-40) cc_final: 0.8143 (t0) REVERT: C 220 PHE cc_start: 0.7717 (m-80) cc_final: 0.7280 (m-80) REVERT: C 237 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7121 (mtm-85) REVERT: C 309 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7976 (mp0) REVERT: C 357 ARG cc_start: 0.7678 (tpp-160) cc_final: 0.7342 (ttt180) outliers start: 52 outliers final: 24 residues processed: 197 average time/residue: 0.9513 time to fit residues: 227.8260 Evaluate side-chains 159 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 2.529 ------------------------------------------------------------------------------- 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 780 GLU 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 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: 3.9990 chunk 186 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 285 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 260 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 394 ASN B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.131041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074576 restraints weight = 45831.416| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.82 r_work: 0.2908 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1790 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= 0.141 Angle : 0.570 9.882 34182 Z= 0.291 Chirality : 0.045 0.234 3960 Planarity : 0.004 0.051 4347 Dihedral : 5.985 57.459 3975 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.46 % Allowed : 12.68 % Favored : 84.86 % 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: 2.34 (0.20), residues: 645 sheet: 0.99 (0.20), residues: 657 loop : -1.16 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 PHE 0.024 0.001 PHE A 133 TYR 0.018 0.001 TYR A 160 ARG 0.005 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 33) link_NAG-ASN : angle 2.62736 ( 99) hydrogen bonds : bond 0.05724 ( 957) hydrogen bonds : angle 4.97383 ( 2619) SS BOND : bond 0.00171 ( 39) SS BOND : angle 1.04021 ( 78) covalent geometry : bond 0.00334 (24990) covalent geometry : angle 0.55110 (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 214 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8828 (p) cc_final: 0.8536 (m) REVERT: A 309 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8331 (mp0) REVERT: A 357 ARG cc_start: 0.7616 (ttp-170) cc_final: 0.7293 (tpp80) REVERT: A 394 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7605 (t0) REVERT: A 558 LYS cc_start: 0.9155 (mmpt) cc_final: 0.8788 (mmpt) REVERT: A 794 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8380 (pp) REVERT: B 121 ASN cc_start: 0.8311 (m-40) cc_final: 0.7923 (t0) REVERT: B 205 SER cc_start: 0.8916 (p) cc_final: 0.8538 (m) REVERT: B 237 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7770 (mpp80) REVERT: B 309 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8442 (mp0) REVERT: B 338 PHE cc_start: 0.8612 (m-80) cc_final: 0.8233 (m-80) REVERT: B 357 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7070 (ttt180) REVERT: C 176 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7999 (pt) REVERT: C 220 PHE cc_start: 0.7723 (m-80) cc_final: 0.7243 (m-80) REVERT: C 309 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7989 (mp0) REVERT: C 357 ARG cc_start: 0.7644 (tpp-160) cc_final: 0.7293 (ttt180) REVERT: C 558 LYS cc_start: 0.9059 (mmpt) cc_final: 0.8747 (mmpt) outliers start: 66 outliers final: 35 residues processed: 201 average time/residue: 0.9363 time to fit residues: 230.6701 Evaluate side-chains 172 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 394 ASN 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 317 ASN Chi-restraints excluded: chain B residue 357 ARG 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 738 CYS Chi-restraints excluded: chain B residue 780 GLU 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: 0.6980 chunk 107 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 19 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** A 394 ASN B 207 HIS B 755 GLN B1002 GLN C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.130917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074897 restraints weight = 45617.197| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.79 r_work: 0.2893 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25062 Z= 0.165 Angle : 0.580 9.273 34182 Z= 0.297 Chirality : 0.046 0.226 3960 Planarity : 0.004 0.055 4347 Dihedral : 5.974 57.895 3975 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: 2.28 (0.20), residues: 645 sheet: 0.74 (0.21), residues: 636 loop : -1.05 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.011 0.001 HIS A 207 PHE 0.018 0.001 PHE C 565 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 33) link_NAG-ASN : angle 2.60527 ( 99) hydrogen bonds : bond 0.06062 ( 957) hydrogen bonds : angle 5.00483 ( 2619) SS BOND : bond 0.00216 ( 39) SS BOND : angle 0.97428 ( 78) covalent geometry : bond 0.00401 (24990) covalent geometry : angle 0.56230 (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 210 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8835 (p) cc_final: 0.8564 (m) REVERT: A 309 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8438 (mp0) REVERT: A 357 ARG cc_start: 0.7580 (ttp-170) cc_final: 0.7311 (tpp80) REVERT: A 558 LYS cc_start: 0.9161 (mmpt) cc_final: 0.8805 (mmpt) REVERT: A 794 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8455 (pp) REVERT: B 121 ASN cc_start: 0.8317 (m-40) cc_final: 0.7918 (t0) REVERT: B 205 SER cc_start: 0.8935 (p) cc_final: 0.8582 (m) REVERT: B 309 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8477 (mp0) REVERT: B 338 PHE cc_start: 0.8633 (m-80) cc_final: 0.8268 (m-80) REVERT: B 357 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7316 (tpt-90) REVERT: B 369 TYR cc_start: 0.8498 (m-80) cc_final: 0.8208 (m-80) REVERT: B 425 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6590 (tt) REVERT: B 1045 LYS cc_start: 0.8855 (tttm) cc_final: 0.8561 (ttmm) REVERT: C 176 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8026 (pt) REVERT: C 309 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8059 (mp0) REVERT: C 512 VAL cc_start: 0.7914 (t) cc_final: 0.7650 (p) REVERT: C 558 LYS cc_start: 0.9064 (mmpt) cc_final: 0.8745 (mmpt) outliers start: 66 outliers final: 34 residues processed: 201 average time/residue: 0.9301 time to fit residues: 229.7271 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 : 2.732 ------------------------------------------------------------------------------- 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 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 207 HIS Chi-restraints excluded: chain B residue 317 ASN 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 780 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 8 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 207 HIS A 901 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.128006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070999 restraints weight = 45576.476| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.83 r_work: 0.2827 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 25062 Z= 0.282 Angle : 0.669 9.182 34182 Z= 0.347 Chirality : 0.049 0.229 3960 Planarity : 0.005 0.079 4347 Dihedral : 6.274 59.833 3972 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.91 % Allowed : 12.57 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3015 helix: 1.89 (0.20), residues: 648 sheet: 0.41 (0.20), residues: 663 loop : -1.15 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.025 0.002 HIS B 207 PHE 0.024 0.002 PHE A 133 TYR 0.025 0.002 TYR A 380 ARG 0.009 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 33) link_NAG-ASN : angle 2.79065 ( 99) hydrogen bonds : bond 0.07700 ( 957) hydrogen bonds : angle 5.28937 ( 2619) SS BOND : bond 0.00310 ( 39) SS BOND : angle 1.19695 ( 78) covalent geometry : bond 0.00704 (24990) covalent geometry : angle 0.65107 (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 219 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 141 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7643 (mtm-85) REVERT: A 309 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8443 (mp0) REVERT: A 314 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8721 (tm-30) REVERT: A 338 PHE cc_start: 0.8592 (m-80) cc_final: 0.8322 (m-80) REVERT: A 357 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7200 (tpp80) REVERT: A 425 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6546 (tt) REVERT: A 558 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8779 (mmpt) REVERT: A 794 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8581 (pp) REVERT: B 205 SER cc_start: 0.8878 (p) cc_final: 0.8591 (m) REVERT: B 237 ARG cc_start: 0.8369 (mtm180) cc_final: 0.7909 (mpp80) REVERT: B 309 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8506 (mp0) REVERT: B 338 PHE cc_start: 0.8701 (m-80) cc_final: 0.8324 (m-80) REVERT: C 100 ILE cc_start: 0.9110 (mm) cc_final: 0.8799 (pt) REVERT: C 176 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8015 (pt) REVERT: C 309 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8094 (mp0) REVERT: C 357 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7434 (ttt180) REVERT: C 425 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6573 (tt) REVERT: C 512 VAL cc_start: 0.8063 (t) cc_final: 0.7844 (p) REVERT: C 558 LYS cc_start: 0.9061 (mmpt) cc_final: 0.8754 (mmpt) outliers start: 78 outliers final: 38 residues processed: 202 average time/residue: 0.9514 time to fit residues: 236.0236 Evaluate side-chains 168 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 2.740 ------------------------------------------------------------------------------- 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 229 LEU 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 318 PHE Chi-restraints excluded: chain A residue 357 ARG 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 207 HIS 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 441 LEU 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 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 176 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 394 ASN 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 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 47 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 901 GLN A1088 HIS B 207 HIS B 755 GLN B 901 GLN C 394 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.130517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.074325 restraints weight = 45662.355| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.81 r_work: 0.2901 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25062 Z= 0.124 Angle : 0.569 9.048 34182 Z= 0.290 Chirality : 0.045 0.237 3960 Planarity : 0.004 0.040 4347 Dihedral : 5.903 58.598 3972 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.94 % Allowed : 13.80 % Favored : 84.27 % 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: 2.26 (0.21), residues: 639 sheet: 0.77 (0.21), residues: 615 loop : -1.10 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.010 0.001 HIS B 207 PHE 0.014 0.001 PHE C 565 TYR 0.016 0.001 TYR B1067 ARG 0.005 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 33) link_NAG-ASN : angle 2.63092 ( 99) hydrogen bonds : bond 0.05429 ( 957) hydrogen bonds : angle 4.98060 ( 2619) SS BOND : bond 0.00205 ( 39) SS BOND : angle 0.87467 ( 78) covalent geometry : bond 0.00282 (24990) covalent geometry : angle 0.55090 (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 200 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8829 (p) cc_final: 0.8553 (m) REVERT: A 309 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8459 (mp0) REVERT: A 338 PHE cc_start: 0.8617 (m-80) cc_final: 0.8368 (m-80) REVERT: A 357 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.7185 (tpp80) REVERT: A 425 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6501 (tt) REVERT: A 558 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8765 (mmpt) REVERT: A 794 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8570 (pp) REVERT: A 902 MET cc_start: 0.9268 (tpp) cc_final: 0.9068 (tpp) REVERT: B 205 SER cc_start: 0.8852 (p) cc_final: 0.8539 (m) REVERT: B 237 ARG cc_start: 0.8357 (mtm180) cc_final: 0.7892 (mpp80) REVERT: B 309 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8507 (mp0) REVERT: B 338 PHE cc_start: 0.8753 (m-80) cc_final: 0.8548 (m-80) REVERT: B 425 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6413 (tt) REVERT: C 237 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7309 (mtm110) REVERT: C 309 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8048 (mp0) REVERT: C 357 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7158 (ttt180) REVERT: C 425 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6458 (tt) REVERT: C 558 LYS cc_start: 0.9068 (mmpt) cc_final: 0.8746 (mmpt) outliers start: 52 outliers final: 29 residues processed: 193 average time/residue: 1.0029 time to fit residues: 234.3575 Evaluate side-chains 157 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 813 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 394 ASN 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 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: 1.9990 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 272 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 273 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.129991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.073116 restraints weight = 45658.318| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.90 r_work: 0.2854 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2431 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 : 0.579 8.528 34182 Z= 0.296 Chirality : 0.045 0.239 3960 Planarity : 0.004 0.039 4347 Dihedral : 5.847 58.303 3972 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.01 % Allowed : 14.02 % Favored : 83.97 % 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: 0.04 (0.15), residues: 3015 helix: 2.07 (0.20), residues: 663 sheet: 0.74 (0.21), residues: 627 loop : -1.13 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.004 0.001 HIS B1064 PHE 0.024 0.001 PHE A 133 TYR 0.020 0.001 TYR C 160 ARG 0.004 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 33) link_NAG-ASN : angle 2.60790 ( 99) hydrogen bonds : bond 0.05698 ( 957) hydrogen bonds : angle 4.95593 ( 2619) SS BOND : bond 0.00190 ( 39) SS BOND : angle 0.89448 ( 78) covalent geometry : bond 0.00328 (24990) covalent geometry : angle 0.56162 (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: 54 poor density : 130 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8765 (p) cc_final: 0.8465 (m) REVERT: A 237 ARG cc_start: 0.8165 (mtm180) cc_final: 0.7492 (mtm-85) REVERT: A 309 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8343 (mp0) REVERT: A 338 PHE cc_start: 0.8597 (m-80) cc_final: 0.8335 (m-80) REVERT: A 357 ARG cc_start: 0.7411 (ttp-170) cc_final: 0.7099 (tpp80) REVERT: A 425 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6436 (tt) REVERT: A 558 LYS cc_start: 0.9101 (mmpt) cc_final: 0.8692 (mmpt) REVERT: A 794 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8471 (pp) REVERT: B 205 SER cc_start: 0.8779 (p) cc_final: 0.8457 (m) REVERT: B 237 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7801 (mpp80) REVERT: B 309 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8343 (mp0) REVERT: B 425 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6372 (tt) REVERT: C 100 ILE cc_start: 0.9119 (mm) cc_final: 0.8849 (tp) REVERT: C 237 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7273 (mtm110) REVERT: C 309 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7834 (mp0) REVERT: C 357 ARG cc_start: 0.7701 (tpp-160) cc_final: 0.7198 (ttt180) REVERT: C 425 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6343 (tt) REVERT: C 558 LYS cc_start: 0.9034 (mmpt) cc_final: 0.8688 (mmpt) outliers start: 54 outliers final: 33 residues processed: 174 average time/residue: 0.9635 time to fit residues: 205.6404 Evaluate side-chains 161 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 2.677 ------------------------------------------------------------------------------- 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 51 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 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 394 ASN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 170 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 B 901 GLN B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.129191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072301 restraints weight = 45730.395| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.90 r_work: 0.2850 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2575 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= 0.165 Angle : 0.598 8.850 34182 Z= 0.306 Chirality : 0.046 0.240 3960 Planarity : 0.004 0.046 4347 Dihedral : 5.906 58.733 3972 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.94 % Allowed : 14.35 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.15), residues: 3015 helix: 2.00 (0.20), residues: 663 sheet: 0.74 (0.21), residues: 624 loop : -1.17 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.005 0.001 HIS B1064 PHE 0.026 0.001 PHE C 133 TYR 0.020 0.001 TYR C 380 ARG 0.003 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 33) link_NAG-ASN : angle 2.64772 ( 99) hydrogen bonds : bond 0.06184 ( 957) hydrogen bonds : angle 5.01021 ( 2619) SS BOND : bond 0.00214 ( 39) SS BOND : angle 0.97133 ( 78) covalent geometry : bond 0.00400 (24990) covalent geometry : angle 0.58082 (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 194 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.9085 (mm) cc_final: 0.8885 (mp) REVERT: A 205 SER cc_start: 0.8838 (p) cc_final: 0.8533 (m) REVERT: A 309 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8347 (mp0) REVERT: A 338 PHE cc_start: 0.8676 (m-80) cc_final: 0.8420 (m-80) REVERT: A 357 ARG cc_start: 0.7318 (ttp-170) cc_final: 0.6992 (tpp80) REVERT: A 425 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6448 (tt) REVERT: A 558 LYS cc_start: 0.9093 (mmpt) cc_final: 0.8704 (mmpt) REVERT: A 794 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8482 (pp) REVERT: B 205 SER cc_start: 0.8916 (p) cc_final: 0.8586 (m) REVERT: B 237 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7313 (mtm-85) REVERT: B 309 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8349 (mp0) REVERT: B 425 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6356 (tt) REVERT: C 173 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7615 (tm130) REVERT: C 309 GLU cc_start: 0.8632 (mm-30) cc_final: 0.7909 (mp0) REVERT: C 425 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6377 (tt) REVERT: C 505 HIS cc_start: 0.7980 (m-70) cc_final: 0.7262 (t-170) REVERT: C 558 LYS cc_start: 0.9034 (mmpt) cc_final: 0.8676 (mmpt) outliers start: 52 outliers final: 34 residues processed: 183 average time/residue: 0.9659 time to fit residues: 215.7693 Evaluate side-chains 169 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 2.645 ------------------------------------------------------------------------------- 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 51 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 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 394 ASN 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 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 232 optimal weight: 20.0000 chunk 212 optimal weight: 5.9990 chunk 294 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 755 GLN B 901 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.129586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.073345 restraints weight = 45639.308| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.79 r_work: 0.2888 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25062 Z= 0.158 Angle : 0.595 9.648 34182 Z= 0.305 Chirality : 0.046 0.258 3960 Planarity : 0.004 0.040 4347 Dihedral : 5.873 58.675 3972 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.64 % Allowed : 14.77 % Favored : 83.59 % 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: 0.00 (0.15), residues: 3015 helix: 1.99 (0.20), residues: 666 sheet: 0.73 (0.21), residues: 624 loop : -1.15 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.006 0.001 HIS A 207 PHE 0.022 0.001 PHE A 133 TYR 0.022 0.001 TYR A 904 ARG 0.003 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 33) link_NAG-ASN : angle 2.64465 ( 99) hydrogen bonds : bond 0.06029 ( 957) hydrogen bonds : angle 4.99069 ( 2619) SS BOND : bond 0.00191 ( 39) SS BOND : angle 0.93879 ( 78) covalent geometry : bond 0.00383 (24990) covalent geometry : angle 0.57753 (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 177 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.9110 (mm) cc_final: 0.8905 (mp) REVERT: A 205 SER cc_start: 0.8850 (p) cc_final: 0.8590 (m) REVERT: A 237 ARG cc_start: 0.8276 (mtm180) cc_final: 0.7596 (mtm110) REVERT: A 309 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8450 (mp0) REVERT: A 338 PHE cc_start: 0.8752 (m-80) cc_final: 0.8484 (m-80) REVERT: A 357 ARG cc_start: 0.7371 (ttp-170) cc_final: 0.6943 (tpp80) REVERT: A 425 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6596 (tt) REVERT: A 558 LYS cc_start: 0.9126 (mmpt) cc_final: 0.8705 (mmpt) REVERT: A 794 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8561 (pp) REVERT: B 100 ILE cc_start: 0.9094 (mm) cc_final: 0.8795 (tp) REVERT: B 205 SER cc_start: 0.8918 (p) cc_final: 0.8642 (m) REVERT: B 237 ARG cc_start: 0.8344 (mtm180) cc_final: 0.7388 (mtm-85) REVERT: B 309 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8486 (mp0) REVERT: B 425 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6407 (tt) REVERT: C 173 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7584 (tm130) REVERT: C 309 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8049 (mp0) REVERT: C 357 ARG cc_start: 0.7546 (tpp-160) cc_final: 0.7188 (ttt180) REVERT: C 425 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6524 (tt) REVERT: C 505 HIS cc_start: 0.7981 (m-70) cc_final: 0.7295 (t-170) REVERT: C 558 LYS cc_start: 0.9066 (mmpt) cc_final: 0.8733 (mmpt) outliers start: 44 outliers final: 33 residues processed: 171 average time/residue: 1.0490 time to fit residues: 217.1969 Evaluate side-chains 167 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 2.611 ------------------------------------------------------------------------------- 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 51 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 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 396 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 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: 0.7980 chunk 151 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 203 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 370 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.130969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.074755 restraints weight = 45558.216| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.85 r_work: 0.2888 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25062 Z= 0.110 Angle : 0.559 8.749 34182 Z= 0.284 Chirality : 0.045 0.252 3960 Planarity : 0.004 0.039 4347 Dihedral : 5.643 57.303 3972 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.49 % Allowed : 14.99 % Favored : 83.52 % 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: 0.14 (0.15), residues: 3015 helix: 2.19 (0.21), residues: 663 sheet: 0.80 (0.21), residues: 624 loop : -1.08 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 PHE 0.020 0.001 PHE C 133 TYR 0.027 0.001 TYR C 380 ARG 0.002 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 33) link_NAG-ASN : angle 2.54529 ( 99) hydrogen bonds : bond 0.04842 ( 957) hydrogen bonds : angle 4.79424 ( 2619) SS BOND : bond 0.00153 ( 39) SS BOND : angle 0.79555 ( 78) covalent geometry : bond 0.00244 (24990) covalent geometry : angle 0.54234 (34005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22020.15 seconds wall clock time: 380 minutes 19.24 seconds (22819.24 seconds total)