Starting phenix.real_space_refine on Tue Apr 7 20:03:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ypb_73292/04_2026/9ypb_73292.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ypb_73292/04_2026/9ypb_73292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ypb_73292/04_2026/9ypb_73292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ypb_73292/04_2026/9ypb_73292.map" model { file = "/net/cci-nas-00/data/ceres_data/9ypb_73292/04_2026/9ypb_73292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ypb_73292/04_2026/9ypb_73292.cif" } resolution = 3.5 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= 0.001 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 127 5.16 5 C 18999 2.51 5 N 4925 2.21 5 O 5807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29858 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1622 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain breaks: 3 Chain: "E" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1575 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain: "F" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1502 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 13, 'TRANS': 179} Chain breaks: 4 Chain: "G" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1551 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Chain: "A" Number of atoms: 7918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7918 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 51, 'TRANS': 961} Chain breaks: 13 Chain: "B" Number of atoms: 7595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7595 Classifications: {'peptide': 973} Link IDs: {'PTRANS': 49, 'TRANS': 923} Chain breaks: 16 Chain: "C" Number of atoms: 7745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7745 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 50, 'TRANS': 941} Chain breaks: 11 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.21, per 1000 atoms: 0.24 Number of scatterers: 29858 At special positions: 0 Unit cell: (129.191, 135.902, 266.77, 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 127 16.00 O 5807 8.00 N 4925 7.00 C 18999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 211 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 194 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 155 " - pdb=" SG CYS F 211 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.01 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " 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 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1134 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7110 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 69 sheets defined 20.2% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'D' and resid 64 through 68 removed outlier: 4.005A pdb=" N LYS D 68 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.630A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.614A pdb=" N HIS E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'G' and resid 122 through 128 Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.568A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.901A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.705A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.083A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.821A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.867A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.344A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.516A pdb=" N GLU A1144 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.587A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.090A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.559A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.068A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.469A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 946 No H-bonds generated for 'chain 'B' and resid 945 through 946' Processing helix chain 'B' and resid 948 through 948 No H-bonds generated for 'chain 'B' and resid 948 through 948' Processing helix chain 'B' and resid 949 through 966 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.700A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.771A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.234A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.618A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.588A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.643A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.397A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.990A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.095A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.730A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 54 removed outlier: 3.945A pdb=" N ARG D 101 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL D 117 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 135 through 139 removed outlier: 3.829A pdb=" N GLY D 154 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 166 through 169 Processing sheet with id=AA6, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.880A pdb=" N GLY E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.880A pdb=" N GLY E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 92 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER E 98 " --> pdb=" O SER E 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.123A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR E 173 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.123A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR E 173 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.657A pdb=" N SER E 193 " --> pdb=" O LYS E 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'F' and resid 59 through 61 Processing sheet with id=AB6, first strand: chain 'F' and resid 135 through 138 Processing sheet with id=AB7, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AB8, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.529A pdb=" N THR G 106 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'G' and resid 47 through 50 removed outlier: 6.739A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 47 through 50 removed outlier: 6.739A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER G 92 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.866A pdb=" N PHE G 119 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR G 173 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.866A pdb=" N PHE G 119 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR G 173 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 154 through 156 removed outlier: 4.736A pdb=" N TRP G 149 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER G 193 " --> pdb=" O LYS G 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AC7, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.556A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.896A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 53 through 55 removed outlier: 4.155A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AD2, first strand: chain 'A' and resid 205 through 206 Processing sheet with id=AD3, first strand: chain 'A' and resid 205 through 206 Processing sheet with id=AD4, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.344A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AD6, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AD7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.642A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.458A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.617A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AE4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE6, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AE7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.626A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.654A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 225 through 230 removed outlier: 6.698A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 310 through 319 removed outlier: 7.034A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 323 through 326 removed outlier: 4.146A pdb=" N ASN B 540 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 325 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASN B 542 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AF4, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.778A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AF6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.491A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.958A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AG1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.916A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.707A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.849A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AG6, first strand: chain 'C' and resid 313 through 317 removed outlier: 5.257A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AG8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AG9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AH1, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.186A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AH3, first strand: chain 'C' and resid 717 through 728 removed outlier: 7.075A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AH5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AH6, first strand: chain 'C' and resid 1094 through 1097 1097 hydrogen bonds defined for protein. 2868 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: 7.33 Time building geometry restraints manager: 3.48 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: 9482 1.34 - 1.46: 7412 1.46 - 1.59: 13474 1.59 - 1.71: 0 1.71 - 1.83: 155 Bond restraints: 30523 Sorted by residual: bond pdb=" N ASP C 111 " pdb=" CA ASP C 111 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.24e+01 bond pdb=" N VAL A1094 " pdb=" CA VAL A1094 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.18e+01 bond pdb=" N ILE A 712 " pdb=" CA ILE A 712 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N ILE C 598 " pdb=" CA ILE C 598 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.12e-02 7.97e+03 9.50e+00 bond pdb=" N VAL A 656 " pdb=" CA VAL A 656 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.37e+00 ... (remaining 30518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 40824 2.37 - 4.74: 656 4.74 - 7.11: 33 7.11 - 9.47: 10 9.47 - 11.84: 2 Bond angle restraints: 41525 Sorted by residual: angle pdb=" CB MET F 123 " pdb=" CG MET F 123 " pdb=" SD MET F 123 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N ASN A 657 " pdb=" CA ASN A 657 " pdb=" C ASN A 657 " ideal model delta sigma weight residual 113.02 108.38 4.64 1.20e+00 6.94e-01 1.49e+01 angle pdb=" N ASN A1098 " pdb=" CA ASN A1098 " pdb=" C ASN A1098 " ideal model delta sigma weight residual 113.02 108.54 4.48 1.20e+00 6.94e-01 1.40e+01 angle pdb=" N TYR D 55 " pdb=" CA TYR D 55 " pdb=" C TYR D 55 " ideal model delta sigma weight residual 107.44 114.59 -7.15 1.93e+00 2.68e-01 1.37e+01 angle pdb=" N LYS C 113 " pdb=" CA LYS C 113 " pdb=" C LYS C 113 " ideal model delta sigma weight residual 111.82 107.54 4.28 1.16e+00 7.43e-01 1.36e+01 ... (remaining 41520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 16263 17.75 - 35.50: 1707 35.50 - 53.26: 397 53.26 - 71.01: 107 71.01 - 88.76: 39 Dihedral angle restraints: 18513 sinusoidal: 7476 harmonic: 11037 Sorted by residual: dihedral pdb=" CB CYS G 135 " pdb=" SG CYS G 135 " pdb=" SG CYS G 194 " pdb=" CB CYS G 194 " ideal model delta sinusoidal sigma weight residual -86.00 -174.71 88.71 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 5.70 87.30 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -5.28 -80.72 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 18510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4155 0.073 - 0.146: 593 0.146 - 0.219: 40 0.219 - 0.292: 3 0.292 - 0.365: 3 Chirality restraints: 4794 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4791 not shown) Planarity restraints: 5345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " -0.084 2.00e-02 2.50e+03 6.90e-02 5.95e+01 pdb=" C7 NAG B1310 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " -0.064 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " 0.109 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.036 2.00e-02 2.50e+03 2.93e-02 1.08e+01 pdb=" C7 NAG C1301 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.046 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 37 " 0.014 2.00e-02 2.50e+03 1.31e-02 4.32e+00 pdb=" CG TRP G 37 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP G 37 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 37 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP G 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 37 " 0.004 2.00e-02 2.50e+03 ... (remaining 5342 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 214 2.50 - 3.10: 22376 3.10 - 3.70: 46822 3.70 - 4.30: 66841 4.30 - 4.90: 110048 Nonbonded interactions: 246301 Sorted by model distance: nonbonded pdb=" OH TYR C 365 " pdb=" CZ PHE C 515 " model vdw 1.901 3.340 nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 2.058 3.040 nonbonded pdb=" O ASN C 540 " pdb=" OD1 ASN C 540 " model vdw 2.099 3.040 nonbonded pdb=" OE1 GLN D 6 " pdb=" OG1 THR D 122 " model vdw 2.125 3.040 nonbonded pdb=" O VAL B 130 " pdb=" OG1 THR B 167 " model vdw 2.133 3.040 ... (remaining 246296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 66 or resid 81 through 94 or resid 103 through \ 143 or resid 159 through 173 or resid 190 through 212 or resid 217 through 241 o \ r resid 264 through 327 or resid 329 through 342 or resid 347 through 379 or res \ id 381 through 413 or resid 415 through 441 or resid 447 through 568 or resid 57 \ 2 through 616 or resid 641 through 827 or resid 855 through 946 or resid 948 thr \ ough 1306)) selection = (chain 'B' and (resid 26 through 94 or resid 103 through 241 or resid 264 throug \ h 379 or resid 381 through 465 or resid 471 through 483 or resid 485 through 568 \ or resid 572 through 827 or resid 855 through 1045 or resid 1047 through 1306)) \ selection = (chain 'C' and (resid 26 through 66 or resid 81 through 143 or resid 159 through \ 173 or resid 190 through 212 or resid 217 through 327 or resid 329 through 342 \ or resid 347 through 413 or resid 415 through 441 or resid 447 through 465 or re \ sid 471 through 483 or resid 485 through 568 or resid 572 through 616 or resid 6 \ 41 through 946 or resid 948 through 1045 or resid 1047 through 1306)) } ncs_group { reference = (chain 'D' and (resid 3 through 145 or resid 154 through 167 or resid 178 throug \ h 196 or resid 211 through 223 or resid 228 through 229)) selection = (chain 'F' and (resid 3 through 56 or resid 61 through 229)) } ncs_group { reference = (chain 'E' and (resid 2 through 87 or resid 90 through 213)) selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.790 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.004 0.041 30594 Z= 0.258 Angle : 0.699 11.842 41692 Z= 0.399 Chirality : 0.049 0.365 4794 Planarity : 0.004 0.075 5320 Dihedral : 15.530 88.758 11265 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 0.94 % Allowed : 22.10 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3694 helix: 1.41 (0.20), residues: 687 sheet: -0.81 (0.17), residues: 902 loop : -1.64 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.026 0.001 TYR A 904 PHE 0.023 0.001 PHE B 133 TRP 0.034 0.002 TRP G 37 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00424 (30523) covalent geometry : angle 0.68955 (41525) SS BOND : bond 0.00414 ( 46) SS BOND : angle 1.22086 ( 92) hydrogen bonds : bond 0.14798 ( 1059) hydrogen bonds : angle 7.05338 ( 2868) link_NAG-ASN : bond 0.00478 ( 25) link_NAG-ASN : angle 2.54037 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 102 GLU cc_start: 0.4799 (tt0) cc_final: 0.4324 (tm-30) REVERT: A 301 CYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7301 (m) REVERT: A 869 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8809 (mtt) REVERT: A 1031 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: B 87 ASN cc_start: 0.8920 (t0) cc_final: 0.8408 (t0) REVERT: B 117 LEU cc_start: 0.9229 (tp) cc_final: 0.8844 (mm) REVERT: B 223 LEU cc_start: 0.8726 (mm) cc_final: 0.8418 (mm) REVERT: B 342 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: B 473 TYR cc_start: 0.8462 (t80) cc_final: 0.8039 (t80) REVERT: B 558 LYS cc_start: 0.9371 (mmtt) cc_final: 0.9144 (mtpt) REVERT: B 779 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8715 (tm-30) REVERT: B 780 GLU cc_start: 0.9035 (tp30) cc_final: 0.8655 (tp30) REVERT: B 786 LYS cc_start: 0.8897 (mttt) cc_final: 0.8657 (mmmm) REVERT: C 756 TYR cc_start: 0.8505 (m-80) cc_final: 0.8169 (m-80) REVERT: C 1002 GLN cc_start: 0.8993 (tt0) cc_final: 0.8770 (tt0) outliers start: 31 outliers final: 18 residues processed: 294 average time/residue: 0.1883 time to fit residues: 88.9027 Evaluate side-chains 228 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.0040 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN F 41 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 762 GLN A1048 HIS B 196 ASN B 207 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C1083 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.127916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.082770 restraints weight = 94072.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085590 restraints weight = 40174.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085702 restraints weight = 19678.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.085753 restraints weight = 20747.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.085932 restraints weight = 18420.710| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30594 Z= 0.204 Angle : 0.625 9.218 41692 Z= 0.320 Chirality : 0.045 0.323 4794 Planarity : 0.004 0.047 5320 Dihedral : 5.521 54.212 4605 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.53 % Rotamer: Outliers : 3.93 % Allowed : 19.81 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3694 helix: 1.64 (0.20), residues: 699 sheet: -0.79 (0.17), residues: 903 loop : -1.52 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 328 TYR 0.036 0.002 TYR G 192 PHE 0.017 0.002 PHE C 429 TRP 0.015 0.002 TRP F 36 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00466 (30523) covalent geometry : angle 0.61719 (41525) SS BOND : bond 0.00358 ( 46) SS BOND : angle 1.11430 ( 92) hydrogen bonds : bond 0.04559 ( 1059) hydrogen bonds : angle 5.87039 ( 2868) link_NAG-ASN : bond 0.00329 ( 25) link_NAG-ASN : angle 2.22340 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 218 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.6812 (m-40) REVERT: E 184 GLU cc_start: 0.5483 (OUTLIER) cc_final: 0.5246 (mp0) REVERT: F 68 LYS cc_start: 0.6648 (mmmt) cc_final: 0.6381 (mmmt) REVERT: F 102 GLU cc_start: 0.4671 (tt0) cc_final: 0.4253 (tm-30) REVERT: G 33 ASN cc_start: 0.8345 (t0) cc_final: 0.8031 (p0) REVERT: A 135 PHE cc_start: 0.9187 (m-80) cc_final: 0.8710 (m-10) REVERT: A 224 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: A 773 GLU cc_start: 0.8645 (tp30) cc_final: 0.8279 (tp30) REVERT: A 869 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8687 (mtm) REVERT: A 1031 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: B 87 ASN cc_start: 0.8913 (t0) cc_final: 0.8382 (t0) REVERT: B 111 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7242 (p0) REVERT: B 117 LEU cc_start: 0.9251 (tp) cc_final: 0.8687 (mp) REVERT: B 223 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8733 (mm) REVERT: B 473 TYR cc_start: 0.8325 (t80) cc_final: 0.7855 (t80) REVERT: B 779 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8157 (tm-30) REVERT: B 931 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9143 (tt) REVERT: C 194 PHE cc_start: 0.8977 (m-80) cc_final: 0.8727 (m-10) REVERT: C 756 TYR cc_start: 0.8288 (m-80) cc_final: 0.7971 (m-80) REVERT: C 1002 GLN cc_start: 0.8275 (tt0) cc_final: 0.8022 (tt0) outliers start: 130 outliers final: 67 residues processed: 326 average time/residue: 0.1656 time to fit residues: 90.3733 Evaluate side-chains 273 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 198 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 18 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 305 optimal weight: 0.0980 chunk 40 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 804 GLN C1071 GLN C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.127867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.082947 restraints weight = 94310.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.084782 restraints weight = 40145.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.085567 restraints weight = 21877.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.085892 restraints weight = 14691.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.086036 restraints weight = 14807.223| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30594 Z= 0.157 Angle : 0.578 9.656 41692 Z= 0.295 Chirality : 0.044 0.298 4794 Planarity : 0.004 0.047 5320 Dihedral : 5.135 54.688 4588 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 3.68 % Allowed : 20.50 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3694 helix: 1.73 (0.20), residues: 710 sheet: -0.76 (0.17), residues: 885 loop : -1.49 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B 238 TRP 0.017 0.001 TRP G 37 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00358 (30523) covalent geometry : angle 0.57003 (41525) SS BOND : bond 0.00257 ( 46) SS BOND : angle 0.96983 ( 92) hydrogen bonds : bond 0.04199 ( 1059) hydrogen bonds : angle 5.55086 ( 2868) link_NAG-ASN : bond 0.00177 ( 25) link_NAG-ASN : angle 2.08395 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 214 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 ASN cc_start: 0.7380 (OUTLIER) cc_final: 0.6848 (m-40) REVERT: E 134 VAL cc_start: 0.5075 (OUTLIER) cc_final: 0.4628 (p) REVERT: F 102 GLU cc_start: 0.4731 (tt0) cc_final: 0.4464 (tm-30) REVERT: G 33 ASN cc_start: 0.8361 (t0) cc_final: 0.8102 (p0) REVERT: A 135 PHE cc_start: 0.9064 (m-80) cc_final: 0.8604 (m-10) REVERT: A 733 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8701 (ptmt) REVERT: A 773 GLU cc_start: 0.8617 (tp30) cc_final: 0.8384 (tp30) REVERT: A 934 ILE cc_start: 0.9637 (tt) cc_final: 0.9422 (tt) REVERT: A 1031 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: B 87 ASN cc_start: 0.8903 (t0) cc_final: 0.8382 (t0) REVERT: B 111 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7215 (p0) REVERT: B 117 LEU cc_start: 0.9203 (tp) cc_final: 0.8763 (mp) REVERT: B 223 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8661 (mm) REVERT: B 319 ARG cc_start: 0.7170 (tpt170) cc_final: 0.6954 (tpt170) REVERT: B 473 TYR cc_start: 0.8278 (t80) cc_final: 0.7795 (t80) REVERT: B 779 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8314 (tm-30) REVERT: C 194 PHE cc_start: 0.8945 (m-80) cc_final: 0.8605 (m-10) REVERT: C 427 ASP cc_start: 0.8802 (p0) cc_final: 0.8528 (p0) REVERT: C 756 TYR cc_start: 0.8260 (m-80) cc_final: 0.7916 (m-80) REVERT: C 955 ASN cc_start: 0.8419 (m110) cc_final: 0.7805 (t0) REVERT: C 1002 GLN cc_start: 0.8255 (tt0) cc_final: 0.8000 (tt0) outliers start: 122 outliers final: 74 residues processed: 322 average time/residue: 0.1712 time to fit residues: 92.0352 Evaluate side-chains 277 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 197 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 60 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 232 optimal weight: 0.3980 chunk 251 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.127019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.080861 restraints weight = 94000.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.083890 restraints weight = 41202.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.084013 restraints weight = 18718.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.084198 restraints weight = 19036.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.084278 restraints weight = 17651.894| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30594 Z= 0.228 Angle : 0.612 9.621 41692 Z= 0.312 Chirality : 0.045 0.325 4794 Planarity : 0.004 0.049 5320 Dihedral : 5.199 55.309 4585 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.66 % Favored : 93.31 % Rotamer: Outliers : 4.32 % Allowed : 20.38 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3694 helix: 1.58 (0.20), residues: 710 sheet: -0.74 (0.17), residues: 870 loop : -1.54 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.024 0.001 TYR B 365 PHE 0.018 0.001 PHE G 64 TRP 0.023 0.001 TRP G 37 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00523 (30523) covalent geometry : angle 0.60442 (41525) SS BOND : bond 0.00538 ( 46) SS BOND : angle 0.97796 ( 92) hydrogen bonds : bond 0.04372 ( 1059) hydrogen bonds : angle 5.56144 ( 2868) link_NAG-ASN : bond 0.00312 ( 25) link_NAG-ASN : angle 2.20188 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 210 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.6795 (m-40) REVERT: E 184 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5407 (mp0) REVERT: F 68 LYS cc_start: 0.6571 (mmmt) cc_final: 0.6273 (mmmt) REVERT: F 106 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.6020 (tt) REVERT: G 33 ASN cc_start: 0.8419 (t0) cc_final: 0.8095 (p0) REVERT: G 50 ILE cc_start: 0.5651 (OUTLIER) cc_final: 0.1016 (mm) REVERT: G 64 PHE cc_start: 0.6273 (m-80) cc_final: 0.6029 (m-10) REVERT: A 81 ASN cc_start: 0.8761 (m-40) cc_final: 0.8406 (m-40) REVERT: A 135 PHE cc_start: 0.9144 (m-80) cc_final: 0.8708 (m-10) REVERT: A 224 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: A 269 TYR cc_start: 0.7165 (m-10) cc_final: 0.6959 (m-10) REVERT: A 773 GLU cc_start: 0.8583 (tp30) cc_final: 0.8219 (tp30) REVERT: A 869 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8716 (mtm) REVERT: A 1019 ARG cc_start: 0.8313 (tpt170) cc_final: 0.8058 (tpp-160) REVERT: A 1031 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: B 87 ASN cc_start: 0.8926 (t0) cc_final: 0.8460 (t0) REVERT: B 111 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7152 (p0) REVERT: B 117 LEU cc_start: 0.9241 (tp) cc_final: 0.8866 (mp) REVERT: B 135 PHE cc_start: 0.7728 (t80) cc_final: 0.7325 (t80) REVERT: B 223 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8714 (mm) REVERT: B 319 ARG cc_start: 0.7177 (tpt170) cc_final: 0.6925 (tpt170) REVERT: B 473 TYR cc_start: 0.8200 (t80) cc_final: 0.7730 (t80) REVERT: B 693 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8928 (pp) REVERT: B 779 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 784 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: C 207 HIS cc_start: 0.6403 (OUTLIER) cc_final: 0.6038 (t70) REVERT: C 427 ASP cc_start: 0.8816 (p0) cc_final: 0.8561 (p0) REVERT: C 756 TYR cc_start: 0.8284 (m-80) cc_final: 0.7988 (m-80) REVERT: C 955 ASN cc_start: 0.8441 (m110) cc_final: 0.8044 (t0) REVERT: C 1002 GLN cc_start: 0.8249 (tt0) cc_final: 0.8043 (tt0) outliers start: 143 outliers final: 90 residues processed: 331 average time/residue: 0.1689 time to fit residues: 94.1257 Evaluate side-chains 299 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 197 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 308 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 354 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 342 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 186 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN F 5 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 440 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.127527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.079754 restraints weight = 94225.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.082181 restraints weight = 37088.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.083590 restraints weight = 20341.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.084458 restraints weight = 13890.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.084914 restraints weight = 11088.659| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30594 Z= 0.142 Angle : 0.575 11.741 41692 Z= 0.291 Chirality : 0.044 0.290 4794 Planarity : 0.004 0.134 5320 Dihedral : 5.011 54.751 4582 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 3.68 % Allowed : 21.23 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3694 helix: 1.75 (0.20), residues: 708 sheet: -0.71 (0.17), residues: 873 loop : -1.48 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG G 56 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE G 64 TRP 0.019 0.001 TRP G 37 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00326 (30523) covalent geometry : angle 0.56800 (41525) SS BOND : bond 0.00349 ( 46) SS BOND : angle 0.88540 ( 92) hydrogen bonds : bond 0.04003 ( 1059) hydrogen bonds : angle 5.34637 ( 2868) link_NAG-ASN : bond 0.00200 ( 25) link_NAG-ASN : angle 2.01992 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 216 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 186 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: E 55 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7098 (m-40) REVERT: F 68 LYS cc_start: 0.6887 (mmmt) cc_final: 0.6610 (mmtt) REVERT: F 106 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6582 (tt) REVERT: G 33 ASN cc_start: 0.8455 (t0) cc_final: 0.8207 (p0) REVERT: G 35 ILE cc_start: 0.7359 (pt) cc_final: 0.6852 (tp) REVERT: A 81 ASN cc_start: 0.8483 (m-40) cc_final: 0.8243 (m-40) REVERT: A 135 PHE cc_start: 0.8299 (m-80) cc_final: 0.7988 (m-10) REVERT: A 224 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: A 229 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8956 (mt) REVERT: A 733 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8793 (ptmt) REVERT: A 869 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8681 (mtm) REVERT: A 1031 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: B 111 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7098 (p0) REVERT: B 117 LEU cc_start: 0.9301 (tp) cc_final: 0.8800 (mp) REVERT: B 135 PHE cc_start: 0.6924 (t80) cc_final: 0.6535 (t80) REVERT: B 473 TYR cc_start: 0.8232 (t80) cc_final: 0.7712 (t80) REVERT: B 693 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8881 (pp) REVERT: B 779 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 817 PHE cc_start: 0.6054 (t80) cc_final: 0.5730 (t80) REVERT: C 207 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6069 (t70) REVERT: C 235 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8418 (tp) REVERT: C 427 ASP cc_start: 0.8647 (p0) cc_final: 0.8375 (p0) REVERT: C 756 TYR cc_start: 0.8170 (m-80) cc_final: 0.7829 (m-80) REVERT: C 955 ASN cc_start: 0.8393 (m110) cc_final: 0.8009 (t0) REVERT: C 1002 GLN cc_start: 0.8247 (tt0) cc_final: 0.8016 (tt0) outliers start: 122 outliers final: 75 residues processed: 321 average time/residue: 0.1727 time to fit residues: 93.5161 Evaluate side-chains 287 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 200 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 937 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 378 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 356 optimal weight: 0.9980 chunk 311 optimal weight: 7.9990 chunk 358 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** E 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.127222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080951 restraints weight = 93835.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.083804 restraints weight = 40327.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.084180 restraints weight = 19200.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.084272 restraints weight = 14080.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084458 restraints weight = 15782.694| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30594 Z= 0.188 Angle : 0.591 11.343 41692 Z= 0.299 Chirality : 0.044 0.369 4794 Planarity : 0.004 0.094 5320 Dihedral : 4.992 54.404 4580 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.31 % Favored : 93.64 % Rotamer: Outliers : 3.86 % Allowed : 21.23 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3694 helix: 1.74 (0.20), residues: 705 sheet: -0.71 (0.17), residues: 875 loop : -1.47 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 56 TYR 0.023 0.001 TYR A 265 PHE 0.027 0.001 PHE C 823 TRP 0.022 0.001 TRP G 37 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00433 (30523) covalent geometry : angle 0.58310 (41525) SS BOND : bond 0.00358 ( 46) SS BOND : angle 0.94624 ( 92) hydrogen bonds : bond 0.04098 ( 1059) hydrogen bonds : angle 5.33753 ( 2868) link_NAG-ASN : bond 0.00214 ( 25) link_NAG-ASN : angle 2.17732 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 214 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.6926 (m-40) REVERT: E 87 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6835 (t0) REVERT: F 68 LYS cc_start: 0.6754 (mmmt) cc_final: 0.6439 (mmtt) REVERT: G 33 ASN cc_start: 0.8462 (t0) cc_final: 0.8023 (p0) REVERT: G 35 ILE cc_start: 0.7340 (pt) cc_final: 0.7000 (tp) REVERT: A 81 ASN cc_start: 0.8735 (m-40) cc_final: 0.8416 (m-40) REVERT: A 131 CYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6311 (m) REVERT: A 135 PHE cc_start: 0.9104 (m-80) cc_final: 0.8689 (m-10) REVERT: A 224 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: A 869 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8727 (mtm) REVERT: A 1031 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: B 87 ASN cc_start: 0.8294 (m110) cc_final: 0.8073 (p0) REVERT: B 111 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7135 (p0) REVERT: B 135 PHE cc_start: 0.7645 (t80) cc_final: 0.7269 (t80) REVERT: B 223 LEU cc_start: 0.8883 (mm) cc_final: 0.8648 (mm) REVERT: B 392 PHE cc_start: 0.8249 (m-80) cc_final: 0.7971 (t80) REVERT: B 473 TYR cc_start: 0.8214 (t80) cc_final: 0.7711 (t80) REVERT: B 693 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8889 (pp) REVERT: B 779 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8275 (tm-30) REVERT: B 784 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: B 1043 CYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8260 (m) REVERT: C 104 TRP cc_start: 0.8267 (m-90) cc_final: 0.7970 (m-90) REVERT: C 207 HIS cc_start: 0.6362 (OUTLIER) cc_final: 0.5976 (t70) REVERT: C 235 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8429 (tp) REVERT: C 427 ASP cc_start: 0.8851 (p0) cc_final: 0.8576 (p0) REVERT: C 756 TYR cc_start: 0.8322 (m-80) cc_final: 0.7997 (m-80) REVERT: C 955 ASN cc_start: 0.8470 (m110) cc_final: 0.7872 (t0) REVERT: C 1002 GLN cc_start: 0.8301 (tt0) cc_final: 0.8033 (tt0) outliers start: 128 outliers final: 92 residues processed: 323 average time/residue: 0.1650 time to fit residues: 89.6690 Evaluate side-chains 306 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 202 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 280 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 224 optimal weight: 10.0000 chunk 256 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 342 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 221 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 751 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.126903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.079205 restraints weight = 93479.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.081582 restraints weight = 36657.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.082990 restraints weight = 20196.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.083798 restraints weight = 13902.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.084268 restraints weight = 11128.716| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30594 Z= 0.128 Angle : 0.574 13.006 41692 Z= 0.290 Chirality : 0.044 0.323 4794 Planarity : 0.004 0.079 5320 Dihedral : 4.850 54.939 4580 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.55 % Favored : 94.40 % Rotamer: Outliers : 3.29 % Allowed : 21.98 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3694 helix: 1.92 (0.20), residues: 703 sheet: -0.63 (0.17), residues: 863 loop : -1.39 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 56 TYR 0.023 0.001 TYR A 265 PHE 0.029 0.001 PHE G 64 TRP 0.036 0.001 TRP D 49 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00291 (30523) covalent geometry : angle 0.56744 (41525) SS BOND : bond 0.00240 ( 46) SS BOND : angle 0.82606 ( 92) hydrogen bonds : bond 0.03819 ( 1059) hydrogen bonds : angle 5.17019 ( 2868) link_NAG-ASN : bond 0.00175 ( 25) link_NAG-ASN : angle 2.06756 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 218 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7169 (m-40) REVERT: E 87 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.6934 (t0) REVERT: F 68 LYS cc_start: 0.7074 (mmmt) cc_final: 0.6738 (mmtt) REVERT: G 33 ASN cc_start: 0.8515 (t0) cc_final: 0.8227 (p0) REVERT: G 35 ILE cc_start: 0.7412 (pt) cc_final: 0.7004 (tp) REVERT: A 81 ASN cc_start: 0.8514 (m-40) cc_final: 0.8278 (m-40) REVERT: A 131 CYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5973 (m) REVERT: A 135 PHE cc_start: 0.8361 (m-80) cc_final: 0.8116 (m-10) REVERT: A 224 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: A 733 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8705 (ptmt) REVERT: A 869 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8686 (mtm) REVERT: A 990 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 1031 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: B 111 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7057 (p0) REVERT: B 135 PHE cc_start: 0.6911 (t80) cc_final: 0.6524 (t80) REVERT: B 473 TYR cc_start: 0.8262 (t80) cc_final: 0.7724 (t80) REVERT: B 693 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8847 (pp) REVERT: B 779 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 1043 CYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8183 (m) REVERT: C 104 TRP cc_start: 0.8136 (m-90) cc_final: 0.7890 (m-90) REVERT: C 207 HIS cc_start: 0.6378 (OUTLIER) cc_final: 0.6036 (t70) REVERT: C 235 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8431 (tp) REVERT: C 427 ASP cc_start: 0.8674 (p0) cc_final: 0.8383 (p0) REVERT: C 756 TYR cc_start: 0.8201 (m-80) cc_final: 0.7882 (m-80) REVERT: C 955 ASN cc_start: 0.8411 (m110) cc_final: 0.8066 (t0) REVERT: C 1002 GLN cc_start: 0.8246 (tt0) cc_final: 0.8001 (tt0) outliers start: 109 outliers final: 71 residues processed: 310 average time/residue: 0.1649 time to fit residues: 86.3859 Evaluate side-chains 286 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 203 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 22 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 203 optimal weight: 0.2980 chunk 266 optimal weight: 1.9990 chunk 291 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.121512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.077425 restraints weight = 90364.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.080013 restraints weight = 37083.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.080310 restraints weight = 23428.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081307 restraints weight = 15029.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.081548 restraints weight = 12278.633| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30594 Z= 0.163 Angle : 0.590 12.201 41692 Z= 0.298 Chirality : 0.044 0.403 4794 Planarity : 0.004 0.069 5320 Dihedral : 4.812 54.548 4578 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 3.17 % Allowed : 22.22 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3694 helix: 1.87 (0.20), residues: 703 sheet: -0.70 (0.17), residues: 879 loop : -1.38 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 56 TYR 0.030 0.001 TYR C 423 PHE 0.029 0.001 PHE G 64 TRP 0.036 0.002 TRP G 37 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00377 (30523) covalent geometry : angle 0.58331 (41525) SS BOND : bond 0.00268 ( 46) SS BOND : angle 0.84822 ( 92) hydrogen bonds : bond 0.03917 ( 1059) hydrogen bonds : angle 5.16901 ( 2868) link_NAG-ASN : bond 0.00197 ( 25) link_NAG-ASN : angle 2.06163 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 219 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.6809 (m-40) REVERT: E 87 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6829 (t0) REVERT: F 68 LYS cc_start: 0.6809 (mmmt) cc_final: 0.6471 (mmtt) REVERT: F 101 ARG cc_start: 0.6675 (ttp-110) cc_final: 0.6195 (ttp-110) REVERT: F 102 GLU cc_start: 0.5057 (tt0) cc_final: 0.4461 (tm-30) REVERT: G 33 ASN cc_start: 0.8515 (t0) cc_final: 0.8022 (p0) REVERT: G 35 ILE cc_start: 0.7364 (pt) cc_final: 0.7070 (tp) REVERT: A 81 ASN cc_start: 0.8668 (m-40) cc_final: 0.8409 (m-40) REVERT: A 131 CYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6224 (m) REVERT: A 135 PHE cc_start: 0.8957 (m-80) cc_final: 0.8703 (m-10) REVERT: A 200 TYR cc_start: 0.8536 (m-80) cc_final: 0.8335 (m-80) REVERT: A 224 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: A 869 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8724 (mtm) REVERT: A 990 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 1031 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: B 111 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7098 (p0) REVERT: B 133 PHE cc_start: 0.8252 (m-10) cc_final: 0.7949 (m-10) REVERT: B 135 PHE cc_start: 0.7546 (t80) cc_final: 0.7160 (t80) REVERT: B 693 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8851 (pp) REVERT: B 779 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 784 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: B 817 PHE cc_start: 0.6035 (t80) cc_final: 0.5723 (t80) REVERT: B 1043 CYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8162 (m) REVERT: C 104 TRP cc_start: 0.8268 (m-90) cc_final: 0.8003 (m-90) REVERT: C 207 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.6031 (t70) REVERT: C 235 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8439 (tp) REVERT: C 427 ASP cc_start: 0.8797 (p0) cc_final: 0.8554 (p0) REVERT: C 607 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: C 756 TYR cc_start: 0.8286 (m-80) cc_final: 0.7983 (m-80) REVERT: C 955 ASN cc_start: 0.8442 (m110) cc_final: 0.8114 (t0) REVERT: C 1002 GLN cc_start: 0.8243 (tt0) cc_final: 0.8012 (tt0) outliers start: 105 outliers final: 82 residues processed: 306 average time/residue: 0.1655 time to fit residues: 85.6830 Evaluate side-chains 302 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 207 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 247 optimal weight: 0.0030 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 336 optimal weight: 4.9990 chunk 297 optimal weight: 8.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.121666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.077569 restraints weight = 90047.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.080457 restraints weight = 36972.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.080790 restraints weight = 19925.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.081481 restraints weight = 13519.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.081768 restraints weight = 11814.245| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30594 Z= 0.156 Angle : 0.594 13.796 41692 Z= 0.300 Chirality : 0.044 0.354 4794 Planarity : 0.004 0.075 5320 Dihedral : 4.799 54.659 4578 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 3.32 % Allowed : 22.34 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3694 helix: 1.89 (0.20), residues: 703 sheet: -0.63 (0.17), residues: 881 loop : -1.38 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 56 TYR 0.032 0.001 TYR C 423 PHE 0.034 0.001 PHE G 64 TRP 0.039 0.001 TRP G 37 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00361 (30523) covalent geometry : angle 0.58670 (41525) SS BOND : bond 0.00245 ( 46) SS BOND : angle 1.02841 ( 92) hydrogen bonds : bond 0.03865 ( 1059) hydrogen bonds : angle 5.12207 ( 2868) link_NAG-ASN : bond 0.00202 ( 25) link_NAG-ASN : angle 2.00262 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 213 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.6989 (m-40) REVERT: E 87 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6832 (t0) REVERT: F 68 LYS cc_start: 0.6941 (mmmt) cc_final: 0.6595 (mmtt) REVERT: F 101 ARG cc_start: 0.6816 (ttp-110) cc_final: 0.6286 (ttp-110) REVERT: F 102 GLU cc_start: 0.5210 (tt0) cc_final: 0.4538 (tm-30) REVERT: G 33 ASN cc_start: 0.8555 (t0) cc_final: 0.8160 (p0) REVERT: G 35 ILE cc_start: 0.7449 (pt) cc_final: 0.7141 (tp) REVERT: G 99 PHE cc_start: 0.5730 (OUTLIER) cc_final: 0.5273 (t80) REVERT: A 81 ASN cc_start: 0.8654 (m-40) cc_final: 0.8394 (m-40) REVERT: A 131 CYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6245 (m) REVERT: A 135 PHE cc_start: 0.8971 (m-80) cc_final: 0.8750 (m-10) REVERT: A 200 TYR cc_start: 0.8477 (m-80) cc_final: 0.8254 (m-80) REVERT: A 224 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: A 869 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8718 (mtm) REVERT: A 990 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 1031 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: B 111 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7056 (p0) REVERT: B 133 PHE cc_start: 0.8270 (m-10) cc_final: 0.7973 (m-10) REVERT: B 135 PHE cc_start: 0.7590 (t80) cc_final: 0.7195 (t80) REVERT: B 392 PHE cc_start: 0.8244 (m-80) cc_final: 0.7982 (t80) REVERT: B 693 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8853 (pp) REVERT: B 784 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8347 (mt0) REVERT: B 931 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9331 (tt) REVERT: B 1043 CYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8196 (m) REVERT: C 104 TRP cc_start: 0.8277 (m-90) cc_final: 0.8019 (m-90) REVERT: C 207 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.5998 (t70) REVERT: C 235 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8437 (tp) REVERT: C 427 ASP cc_start: 0.8793 (p0) cc_final: 0.8543 (p0) REVERT: C 756 TYR cc_start: 0.8277 (m-80) cc_final: 0.7971 (m-80) REVERT: C 955 ASN cc_start: 0.8416 (m110) cc_final: 0.8084 (t0) REVERT: C 1002 GLN cc_start: 0.8212 (tt0) cc_final: 0.7994 (tt0) outliers start: 110 outliers final: 83 residues processed: 303 average time/residue: 0.1680 time to fit residues: 85.4676 Evaluate side-chains 301 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 204 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 93 optimal weight: 0.8980 chunk 370 optimal weight: 1.9990 chunk 296 optimal weight: 0.0970 chunk 216 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 319 optimal weight: 0.0980 chunk 236 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.122142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.079606 restraints weight = 90412.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.082259 restraints weight = 39846.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.081691 restraints weight = 21307.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.082071 restraints weight = 23940.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.082219 restraints weight = 19124.949| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30594 Z= 0.139 Angle : 0.592 13.647 41692 Z= 0.298 Chirality : 0.044 0.306 4794 Planarity : 0.004 0.077 5320 Dihedral : 4.752 55.092 4578 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 3.11 % Allowed : 22.46 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3694 helix: 1.92 (0.20), residues: 703 sheet: -0.59 (0.17), residues: 878 loop : -1.36 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 56 TYR 0.025 0.001 TYR C 423 PHE 0.049 0.001 PHE B 817 TRP 0.040 0.002 TRP G 37 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00319 (30523) covalent geometry : angle 0.58397 (41525) SS BOND : bond 0.00233 ( 46) SS BOND : angle 1.33499 ( 92) hydrogen bonds : bond 0.03766 ( 1059) hydrogen bonds : angle 5.06426 ( 2868) link_NAG-ASN : bond 0.00175 ( 25) link_NAG-ASN : angle 1.94423 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7388 Ramachandran restraints generated. 3694 Oldfield, 0 Emsley, 3694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 206 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 161 PHE cc_start: 0.7994 (t80) cc_final: 0.7771 (m-80) REVERT: E 55 ASN cc_start: 0.7408 (OUTLIER) cc_final: 0.6803 (m-40) REVERT: E 87 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6853 (t0) REVERT: F 68 LYS cc_start: 0.6863 (mmmt) cc_final: 0.6525 (mmtt) REVERT: F 102 GLU cc_start: 0.5194 (tt0) cc_final: 0.4689 (tm-30) REVERT: G 33 ASN cc_start: 0.8617 (t0) cc_final: 0.8163 (p0) REVERT: G 35 ILE cc_start: 0.7386 (pt) cc_final: 0.7117 (tp) REVERT: G 99 PHE cc_start: 0.5846 (OUTLIER) cc_final: 0.5281 (t80) REVERT: A 81 ASN cc_start: 0.8787 (m-40) cc_final: 0.8453 (m-40) REVERT: A 131 CYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6354 (m) REVERT: A 224 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: A 869 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8734 (mtm) REVERT: A 950 ASP cc_start: 0.7924 (t0) cc_final: 0.7385 (t0) REVERT: A 990 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 1031 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: B 111 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7026 (p0) REVERT: B 133 PHE cc_start: 0.8315 (m-10) cc_final: 0.8021 (m-10) REVERT: B 135 PHE cc_start: 0.7859 (t80) cc_final: 0.7505 (t80) REVERT: B 265 TYR cc_start: 0.4015 (OUTLIER) cc_final: 0.3685 (m-80) REVERT: B 693 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8850 (pp) REVERT: B 784 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: B 931 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9322 (tt) REVERT: C 104 TRP cc_start: 0.8317 (m-90) cc_final: 0.8048 (m-90) REVERT: C 207 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5783 (t70) REVERT: C 235 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8360 (tp) REVERT: C 427 ASP cc_start: 0.8906 (p0) cc_final: 0.8650 (p0) REVERT: C 756 TYR cc_start: 0.8282 (m-80) cc_final: 0.7996 (m-80) REVERT: C 955 ASN cc_start: 0.8445 (m110) cc_final: 0.8049 (t0) REVERT: C 1002 GLN cc_start: 0.8297 (tt0) cc_final: 0.8041 (tt0) outliers start: 103 outliers final: 86 residues processed: 294 average time/residue: 0.1664 time to fit residues: 82.8927 Evaluate side-chains 300 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 200 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 247 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 202 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 245 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.119183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.077767 restraints weight = 91402.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.078310 restraints weight = 45327.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.077827 restraints weight = 27742.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.078227 restraints weight = 25342.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.078401 restraints weight = 21318.719| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30594 Z= 0.275 Angle : 0.672 12.839 41692 Z= 0.340 Chirality : 0.046 0.339 4794 Planarity : 0.004 0.075 5320 Dihedral : 5.152 57.431 4578 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.53 % Rotamer: Outliers : 3.44 % Allowed : 22.25 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3694 helix: 1.58 (0.19), residues: 701 sheet: -0.76 (0.17), residues: 876 loop : -1.47 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 408 TYR 0.028 0.002 TYR D 191 PHE 0.033 0.002 PHE B 817 TRP 0.041 0.002 TRP G 37 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00634 (30523) covalent geometry : angle 0.66235 (41525) SS BOND : bond 0.00338 ( 46) SS BOND : angle 1.52022 ( 92) hydrogen bonds : bond 0.04455 ( 1059) hydrogen bonds : angle 5.38400 ( 2868) link_NAG-ASN : bond 0.00392 ( 25) link_NAG-ASN : angle 2.27164 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5817.10 seconds wall clock time: 101 minutes 11.10 seconds (6071.10 seconds total)