Starting phenix.real_space_refine on Mon Aug 25 02:31:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmd_37650/08_2025/8wmd_37650_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmd_37650/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wmd_37650/08_2025/8wmd_37650_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmd_37650/08_2025/8wmd_37650_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wmd_37650/08_2025/8wmd_37650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmd_37650/08_2025/8wmd_37650.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C Time building chain proxies: 8.69, per 1000 atoms: 0.36 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 B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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: 2.01 Conformation dependent library (CDL) restraints added in 834.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.94 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: 4.99 Time building geometry restraints manager: 2.72 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.090 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- 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 : 4.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 983 TYR 0.014 0.001 TYR B1067 PHE 0.008 0.001 PHE A 400 TRP 0.007 0.001 TRP C 886 HIS 0.002 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00284 (24990) covalent geometry : angle 0.51917 (34005) SS BOND : bond 0.00227 ( 39) SS BOND : angle 0.70776 ( 78) hydrogen bonds : bond 0.13255 ( 957) hydrogen bonds : angle 5.77389 ( 2619) link_NAG-ASN : bond 0.00834 ( 33) link_NAG-ASN : angle 4.01309 ( 99) *********************** 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 : 0.959 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: 0.5428 time to fit residues: 189.6177 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 : 0.953 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 121 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 755 GLN B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.132095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075839 restraints weight = 45803.618| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.82 r_work: 0.2936 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25062 Z= 0.151 Angle : 0.605 12.995 34182 Z= 0.304 Chirality : 0.046 0.272 3960 Planarity : 0.005 0.071 4347 Dihedral : 6.438 57.509 3985 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.05 % Allowed : 11.93 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.15), residues: 3015 helix: 2.41 (0.21), residues: 648 sheet: 0.96 (0.20), residues: 657 loop : -1.17 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.018 0.001 TYR A1067 PHE 0.030 0.001 PHE C 133 TRP 0.013 0.001 TRP B 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00349 (24990) covalent geometry : angle 0.58199 (34005) SS BOND : bond 0.00182 ( 39) SS BOND : angle 0.95714 ( 78) hydrogen bonds : bond 0.05728 ( 957) hydrogen bonds : angle 5.04291 ( 2619) link_NAG-ASN : bond 0.00450 ( 33) link_NAG-ASN : angle 3.02132 ( 99) *********************** 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 214 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8762 (p) cc_final: 0.8453 (m) REVERT: A 237 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7434 (mtm-85) REVERT: A 309 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8079 (mp0) REVERT: A 357 ARG cc_start: 0.7511 (tpp-160) cc_final: 0.7189 (tpp80) REVERT: A 558 LYS cc_start: 0.9123 (mmpt) cc_final: 0.8769 (mmpt) REVERT: A 794 ILE cc_start: 0.8481 (tt) cc_final: 0.8277 (pp) REVERT: B 121 ASN cc_start: 0.8416 (m-40) cc_final: 0.8106 (t0) REVERT: B 205 SER cc_start: 0.8893 (p) cc_final: 0.8534 (m) REVERT: B 237 ARG cc_start: 0.8178 (mtm180) cc_final: 0.7283 (mtm110) REVERT: B 309 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8367 (mp0) REVERT: B 357 ARG cc_start: 0.7554 (tpp-160) cc_final: 0.7038 (ttt180) REVERT: C 121 ASN cc_start: 0.8471 (m-40) cc_final: 0.8133 (t0) REVERT: C 210 ILE cc_start: 0.8107 (tp) cc_final: 0.7891 (pt) REVERT: C 220 PHE cc_start: 0.7500 (m-80) cc_final: 0.7104 (m-80) REVERT: C 237 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7435 (mtm110) REVERT: C 309 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7967 (mp0) REVERT: C 357 ARG cc_start: 0.7483 (tpp-160) cc_final: 0.6936 (ttt180) REVERT: C 571 ASP cc_start: 0.8661 (t0) cc_final: 0.8457 (t0) REVERT: C 1045 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8349 (tttt) outliers start: 55 outliers final: 24 residues processed: 201 average time/residue: 0.5599 time to fit residues: 134.0052 Evaluate side-chains 158 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 171 VAL 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 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 341 VAL Chi-restraints excluded: chain C residue 394 ASN 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 1045 LYS 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 101 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 282 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 297 optimal weight: 0.4980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 394 ASN B 164 ASN B 343 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C1088 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.130862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074329 restraints weight = 45838.921| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.81 r_work: 0.2904 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1635 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= 0.169 Angle : 0.590 10.224 34182 Z= 0.301 Chirality : 0.046 0.228 3960 Planarity : 0.004 0.060 4347 Dihedral : 6.116 57.499 3975 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.98 % Allowed : 12.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.15), residues: 3015 helix: 2.33 (0.20), residues: 645 sheet: 0.95 (0.21), residues: 657 loop : -1.13 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE C 565 TRP 0.011 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00407 (24990) covalent geometry : angle 0.57105 (34005) SS BOND : bond 0.00196 ( 39) SS BOND : angle 0.95241 ( 78) hydrogen bonds : bond 0.06089 ( 957) hydrogen bonds : angle 5.03122 ( 2619) link_NAG-ASN : bond 0.00456 ( 33) link_NAG-ASN : angle 2.76630 ( 99) *********************** 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: 53 poor density : 155 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8796 (p) cc_final: 0.8537 (m) REVERT: A 309 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8134 (mp0) REVERT: A 357 ARG cc_start: 0.7599 (tpp-160) cc_final: 0.7193 (tpp80) REVERT: A 394 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7410 (t0) REVERT: A 512 VAL cc_start: 0.8110 (t) cc_final: 0.7870 (p) REVERT: A 558 LYS cc_start: 0.9141 (mmpt) cc_final: 0.8772 (mmpt) REVERT: A 794 ILE cc_start: 0.8586 (tt) cc_final: 0.8355 (pp) REVERT: B 121 ASN cc_start: 0.8349 (m-40) cc_final: 0.7967 (t0) REVERT: B 205 SER cc_start: 0.8928 (p) cc_final: 0.8617 (m) REVERT: B 237 ARG cc_start: 0.8186 (mtm180) cc_final: 0.7764 (mpp80) REVERT: B 309 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8438 (mp0) REVERT: B 338 PHE cc_start: 0.8622 (m-80) cc_final: 0.8220 (m-80) REVERT: B 357 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.7063 (ttt180) REVERT: B 1045 LYS cc_start: 0.8856 (tttm) cc_final: 0.8551 (ttmm) REVERT: C 121 ASN cc_start: 0.8519 (m-40) cc_final: 0.8149 (t0) REVERT: C 220 PHE cc_start: 0.7641 (m-80) cc_final: 0.7229 (m-80) REVERT: C 309 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7981 (mp0) REVERT: C 357 ARG cc_start: 0.7504 (ttp-170) cc_final: 0.7182 (ttt180) outliers start: 53 outliers final: 26 residues processed: 198 average time/residue: 0.4975 time to fit residues: 119.5729 Evaluate side-chains 164 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 396 TYR Chi-restraints excluded: chain B residue 430 THR 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 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 287 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 293 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 285 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 207 HIS B 755 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.131225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075551 restraints weight = 45365.471| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.03 r_work: 0.2883 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25062 Z= 0.156 Angle : 0.578 9.782 34182 Z= 0.296 Chirality : 0.046 0.232 3960 Planarity : 0.004 0.054 4347 Dihedral : 6.013 57.684 3975 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.76 % Allowed : 12.23 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3015 helix: 2.31 (0.20), residues: 645 sheet: 0.75 (0.21), residues: 636 loop : -1.03 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.019 0.001 TYR C 160 PHE 0.023 0.001 PHE B 133 TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00373 (24990) covalent geometry : angle 0.55945 (34005) SS BOND : bond 0.00359 ( 39) SS BOND : angle 1.11299 ( 78) hydrogen bonds : bond 0.05927 ( 957) hydrogen bonds : angle 4.99179 ( 2619) link_NAG-ASN : bond 0.00448 ( 33) link_NAG-ASN : angle 2.64252 ( 99) *********************** 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 223 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8846 (p) cc_final: 0.8557 (m) REVERT: A 309 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8357 (mp0) REVERT: A 357 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7261 (tpp80) REVERT: A 558 LYS cc_start: 0.9153 (mmpt) cc_final: 0.8787 (mmpt) REVERT: A 794 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8420 (pp) REVERT: B 121 ASN cc_start: 0.8318 (m-40) cc_final: 0.7920 (t0) REVERT: B 205 SER cc_start: 0.8934 (p) cc_final: 0.8549 (m) REVERT: B 309 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8465 (mp0) REVERT: B 338 PHE cc_start: 0.8624 (m-80) cc_final: 0.8235 (m-80) REVERT: B 357 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7385 (tpp-160) REVERT: C 176 LEU cc_start: 0.8202 (mm) cc_final: 0.7969 (pt) REVERT: C 220 PHE cc_start: 0.7754 (m-80) cc_final: 0.7522 (m-80) REVERT: C 309 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8033 (mp0) REVERT: C 357 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.7363 (tpp-160) REVERT: C 558 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8712 (mmpt) outliers start: 74 outliers final: 37 residues processed: 211 average time/residue: 0.4752 time to fit residues: 122.7073 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 : 1.017 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 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 357 ARG 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 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 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 259 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 70 optimal weight: 1.9990 chunk 168 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS B 207 HIS B 394 ASN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.131045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.074831 restraints weight = 45568.784| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.81 r_work: 0.2913 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25062 Z= 0.125 Angle : 0.561 9.251 34182 Z= 0.285 Chirality : 0.045 0.237 3960 Planarity : 0.004 0.043 4347 Dihedral : 5.901 57.459 3975 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.13 % Allowed : 13.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.15), residues: 3015 helix: 2.37 (0.20), residues: 645 sheet: 0.91 (0.21), residues: 657 loop : -1.08 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.018 0.001 TYR C 160 PHE 0.019 0.001 PHE C 133 TRP 0.007 0.001 TRP A 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00291 (24990) covalent geometry : angle 0.54317 (34005) SS BOND : bond 0.00220 ( 39) SS BOND : angle 0.91999 ( 78) hydrogen bonds : bond 0.05439 ( 957) hydrogen bonds : angle 4.91528 ( 2619) link_NAG-ASN : bond 0.00451 ( 33) link_NAG-ASN : angle 2.58521 ( 99) *********************** 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 199 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8779 (p) cc_final: 0.8551 (m) REVERT: A 237 ARG cc_start: 0.8298 (mtm180) cc_final: 0.7716 (mpp80) REVERT: A 309 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8357 (mp0) REVERT: A 357 ARG cc_start: 0.7602 (ttp-170) cc_final: 0.7242 (tpp80) REVERT: A 380 TYR cc_start: 0.8601 (m-80) cc_final: 0.8197 (m-80) REVERT: A 425 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6626 (tt) REVERT: A 558 LYS cc_start: 0.9155 (mmpt) cc_final: 0.8797 (mmpt) REVERT: A 794 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8452 (pp) REVERT: A 1045 LYS cc_start: 0.8874 (tttm) cc_final: 0.8578 (ttmm) REVERT: B 121 ASN cc_start: 0.8307 (m-40) cc_final: 0.7910 (t0) REVERT: B 205 SER cc_start: 0.8825 (p) cc_final: 0.8535 (m) REVERT: B 237 ARG cc_start: 0.8219 (mtm180) cc_final: 0.7762 (mpp80) REVERT: B 309 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8451 (mp0) REVERT: B 338 PHE cc_start: 0.8626 (m-80) cc_final: 0.8270 (m-80) REVERT: B 425 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6633 (tt) REVERT: B 1045 LYS cc_start: 0.8852 (tttm) cc_final: 0.8558 (ttmm) REVERT: C 176 LEU cc_start: 0.8181 (mm) cc_final: 0.7974 (pt) REVERT: C 220 PHE cc_start: 0.7800 (m-80) cc_final: 0.7555 (m-80) REVERT: C 309 GLU cc_start: 0.8612 (mm-30) cc_final: 0.7975 (mp0) REVERT: C 558 LYS cc_start: 0.9010 (mmpt) cc_final: 0.8693 (mmpt) outliers start: 57 outliers final: 34 residues processed: 188 average time/residue: 0.4643 time to fit residues: 106.3539 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 : 0.872 ------------------------------------------------------------------------------- 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 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 738 CYS 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 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 430 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 48 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 0.0030 chunk 54 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 291 optimal weight: 0.3980 chunk 299 optimal weight: 0.3980 chunk 205 optimal weight: 5.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.131700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075782 restraints weight = 45693.653| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.81 r_work: 0.2928 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25062 Z= 0.111 Angle : 0.543 8.789 34182 Z= 0.276 Chirality : 0.045 0.246 3960 Planarity : 0.004 0.038 4347 Dihedral : 5.695 56.926 3973 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.54 % Allowed : 12.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.15), residues: 3015 helix: 2.43 (0.21), residues: 645 sheet: 0.95 (0.21), residues: 657 loop : -1.06 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.018 0.001 TYR A 160 PHE 0.026 0.001 PHE A 133 TRP 0.007 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00248 (24990) covalent geometry : angle 0.52594 (34005) SS BOND : bond 0.00201 ( 39) SS BOND : angle 0.80352 ( 78) hydrogen bonds : bond 0.04942 ( 957) hydrogen bonds : angle 4.79887 ( 2619) link_NAG-ASN : bond 0.00452 ( 33) link_NAG-ASN : angle 2.51086 ( 99) *********************** 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 215 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 147 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8826 (p) cc_final: 0.8595 (m) REVERT: A 309 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8416 (mp0) REVERT: A 338 PHE cc_start: 0.8551 (m-80) cc_final: 0.8317 (m-80) REVERT: A 357 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.7178 (tpp80) REVERT: A 380 TYR cc_start: 0.8551 (m-80) cc_final: 0.8141 (m-80) REVERT: A 425 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6595 (tt) REVERT: A 558 LYS cc_start: 0.9156 (mmpt) cc_final: 0.8789 (mmpt) REVERT: A 794 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8436 (pp) REVERT: A 1045 LYS cc_start: 0.8833 (tttm) cc_final: 0.8551 (ttmm) REVERT: B 121 ASN cc_start: 0.8301 (m-40) cc_final: 0.7889 (t0) REVERT: B 205 SER cc_start: 0.8737 (p) cc_final: 0.8497 (m) REVERT: B 237 ARG cc_start: 0.8343 (mtm180) cc_final: 0.7874 (mpp80) REVERT: B 309 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8454 (mp0) REVERT: B 357 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7403 (ttt180) REVERT: B 425 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6610 (tt) REVERT: B 1045 LYS cc_start: 0.8839 (tttm) cc_final: 0.8556 (ttmm) REVERT: C 176 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7971 (pt) REVERT: C 220 PHE cc_start: 0.7811 (m-80) cc_final: 0.7603 (m-80) REVERT: C 309 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7974 (mp0) REVERT: C 512 VAL cc_start: 0.7928 (t) cc_final: 0.7658 (p) REVERT: C 558 LYS cc_start: 0.9022 (mmpt) cc_final: 0.8712 (mmpt) outliers start: 68 outliers final: 35 residues processed: 205 average time/residue: 0.5142 time to fit residues: 127.1143 Evaluate side-chains 169 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS 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 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 143 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 243 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 901 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 901 GLN B1002 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.129048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.072629 restraints weight = 45619.202| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.80 r_work: 0.2853 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 25062 Z= 0.266 Angle : 0.655 8.573 34182 Z= 0.339 Chirality : 0.049 0.240 3960 Planarity : 0.005 0.069 4347 Dihedral : 6.106 59.206 3973 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.31 % Allowed : 13.50 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 3015 helix: 2.00 (0.20), residues: 648 sheet: 0.49 (0.21), residues: 636 loop : -1.07 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.028 0.002 TYR A 904 PHE 0.017 0.002 PHE C1121 TRP 0.008 0.001 TRP C 886 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00664 (24990) covalent geometry : angle 0.63778 (34005) SS BOND : bond 0.00279 ( 39) SS BOND : angle 1.16515 ( 78) hydrogen bonds : bond 0.07411 ( 957) hydrogen bonds : angle 5.18192 ( 2619) link_NAG-ASN : bond 0.00499 ( 33) link_NAG-ASN : angle 2.69678 ( 99) *********************** 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 201 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 139 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8920 (p) cc_final: 0.8679 (m) REVERT: A 309 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8442 (mp0) REVERT: A 314 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8703 (tm-30) REVERT: A 338 PHE cc_start: 0.8616 (m-80) cc_final: 0.8338 (m-80) REVERT: A 357 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.7233 (tpp80) REVERT: A 425 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6613 (tt) REVERT: A 558 LYS cc_start: 0.9148 (mmpt) cc_final: 0.8741 (mmpt) REVERT: A 794 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8524 (pp) REVERT: B 205 SER cc_start: 0.8896 (p) cc_final: 0.8691 (m) REVERT: B 237 ARG cc_start: 0.8370 (mtm180) cc_final: 0.7912 (mpp80) REVERT: B 309 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8512 (mp0) REVERT: B 357 ARG cc_start: 0.7783 (tpp-160) cc_final: 0.7527 (tpp80) REVERT: C 100 ILE cc_start: 0.8887 (tp) cc_final: 0.8293 (pt) REVERT: C 176 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8010 (pt) REVERT: C 237 ARG cc_start: 0.8328 (mtm180) cc_final: 0.7364 (mtm110) REVERT: C 309 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8104 (mp0) REVERT: C 512 VAL cc_start: 0.7970 (t) cc_final: 0.7736 (p) REVERT: C 558 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8766 (mmpt) outliers start: 62 outliers final: 36 residues processed: 188 average time/residue: 0.4256 time to fit residues: 97.4895 Evaluate side-chains 163 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 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 318 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 168 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 245 optimal weight: 0.0570 chunk 250 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- 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 901 GLN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.130438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074497 restraints weight = 45433.183| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.80 r_work: 0.2887 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2437 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= 0.156 Angle : 0.588 8.754 34182 Z= 0.300 Chirality : 0.046 0.240 3960 Planarity : 0.004 0.041 4347 Dihedral : 5.920 58.777 3972 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.98 % Allowed : 14.17 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.15), residues: 3015 helix: 1.99 (0.20), residues: 663 sheet: 0.66 (0.21), residues: 630 loop : -1.13 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.029 0.001 TYR A 380 PHE 0.025 0.001 PHE A 133 TRP 0.007 0.001 TRP C 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00377 (24990) covalent geometry : angle 0.57018 (34005) SS BOND : bond 0.00215 ( 39) SS BOND : angle 0.92686 ( 78) hydrogen bonds : bond 0.05916 ( 957) hydrogen bonds : angle 5.00627 ( 2619) link_NAG-ASN : bond 0.00461 ( 33) link_NAG-ASN : angle 2.64126 ( 99) *********************** 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 195 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8862 (p) cc_final: 0.8618 (m) REVERT: A 237 ARG cc_start: 0.8282 (mtm180) cc_final: 0.7600 (mtm110) REVERT: A 309 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8454 (mp0) REVERT: A 338 PHE cc_start: 0.8684 (m-80) cc_final: 0.8427 (m-80) REVERT: A 357 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.7186 (tpp80) REVERT: A 425 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6557 (tt) REVERT: A 558 LYS cc_start: 0.9138 (mmpt) cc_final: 0.8702 (mmpt) REVERT: A 794 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8583 (pp) REVERT: B 205 SER cc_start: 0.8900 (p) cc_final: 0.8581 (m) REVERT: B 237 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7892 (mpp80) REVERT: B 309 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8508 (mp0) REVERT: B 357 ARG cc_start: 0.7688 (tpp-160) cc_final: 0.7392 (tpp80) REVERT: B 425 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6502 (tt) REVERT: B 1045 LYS cc_start: 0.8867 (tttm) cc_final: 0.8587 (ttmm) REVERT: C 176 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8035 (pt) REVERT: C 309 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8052 (mp0) REVERT: C 558 LYS cc_start: 0.9068 (mmpt) cc_final: 0.8754 (mmpt) outliers start: 53 outliers final: 34 residues processed: 186 average time/residue: 0.4434 time to fit residues: 100.7858 Evaluate side-chains 168 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 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 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 293 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 72 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 370 ASN C 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.129760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073242 restraints weight = 45685.634| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.84 r_work: 0.2921 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25062 Z= 0.155 Angle : 0.593 8.986 34182 Z= 0.303 Chirality : 0.046 0.248 3960 Planarity : 0.004 0.044 4347 Dihedral : 5.891 58.627 3972 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.94 % Allowed : 14.28 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3015 helix: 2.03 (0.20), residues: 663 sheet: 0.70 (0.21), residues: 624 loop : -1.13 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.026 0.002 TYR A 380 PHE 0.017 0.001 PHE C 133 TRP 0.007 0.001 TRP B 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00374 (24990) covalent geometry : angle 0.57568 (34005) SS BOND : bond 0.00207 ( 39) SS BOND : angle 0.93367 ( 78) hydrogen bonds : bond 0.05974 ( 957) hydrogen bonds : angle 4.99765 ( 2619) link_NAG-ASN : bond 0.00467 ( 33) link_NAG-ASN : angle 2.63210 ( 99) *********************** 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 193 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8834 (p) cc_final: 0.8558 (m) REVERT: A 237 ARG cc_start: 0.8267 (mtm180) cc_final: 0.7603 (mtm110) REVERT: A 309 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8401 (mp0) REVERT: A 314 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: A 338 PHE cc_start: 0.8699 (m-80) cc_final: 0.8438 (m-80) REVERT: A 357 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7114 (tpp80) REVERT: A 425 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6522 (tt) REVERT: A 558 LYS cc_start: 0.9121 (mmpt) cc_final: 0.8732 (mmpt) REVERT: A 794 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8537 (pp) REVERT: B 205 SER cc_start: 0.8889 (p) cc_final: 0.8589 (m) REVERT: B 237 ARG cc_start: 0.8306 (mtm180) cc_final: 0.7860 (mpp80) REVERT: B 309 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8412 (mp0) REVERT: B 357 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7293 (tpp80) REVERT: B 425 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6490 (tt) REVERT: B 1045 LYS cc_start: 0.8859 (tttm) cc_final: 0.8546 (ttmm) REVERT: C 100 ILE cc_start: 0.9084 (mm) cc_final: 0.8873 (tp) REVERT: C 176 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8014 (pt) REVERT: C 237 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7306 (mtm110) REVERT: C 309 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7945 (mp0) REVERT: C 558 LYS cc_start: 0.9052 (mmpt) cc_final: 0.8724 (mmpt) outliers start: 52 outliers final: 36 residues processed: 183 average time/residue: 0.4504 time to fit residues: 100.4794 Evaluate side-chains 172 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 121 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN 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 317 ASN Chi-restraints excluded: chain B residue 394 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 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 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 67 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 270 optimal weight: 0.4980 chunk 273 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.130198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073665 restraints weight = 45597.338| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.89 r_work: 0.2878 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25062 Z= 0.127 Angle : 0.580 9.175 34182 Z= 0.297 Chirality : 0.045 0.251 3960 Planarity : 0.004 0.038 4347 Dihedral : 5.793 58.019 3972 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.72 % Allowed : 14.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.15), residues: 3015 helix: 2.12 (0.21), residues: 663 sheet: 0.74 (0.21), residues: 624 loop : -1.10 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.021 0.001 TYR C 380 PHE 0.026 0.001 PHE A 133 TRP 0.007 0.001 TRP B 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00294 (24990) covalent geometry : angle 0.56302 (34005) SS BOND : bond 0.00175 ( 39) SS BOND : angle 0.88403 ( 78) hydrogen bonds : bond 0.05451 ( 957) hydrogen bonds : angle 4.91174 ( 2619) link_NAG-ASN : bond 0.00564 ( 33) link_NAG-ASN : angle 2.61305 ( 99) ********************** 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 185 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8775 (p) cc_final: 0.8470 (m) REVERT: A 309 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8338 (mp0) REVERT: A 338 PHE cc_start: 0.8677 (m-80) cc_final: 0.8411 (m-80) REVERT: A 357 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.6995 (tpp80) REVERT: A 425 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6470 (tt) REVERT: A 558 LYS cc_start: 0.9103 (mmpt) cc_final: 0.8698 (mmpt) REVERT: A 794 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8479 (pp) REVERT: B 205 SER cc_start: 0.8773 (p) cc_final: 0.8407 (m) REVERT: B 237 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7801 (mpp80) REVERT: B 309 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8363 (mp0) REVERT: B 338 PHE cc_start: 0.8724 (m-80) cc_final: 0.8514 (m-80) REVERT: B 357 ARG cc_start: 0.7610 (tpp-160) cc_final: 0.7305 (tpp80) REVERT: B 425 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6348 (tt) REVERT: B 1045 LYS cc_start: 0.8821 (tttm) cc_final: 0.8485 (ttmm) REVERT: C 176 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7977 (pt) REVERT: C 237 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7448 (mtm110) REVERT: C 309 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7890 (mp0) REVERT: C 505 HIS cc_start: 0.8029 (m-70) cc_final: 0.7286 (t-170) REVERT: C 558 LYS cc_start: 0.9031 (mmpt) cc_final: 0.8690 (mmpt) outliers start: 46 outliers final: 35 residues processed: 177 average time/residue: 0.4444 time to fit residues: 96.1608 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 : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 394 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 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 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 430 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 146 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.129732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.073017 restraints weight = 45373.391| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.93 r_work: 0.2846 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25062 Z= 0.140 Angle : 0.586 9.439 34182 Z= 0.300 Chirality : 0.046 0.251 3960 Planarity : 0.004 0.061 4347 Dihedral : 5.767 57.992 3972 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.75 % Allowed : 14.77 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.15), residues: 3015 helix: 2.10 (0.21), residues: 663 sheet: 0.73 (0.21), residues: 624 loop : -1.10 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 498 TYR 0.025 0.001 TYR A 904 PHE 0.026 0.001 PHE C 133 TRP 0.006 0.001 TRP B 886 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00332 (24990) covalent geometry : angle 0.56918 (34005) SS BOND : bond 0.00185 ( 39) SS BOND : angle 0.90704 ( 78) hydrogen bonds : bond 0.05651 ( 957) hydrogen bonds : angle 4.92162 ( 2619) link_NAG-ASN : bond 0.00472 ( 33) link_NAG-ASN : angle 2.58855 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12146.42 seconds wall clock time: 206 minutes 47.92 seconds (12407.92 seconds total)