Starting phenix.real_space_refine on Wed Feb 4 14:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lto_63374/02_2026/9lto_63374.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lto_63374/02_2026/9lto_63374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lto_63374/02_2026/9lto_63374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lto_63374/02_2026/9lto_63374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lto_63374/02_2026/9lto_63374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lto_63374/02_2026/9lto_63374.map" } resolution = 2.92 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= 0.033 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 51 5.16 5 C 6948 2.51 5 N 1897 2.21 5 O 1977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10873 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 773 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 131} Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 496 Unresolved non-hydrogen dihedrals: 322 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 5, 'TRP:plan': 3, 'PHE:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 210 Chain: "S" Number of atoms: 5714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 5714 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 745} Chain breaks: 4 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 280 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 28, 'ARG:plan': 3, 'ASP:plan': 12, 'ASN:plan1': 5, 'PHE:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 230 Chain: "B" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3985 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 505} Chain breaks: 2 Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 472 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 14, 'GLN:plan1': 5, 'HIS:plan': 6, 'GLU:plan': 17, 'ASP:plan': 10, 'ASN:plan1': 7, 'PHE:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 270 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 401 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 2.17, per 1000 atoms: 0.20 Number of scatterers: 10873 At special positions: 0 Unit cell: (124.95, 109.65, 114.75, 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 51 16.00 O 1977 8.00 N 1897 7.00 C 6948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 18 " - pdb=" SG CYS S 313 " 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 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 447.5 milliseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 26 sheets defined 18.1% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 152 through 166 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.104A pdb=" N HIS A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 385 removed outlier: 3.729A pdb=" N GLY S 385 " --> pdb=" O PHE S 382 " (cutoff:3.500A) Processing helix chain 'S' and resid 1044 through 1059 removed outlier: 3.581A pdb=" N LEU S1050 " --> pdb=" O SER S1046 " (cutoff:3.500A) Processing helix chain 'S' and resid 1069 through 1074 Processing helix chain 'S' and resid 1090 through 1097 removed outlier: 3.660A pdb=" N ILE S1094 " --> pdb=" O ASP S1090 " (cutoff:3.500A) Processing helix chain 'S' and resid 1098 through 1100 No H-bonds generated for 'chain 'S' and resid 1098 through 1100' Processing helix chain 'S' and resid 1101 through 1107 Processing helix chain 'S' and resid 1125 through 1132 removed outlier: 3.980A pdb=" N LYS S1131 " --> pdb=" O ASP S1127 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL S1132 " --> pdb=" O ASP S1128 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 26 Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 110 through 124 removed outlier: 5.173A pdb=" N PHE B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.624A pdb=" N THR B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.692A pdb=" N ARG B 288 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP B 289 " --> pdb=" O PRO B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 285 through 289' Processing helix chain 'B' and resid 293 through 311 removed outlier: 3.519A pdb=" N ASP B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.692A pdb=" N LYS B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 393 through 399 removed outlier: 3.825A pdb=" N PHE B 397 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'D' and resid 53 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA2, first strand: chain 'S' and resid 4 through 10 removed outlier: 6.480A pdb=" N ILE S1037 " --> pdb=" O ALA S 9 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY S1038 " --> pdb=" O LEU S1029 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU S1029 " --> pdb=" O GLY S1038 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL S1040 " --> pdb=" O SER S1027 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER S1027 " --> pdb=" O VAL S1040 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER S1027 " --> pdb=" O HIS S1009 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N HIS S1009 " --> pdb=" O SER S1027 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU S1029 " --> pdb=" O PHE S1007 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE S1007 " --> pdb=" O LEU S1029 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY S1031 " --> pdb=" O ASN S1005 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 17 through 21 removed outlier: 3.579A pdb=" N GLY S 17 " --> pdb=" O ALA S 34 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU S 39 " --> pdb=" O GLU S 54 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU S 54 " --> pdb=" O LEU S 39 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE S 41 " --> pdb=" O VAL S 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 61 through 67 removed outlier: 4.057A pdb=" N ASN S 85 " --> pdb=" O THR S 81 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA S 86 " --> pdb=" O HIS S 105 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N HIS S 105 " --> pdb=" O ALA S 86 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE S 88 " --> pdb=" O ARG S 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 121 through 124 removed outlier: 3.690A pdb=" N ILE S 121 " --> pdb=" O ARG S 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 164 through 169 removed outlier: 5.721A pdb=" N VAL S 164 " --> pdb=" O GLN S 183 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN S 183 " --> pdb=" O VAL S 164 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS S 189 " --> pdb=" O TYR S 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 164 through 169 removed outlier: 5.721A pdb=" N VAL S 164 " --> pdb=" O GLN S 183 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN S 183 " --> pdb=" O VAL S 164 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER S 196 " --> pdb=" O GLU S 201 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU S 201 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 218 through 221 removed outlier: 3.542A pdb=" N MET S 218 " --> pdb=" O ILE S 232 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE S 237 " --> pdb=" O ILE S 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 258 through 263 removed outlier: 6.697A pdb=" N GLY S 274 " --> pdb=" O VAL S 259 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS S 261 " --> pdb=" O LEU S 272 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU S 272 " --> pdb=" O HIS S 261 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG S 263 " --> pdb=" O ARG S 270 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG S 270 " --> pdb=" O ARG S 263 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU S 273 " --> pdb=" O PHE S 281 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG S 279 " --> pdb=" O ASP S 275 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP S 299 " --> pdb=" O GLU S 286 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU S 288 " --> pdb=" O LEU S 297 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU S 297 " --> pdb=" O GLU S 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 258 through 263 removed outlier: 6.697A pdb=" N GLY S 274 " --> pdb=" O VAL S 259 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS S 261 " --> pdb=" O LEU S 272 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU S 272 " --> pdb=" O HIS S 261 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG S 263 " --> pdb=" O ARG S 270 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG S 270 " --> pdb=" O ARG S 263 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU S 273 " --> pdb=" O PHE S 281 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG S 279 " --> pdb=" O ASP S 275 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY S 306 " --> pdb=" O LEU S 280 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 315 through 316 removed outlier: 3.740A pdb=" N GLU S 351 " --> pdb=" O LEU S 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 720 through 727 removed outlier: 6.524A pdb=" N LEU S 736 " --> pdb=" O ARG S 722 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE S 724 " --> pdb=" O GLY S 734 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY S 734 " --> pdb=" O ILE S 724 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TYR S 726 " --> pdb=" O CYS S 732 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N CYS S 732 " --> pdb=" O TYR S 726 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL S 742 " --> pdb=" O THR S 749 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 720 through 727 removed outlier: 6.524A pdb=" N LEU S 736 " --> pdb=" O ARG S 722 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE S 724 " --> pdb=" O GLY S 734 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY S 734 " --> pdb=" O ILE S 724 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TYR S 726 " --> pdb=" O CYS S 732 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N CYS S 732 " --> pdb=" O TYR S 726 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS S 803 " --> pdb=" O ILE S 793 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER S 762 " --> pdb=" O ALA S 804 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN S 806 " --> pdb=" O SER S 762 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER S 764 " --> pdb=" O GLN S 806 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 815 through 819 removed outlier: 4.010A pdb=" N ARG S 847 " --> pdb=" O THR S 833 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL S 866 " --> pdb=" O GLY S 846 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA S 862 " --> pdb=" O VAL S 850 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN S 852 " --> pdb=" O THR S 860 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N THR S 860 " --> pdb=" O GLN S 852 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER S 854 " --> pdb=" O LEU S 858 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU S 858 " --> pdb=" O SER S 854 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 870 through 876 removed outlier: 4.848A pdb=" N SER S 872 " --> pdb=" O SER S 883 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N CYS S 903 " --> pdb=" O LEU S 890 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU S 892 " --> pdb=" O THR S 901 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR S 901 " --> pdb=" O GLU S 892 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 911 through 917 removed outlier: 3.505A pdb=" N TYR S 913 " --> pdb=" O GLY S 924 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA S 946 " --> pdb=" O LEU S 932 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA S 934 " --> pdb=" O GLU S 944 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU S 944 " --> pdb=" O ALA S 934 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 954 through 959 removed outlier: 7.053A pdb=" N ALA S 968 " --> pdb=" O SER S 955 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL S 957 " --> pdb=" O LEU S 966 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU S 966 " --> pdb=" O VAL S 957 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE S 959 " --> pdb=" O ASN S 964 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASN S 964 " --> pdb=" O ILE S 959 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE S 975 " --> pdb=" O GLY S 967 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN S 973 " --> pdb=" O GLU S 969 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU S 974 " --> pdb=" O LEU S 997 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU S 997 " --> pdb=" O LEU S 974 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL S 976 " --> pdb=" O VAL S 995 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 1076 through 1077 Processing sheet with id=AC1, first strand: chain 'S' and resid 1113 through 1114 Processing sheet with id=AC2, first strand: chain 'B' and resid 104 through 105 removed outlier: 7.223A pdb=" N THR B 51 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.983A pdb=" N ILE B 73 " --> pdb=" O ARG B 63 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE B 65 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 71 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 82 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 130 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 84 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AC5, first strand: chain 'B' and resid 139 through 140 removed outlier: 4.229A pdb=" N SER B 192 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU B 189 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS B 210 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR B 191 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR B 208 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 193 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 206 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 195 " --> pdb=" O CYS B 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 222 through 225 removed outlier: 6.686A pdb=" N GLN B 243 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP B 252 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 329 through 336 removed outlier: 5.329A pdb=" N MET B 331 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR B 347 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 333 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 345 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 466 through 468 removed outlier: 3.824A pdb=" N PHE B 499 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 491 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 497 " --> pdb=" O ALA B 491 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1056 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: 1.81 Time building geometry restraints manager: 0.74 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: 3626 1.34 - 1.46: 2599 1.46 - 1.58: 4801 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 11101 Sorted by residual: bond pdb=" CB TRP B 332 " pdb=" CG TRP B 332 " ideal model delta sigma weight residual 1.498 1.547 -0.049 3.10e-02 1.04e+03 2.46e+00 bond pdb=" CA PHE B 343 " pdb=" CB PHE B 343 " ideal model delta sigma weight residual 1.528 1.548 -0.021 1.39e-02 5.18e+03 2.25e+00 bond pdb=" CB ASN S1111 " pdb=" CG ASN S1111 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 bond pdb=" CB PRO B 290 " pdb=" CG PRO B 290 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.69e+00 bond pdb=" CA ILE S 98 " pdb=" CB ILE S 98 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.34e+00 ... (remaining 11096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 14991 2.47 - 4.94: 128 4.94 - 7.41: 12 7.41 - 9.88: 2 9.88 - 12.35: 2 Bond angle restraints: 15135 Sorted by residual: angle pdb=" CA LYS B 333 " pdb=" CB LYS B 333 " pdb=" CG LYS B 333 " ideal model delta sigma weight residual 114.10 125.39 -11.29 2.00e+00 2.50e-01 3.18e+01 angle pdb=" CB MET B 314 " pdb=" CG MET B 314 " pdb=" SD MET B 314 " ideal model delta sigma weight residual 112.70 125.05 -12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C LYS B 333 " pdb=" CA LYS B 333 " pdb=" CB LYS B 333 " ideal model delta sigma weight residual 111.60 105.19 6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N LYS B 333 " pdb=" CA LYS B 333 " pdb=" CB LYS B 333 " ideal model delta sigma weight residual 110.51 115.65 -5.14 1.61e+00 3.86e-01 1.02e+01 angle pdb=" CA PRO B 290 " pdb=" N PRO B 290 " pdb=" CD PRO B 290 " ideal model delta sigma weight residual 112.00 107.54 4.46 1.40e+00 5.10e-01 1.01e+01 ... (remaining 15130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5773 17.88 - 35.76: 605 35.76 - 53.64: 165 53.64 - 71.52: 25 71.52 - 89.40: 9 Dihedral angle restraints: 6577 sinusoidal: 2222 harmonic: 4355 Sorted by residual: dihedral pdb=" CA PHE S 180 " pdb=" C PHE S 180 " pdb=" N VAL S 181 " pdb=" CA VAL S 181 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LYS B 333 " pdb=" C LYS B 333 " pdb=" N MET B 334 " pdb=" CA MET B 334 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA THR S 45 " pdb=" C THR S 45 " pdb=" N ALA S 46 " pdb=" CA ALA S 46 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1324 0.048 - 0.097: 338 0.097 - 0.145: 91 0.145 - 0.194: 2 0.194 - 0.242: 1 Chirality restraints: 1756 Sorted by residual: chirality pdb=" CG LEU B 326 " pdb=" CB LEU B 326 " pdb=" CD1 LEU B 326 " pdb=" CD2 LEU B 326 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B 344 " pdb=" CA ILE B 344 " pdb=" CG1 ILE B 344 " pdb=" CG2 ILE B 344 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA ASN S1111 " pdb=" N ASN S1111 " pdb=" C ASN S1111 " pdb=" CB ASN S1111 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1753 not shown) Planarity restraints: 1978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 289 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO B 290 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO B 290 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 290 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU S 728 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" CD GLU S 728 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU S 728 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU S 728 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 265 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO S 266 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO S 266 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO S 266 " -0.020 5.00e-02 4.00e+02 ... (remaining 1975 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 435 2.72 - 3.26: 10062 3.26 - 3.81: 16656 3.81 - 4.35: 19638 4.35 - 4.90: 34972 Nonbonded interactions: 81763 Sorted by model distance: nonbonded pdb=" OG SER B 76 " pdb=" OD1 ASP B 78 " model vdw 2.173 3.040 nonbonded pdb=" OG SER S 2 " pdb=" OD1 ASN S 4 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP B 212 " pdb=" N LYS B 213 " model vdw 2.240 3.120 nonbonded pdb=" O LYS B 31 " pdb=" OG1 THR B 34 " model vdw 2.250 3.040 nonbonded pdb=" N GLU B 339 " pdb=" OE1 GLU B 339 " model vdw 2.271 3.120 ... (remaining 81758 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11102 Z= 0.143 Angle : 0.620 12.350 15137 Z= 0.341 Chirality : 0.045 0.242 1756 Planarity : 0.004 0.119 1978 Dihedral : 16.280 89.400 3758 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.40 % Allowed : 27.46 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.36 (0.22), residues: 1476 helix: 1.00 (0.36), residues: 250 sheet: -0.48 (0.26), residues: 427 loop : -1.83 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 198 TYR 0.013 0.001 TYR B 455 PHE 0.015 0.001 PHE B 343 TRP 0.009 0.001 TRP B 472 HIS 0.002 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00304 (11101) covalent geometry : angle 0.61937 (15135) SS BOND : bond 0.00152 ( 1) SS BOND : angle 1.39649 ( 2) hydrogen bonds : bond 0.12892 ( 375) hydrogen bonds : angle 5.89021 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 218 MET cc_start: 0.6297 (mtt) cc_final: 0.5875 (mtm) REVERT: B 374 GLU cc_start: 0.8644 (pt0) cc_final: 0.8440 (pm20) REVERT: B 398 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6909 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 82 average time/residue: 0.4501 time to fit residues: 40.3386 Evaluate side-chains 78 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 64 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 398 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.0370 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 332 GLN S 805 HIS S 970 ASN B 115 ASN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS D 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.106273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.082600 restraints weight = 33457.400| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.52 r_work: 0.3293 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11102 Z= 0.115 Angle : 0.550 7.363 15137 Z= 0.281 Chirality : 0.044 0.206 1756 Planarity : 0.004 0.072 1978 Dihedral : 4.340 46.813 1609 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.69 % Allowed : 25.47 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.26 (0.22), residues: 1476 helix: 1.00 (0.35), residues: 257 sheet: -0.40 (0.27), residues: 422 loop : -1.75 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 198 TYR 0.012 0.001 TYR B 460 PHE 0.014 0.001 PHE B 242 TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00263 (11101) covalent geometry : angle 0.55041 (15135) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.87348 ( 2) hydrogen bonds : bond 0.03244 ( 375) hydrogen bonds : angle 4.90081 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8758 (OUTLIER) REVERT: S 90 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: S 218 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.5232 (mtm) REVERT: S 728 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 226 LYS cc_start: 0.9299 (mttt) cc_final: 0.8914 (mppt) REVERT: B 374 GLU cc_start: 0.8996 (pt0) cc_final: 0.8643 (pm20) REVERT: B 387 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 410 CYS cc_start: 0.8415 (p) cc_final: 0.7895 (m) REVERT: B 447 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7339 (tm-30) outliers start: 27 outliers final: 2 residues processed: 102 average time/residue: 0.4399 time to fit residues: 49.5385 Evaluate side-chains 89 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 63 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.0050 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 30 ASN S 332 GLN ** S 970 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 = 0.3947 r_free = 0.3947 target = 0.107479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.084428 restraints weight = 33089.599| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.26 r_work: 0.3350 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11102 Z= 0.094 Angle : 0.520 7.735 15137 Z= 0.265 Chirality : 0.044 0.211 1756 Planarity : 0.004 0.056 1978 Dihedral : 3.895 28.414 1600 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.08 % Allowed : 25.67 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.15 (0.22), residues: 1476 helix: 1.03 (0.35), residues: 261 sheet: -0.32 (0.27), residues: 422 loop : -1.68 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 198 TYR 0.009 0.001 TYR B 460 PHE 0.009 0.001 PHE B 242 TRP 0.009 0.001 TRP B 332 HIS 0.004 0.000 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00216 (11101) covalent geometry : angle 0.52014 (15135) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.54776 ( 2) hydrogen bonds : bond 0.02850 ( 375) hydrogen bonds : angle 4.64338 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.432 Fit side-chains REVERT: A 92 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8743 (OUTLIER) REVERT: S 218 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.5431 (mtm) REVERT: S 728 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7585 (tm-30) REVERT: B 143 GLU cc_start: 0.8402 (mp0) cc_final: 0.8099 (mp0) REVERT: B 226 LYS cc_start: 0.9305 (mttt) cc_final: 0.8944 (mppt) REVERT: B 308 GLU cc_start: 0.7999 (tt0) cc_final: 0.7778 (pp20) REVERT: B 374 GLU cc_start: 0.8993 (pt0) cc_final: 0.8781 (pm20) REVERT: B 385 GLU cc_start: 0.9131 (tp30) cc_final: 0.8710 (tp30) REVERT: B 387 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8831 (mm) REVERT: B 447 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7432 (tm-30) REVERT: B 500 GLU cc_start: 0.8060 (mp0) cc_final: 0.7317 (tm-30) outliers start: 31 outliers final: 7 residues processed: 115 average time/residue: 0.4412 time to fit residues: 55.8966 Evaluate side-chains 94 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 78 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 128 optimal weight: 0.0970 chunk 9 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 332 GLN S 970 ASN B 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.082686 restraints weight = 33300.404| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 4.25 r_work: 0.3311 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11102 Z= 0.144 Angle : 0.550 8.285 15137 Z= 0.281 Chirality : 0.044 0.211 1756 Planarity : 0.004 0.047 1978 Dihedral : 3.947 29.653 1600 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.99 % Allowed : 26.57 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.09 (0.22), residues: 1476 helix: 1.23 (0.35), residues: 255 sheet: -0.36 (0.27), residues: 422 loop : -1.62 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 198 TYR 0.014 0.001 TYR B 460 PHE 0.017 0.001 PHE A 104 TRP 0.009 0.001 TRP B 304 HIS 0.004 0.001 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00335 (11101) covalent geometry : angle 0.55017 (15135) SS BOND : bond 0.00501 ( 1) SS BOND : angle 1.12127 ( 2) hydrogen bonds : bond 0.03120 ( 375) hydrogen bonds : angle 4.67328 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.318 Fit side-chains REVERT: A 92 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8702 (OUTLIER) REVERT: S 90 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: S 218 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.5557 (mtm) REVERT: S 728 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7678 (tm-30) REVERT: S 835 MET cc_start: 0.8289 (tpp) cc_final: 0.7970 (tpp) REVERT: B 143 GLU cc_start: 0.8426 (mp0) cc_final: 0.8059 (mp0) REVERT: B 226 LYS cc_start: 0.9302 (mttt) cc_final: 0.8946 (mppt) REVERT: B 308 GLU cc_start: 0.7997 (tt0) cc_final: 0.7781 (pp20) REVERT: B 374 GLU cc_start: 0.8998 (pt0) cc_final: 0.8773 (pm20) REVERT: B 385 GLU cc_start: 0.9119 (tp30) cc_final: 0.8642 (tp30) REVERT: B 387 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8842 (mm) REVERT: B 447 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 500 GLU cc_start: 0.8104 (mp0) cc_final: 0.7368 (tm-30) outliers start: 30 outliers final: 16 residues processed: 110 average time/residue: 0.4365 time to fit residues: 52.6797 Evaluate side-chains 99 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 321 VAL Chi-restraints excluded: chain S residue 338 VAL Chi-restraints excluded: chain S residue 863 GLU Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 1006 VAL Chi-restraints excluded: chain S residue 1093 LEU Chi-restraints excluded: chain S residue 1105 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 456 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.0370 chunk 68 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 37 optimal weight: 0.0020 chunk 10 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.107383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.084308 restraints weight = 32870.963| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 4.27 r_work: 0.3351 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11102 Z= 0.090 Angle : 0.526 8.033 15137 Z= 0.267 Chirality : 0.044 0.233 1756 Planarity : 0.004 0.049 1978 Dihedral : 3.821 28.223 1600 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.18 % Allowed : 26.57 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.22), residues: 1476 helix: 1.50 (0.35), residues: 253 sheet: -0.23 (0.26), residues: 430 loop : -1.63 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 198 TYR 0.009 0.001 TYR B 87 PHE 0.010 0.001 PHE B 124 TRP 0.010 0.001 TRP B 304 HIS 0.003 0.000 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00204 (11101) covalent geometry : angle 0.52580 (15135) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.62903 ( 2) hydrogen bonds : bond 0.02640 ( 375) hydrogen bonds : angle 4.45522 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.389 Fit side-chains REVERT: A 92 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8666 (OUTLIER) REVERT: S 90 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: S 139 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8796 (mt) REVERT: S 198 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8729 (ttp80) REVERT: S 218 MET cc_start: 0.5866 (OUTLIER) cc_final: 0.5589 (mtm) REVERT: S 728 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7723 (tm-30) REVERT: S 835 MET cc_start: 0.8133 (tpp) cc_final: 0.7885 (tpp) REVERT: B 143 GLU cc_start: 0.8406 (mp0) cc_final: 0.8083 (mp0) REVERT: B 226 LYS cc_start: 0.9284 (mttt) cc_final: 0.8941 (mppt) REVERT: B 308 GLU cc_start: 0.8035 (tt0) cc_final: 0.7822 (pp20) REVERT: B 374 GLU cc_start: 0.8986 (pt0) cc_final: 0.8775 (pm20) REVERT: B 385 GLU cc_start: 0.9116 (tp30) cc_final: 0.8638 (tp30) REVERT: B 387 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 447 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 500 GLU cc_start: 0.8075 (mp0) cc_final: 0.7376 (tm-30) outliers start: 32 outliers final: 11 residues processed: 111 average time/residue: 0.4653 time to fit residues: 56.7577 Evaluate side-chains 97 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 1006 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 1 optimal weight: 40.0000 chunk 134 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 332 GLN ** S 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.104017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.080707 restraints weight = 33570.155| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 4.22 r_work: 0.3266 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11102 Z= 0.217 Angle : 0.607 9.802 15137 Z= 0.312 Chirality : 0.046 0.200 1756 Planarity : 0.004 0.040 1978 Dihedral : 4.163 31.089 1600 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.38 % Allowed : 26.77 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.10 (0.22), residues: 1476 helix: 1.18 (0.35), residues: 265 sheet: -0.30 (0.26), residues: 437 loop : -1.72 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 198 TYR 0.019 0.001 TYR B 460 PHE 0.013 0.002 PHE S1088 TRP 0.012 0.002 TRP B 304 HIS 0.005 0.001 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00507 (11101) covalent geometry : angle 0.60715 (15135) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.14138 ( 2) hydrogen bonds : bond 0.03550 ( 375) hydrogen bonds : angle 4.80246 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8704 (mm) REVERT: S 90 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: S 728 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 143 GLU cc_start: 0.8479 (mp0) cc_final: 0.8104 (mp0) REVERT: B 226 LYS cc_start: 0.9291 (mttt) cc_final: 0.8914 (mppt) REVERT: B 385 GLU cc_start: 0.9109 (tp30) cc_final: 0.8633 (tp30) REVERT: B 387 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 447 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 500 GLU cc_start: 0.8173 (mp0) cc_final: 0.7406 (tm-30) outliers start: 34 outliers final: 15 residues processed: 109 average time/residue: 0.3927 time to fit residues: 47.5427 Evaluate side-chains 100 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 338 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 1006 VAL Chi-restraints excluded: chain S residue 1093 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 6 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 132 optimal weight: 30.0000 chunk 143 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 30 ASN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.102440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.079095 restraints weight = 33561.856| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.22 r_work: 0.3233 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11102 Z= 0.259 Angle : 0.644 9.990 15137 Z= 0.333 Chirality : 0.047 0.212 1756 Planarity : 0.004 0.039 1978 Dihedral : 4.508 33.108 1600 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.88 % Allowed : 27.46 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.23 (0.22), residues: 1476 helix: 1.22 (0.34), residues: 259 sheet: -0.51 (0.25), residues: 450 loop : -1.76 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 198 TYR 0.018 0.002 TYR B 460 PHE 0.015 0.002 PHE S 180 TRP 0.018 0.002 TRP B 472 HIS 0.005 0.001 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00602 (11101) covalent geometry : angle 0.64397 (15135) SS BOND : bond 0.00223 ( 1) SS BOND : angle 1.12418 ( 2) hydrogen bonds : bond 0.03788 ( 375) hydrogen bonds : angle 5.03675 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 0.402 Fit side-chains REVERT: A 92 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8689 (mm) REVERT: S 90 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: S 728 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 143 GLU cc_start: 0.8492 (mp0) cc_final: 0.8062 (mp0) REVERT: B 226 LYS cc_start: 0.9287 (mttt) cc_final: 0.8903 (mppt) REVERT: B 374 GLU cc_start: 0.8911 (pt0) cc_final: 0.8662 (pm20) REVERT: B 385 GLU cc_start: 0.9069 (tp30) cc_final: 0.8645 (tp30) REVERT: B 447 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7556 (tm-30) REVERT: B 500 GLU cc_start: 0.8232 (mp0) cc_final: 0.7409 (tm-30) outliers start: 39 outliers final: 21 residues processed: 107 average time/residue: 0.4442 time to fit residues: 52.5925 Evaluate side-chains 97 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 180 PHE Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 321 VAL Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 338 VAL Chi-restraints excluded: chain S residue 863 GLU Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 930 VAL Chi-restraints excluded: chain S residue 1006 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain D residue 54 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 138 optimal weight: 0.0470 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.105234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082060 restraints weight = 33146.900| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 4.27 r_work: 0.3307 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11102 Z= 0.103 Angle : 0.568 10.906 15137 Z= 0.287 Chirality : 0.045 0.250 1756 Planarity : 0.003 0.043 1978 Dihedral : 4.155 30.566 1600 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.79 % Allowed : 28.36 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.07 (0.22), residues: 1476 helix: 1.44 (0.35), residues: 259 sheet: -0.47 (0.25), residues: 461 loop : -1.67 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 198 TYR 0.009 0.001 TYR B 87 PHE 0.010 0.001 PHE B 525 TRP 0.019 0.002 TRP B 472 HIS 0.005 0.001 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00237 (11101) covalent geometry : angle 0.56766 (15135) SS BOND : bond 0.00109 ( 1) SS BOND : angle 1.21544 ( 2) hydrogen bonds : bond 0.02796 ( 375) hydrogen bonds : angle 4.61344 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8635 (mm) REVERT: S 90 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8378 (tm-30) REVERT: S 218 MET cc_start: 0.5871 (mtt) cc_final: 0.5572 (mtm) REVERT: S 728 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 143 GLU cc_start: 0.8412 (mp0) cc_final: 0.7984 (mp0) REVERT: B 158 SER cc_start: 0.8301 (t) cc_final: 0.7568 (p) REVERT: B 226 LYS cc_start: 0.9278 (mttt) cc_final: 0.8896 (mppt) REVERT: B 385 GLU cc_start: 0.9047 (tp30) cc_final: 0.8658 (tp30) REVERT: B 447 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 500 GLU cc_start: 0.8137 (mp0) cc_final: 0.7390 (tm-30) outliers start: 28 outliers final: 15 residues processed: 107 average time/residue: 0.4046 time to fit residues: 47.6745 Evaluate side-chains 95 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 321 VAL Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 1006 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 456 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 50.0000 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 2 optimal weight: 50.0000 chunk 25 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 332 GLN S 970 ASN S1070 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.103975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080747 restraints weight = 33130.267| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 4.24 r_work: 0.3276 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11102 Z= 0.166 Angle : 0.614 10.223 15137 Z= 0.310 Chirality : 0.045 0.262 1756 Planarity : 0.004 0.052 1978 Dihedral : 4.162 30.513 1600 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.49 % Allowed : 28.46 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.10 (0.22), residues: 1476 helix: 1.32 (0.34), residues: 259 sheet: -0.44 (0.25), residues: 463 loop : -1.70 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG S 198 TYR 0.015 0.001 TYR B 460 PHE 0.014 0.001 PHE S 180 TRP 0.039 0.002 TRP B 304 HIS 0.004 0.001 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00391 (11101) covalent geometry : angle 0.61399 (15135) SS BOND : bond 0.00327 ( 1) SS BOND : angle 1.43430 ( 2) hydrogen bonds : bond 0.03182 ( 375) hydrogen bonds : angle 4.71719 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.306 Fit side-chains REVERT: A 92 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8622 (mm) REVERT: S 90 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8379 (tm-30) REVERT: S 218 MET cc_start: 0.6056 (mtt) cc_final: 0.5753 (mtm) REVERT: S 728 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 143 GLU cc_start: 0.8485 (mp0) cc_final: 0.8115 (mp0) REVERT: B 226 LYS cc_start: 0.9276 (mttt) cc_final: 0.8904 (mppt) REVERT: B 385 GLU cc_start: 0.9056 (tp30) cc_final: 0.8600 (tp30) REVERT: B 447 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 500 GLU cc_start: 0.8135 (mp0) cc_final: 0.7405 (tm-30) outliers start: 25 outliers final: 14 residues processed: 93 average time/residue: 0.4197 time to fit residues: 42.9297 Evaluate side-chains 84 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 321 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 1006 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 89 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 70.0000 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 44 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 0.0870 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.106106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.082969 restraints weight = 33012.871| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.26 r_work: 0.3321 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11102 Z= 0.104 Angle : 0.605 13.697 15137 Z= 0.300 Chirality : 0.045 0.265 1756 Planarity : 0.003 0.059 1978 Dihedral : 4.050 28.626 1600 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.69 % Allowed : 29.35 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.99 (0.22), residues: 1476 helix: 1.39 (0.35), residues: 259 sheet: -0.25 (0.26), residues: 445 loop : -1.67 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG S 198 TYR 0.009 0.001 TYR B 460 PHE 0.017 0.001 PHE B 320 TRP 0.028 0.002 TRP B 304 HIS 0.002 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00245 (11101) covalent geometry : angle 0.60484 (15135) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.99822 ( 2) hydrogen bonds : bond 0.02755 ( 375) hydrogen bonds : angle 4.53100 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.416 Fit side-chains REVERT: A 92 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8706 (mm) REVERT: S 90 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: S 218 MET cc_start: 0.5952 (mtt) cc_final: 0.5728 (mtm) REVERT: S 728 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7999 (tm-30) REVERT: B 158 SER cc_start: 0.8269 (t) cc_final: 0.7512 (p) REVERT: B 226 LYS cc_start: 0.9274 (mttt) cc_final: 0.8906 (mppt) REVERT: B 385 GLU cc_start: 0.9057 (tp30) cc_final: 0.8580 (tp30) REVERT: B 447 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7646 (tm-30) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.4156 time to fit residues: 42.3992 Evaluate side-chains 92 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 121 ILE Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 195 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 321 VAL Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 1006 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 109 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.104182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080982 restraints weight = 33363.301| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.29 r_work: 0.3279 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11102 Z= 0.177 Angle : 0.628 10.522 15137 Z= 0.315 Chirality : 0.046 0.272 1756 Planarity : 0.003 0.039 1978 Dihedral : 4.137 30.078 1600 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.99 % Allowed : 28.96 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1476 helix: 1.26 (0.34), residues: 265 sheet: -0.25 (0.26), residues: 442 loop : -1.72 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 198 TYR 0.015 0.001 TYR B 460 PHE 0.013 0.001 PHE S 281 TRP 0.029 0.002 TRP B 304 HIS 0.003 0.001 HIS S1070 Details of bonding type rmsd covalent geometry : bond 0.00416 (11101) covalent geometry : angle 0.62801 (15135) SS BOND : bond 0.00274 ( 1) SS BOND : angle 1.24160 ( 2) hydrogen bonds : bond 0.03228 ( 375) hydrogen bonds : angle 4.65051 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3878.70 seconds wall clock time: 66 minutes 33.05 seconds (3993.05 seconds total)