Starting phenix.real_space_refine on Wed Feb 4 08:28:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejc_48100/02_2026/9ejc_48100.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejc_48100/02_2026/9ejc_48100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ejc_48100/02_2026/9ejc_48100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejc_48100/02_2026/9ejc_48100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ejc_48100/02_2026/9ejc_48100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejc_48100/02_2026/9ejc_48100.map" } resolution = 2.98 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 ------------------------------------------------------------------------------- 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= 0.066 sd= 0.101 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 70 5.16 5 C 6030 2.51 5 N 1630 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 9492 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2408 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain: "F" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 544 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 2.12, per 1000 atoms: 0.22 Number of scatterers: 9492 At special positions: 0 Unit cell: (95.04, 118.8, 150.48, 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 70 16.00 O 1762 8.00 N 1630 7.00 C 6030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS F 22 " distance=2.04 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 286 " distance=2.03 Simple disulfide: pdb=" SG CYS E 118 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 35 " distance=2.03 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " 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: 0.65 Conformation dependent library (CDL) restraints added in 228.0 milliseconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 37.4% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.825A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.757A pdb=" N ALA C 23 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN C 24 " --> pdb=" O MET C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 20 through 24' Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 46 through 75 Processing helix chain 'E' and resid 76 through 79 removed outlier: 4.185A pdb=" N ALA E 79 " --> pdb=" O ARG E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 79' Processing helix chain 'E' and resid 80 through 91 removed outlier: 3.826A pdb=" N LEU E 91 " --> pdb=" O LEU E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 109 removed outlier: 4.138A pdb=" N MET E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 113 removed outlier: 3.763A pdb=" N ILE E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 116 through 149 removed outlier: 4.437A pdb=" N ASP E 132 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 156 removed outlier: 3.612A pdb=" N LYS E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 157 through 180 removed outlier: 4.100A pdb=" N GLY E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 220 removed outlier: 3.548A pdb=" N ARG E 212 " --> pdb=" O ARG E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 241 removed outlier: 3.974A pdb=" N ARG E 240 " --> pdb=" O CYS E 236 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 280 Proline residue: E 266 - end of helix Processing helix chain 'E' and resid 285 through 317 removed outlier: 3.500A pdb=" N LEU E 301 " --> pdb=" O ALA E 297 " (cutoff:3.500A) Proline residue: E 311 - end of helix Processing helix chain 'E' and resid 319 through 330 removed outlier: 3.585A pdb=" N TYR E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY E 327 " --> pdb=" O GLN E 323 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU E 328 " --> pdb=" O ARG E 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 5 removed outlier: 4.257A pdb=" N ALA F 4 " --> pdb=" O ALA F 1 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 72 removed outlier: 5.340A pdb=" N GLU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS F 65 " --> pdb=" O LYS F 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.654A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.956A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.952A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.176A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.001A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.504A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 4.135A pdb=" N VAL D 212 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.989A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.827A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.634A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.629A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.552A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.639A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.681A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 183 through 186 removed outlier: 3.623A pdb=" N SER E 184 " --> pdb=" O TYR E 197 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET E 195 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 26 through 27 removed outlier: 4.060A pdb=" N ASN F 27 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE F 41 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL F 40 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.123A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.632A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.132A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 97 " --> pdb=" O HIS D 35 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.700A pdb=" N VAL D 143 " --> pdb=" O ILE D 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.913A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 214 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.913A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR D 226 " --> pdb=" O GLN D 219 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1233 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: 1.31 Time building geometry restraints manager: 0.89 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: 3071 1.34 - 1.46: 2275 1.46 - 1.58: 4237 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9679 Sorted by residual: bond pdb=" N ASP D 1 " pdb=" CA ASP D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ASP B 5 " pdb=" CA ASP B 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ALA F 1 " pdb=" CA ALA F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N CYS E 30 " pdb=" CA CYS E 30 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 ... (remaining 9674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 12728 1.21 - 2.41: 309 2.41 - 3.62: 61 3.62 - 4.83: 8 4.83 - 6.03: 2 Bond angle restraints: 13108 Sorted by residual: angle pdb=" CA ARG E 279 " pdb=" CB ARG E 279 " pdb=" CG ARG E 279 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.10e+00 angle pdb=" C VAL E 309 " pdb=" CA VAL E 309 " pdb=" CB VAL E 309 " ideal model delta sigma weight residual 111.88 108.56 3.32 1.37e+00 5.33e-01 5.89e+00 angle pdb=" CA ASN E 31 " pdb=" C ASN E 31 " pdb=" N PHE E 32 " ideal model delta sigma weight residual 114.76 117.35 -2.59 1.14e+00 7.69e-01 5.18e+00 angle pdb=" N VAL E 38 " pdb=" CA VAL E 38 " pdb=" C VAL E 38 " ideal model delta sigma weight residual 113.71 111.64 2.07 9.50e-01 1.11e+00 4.74e+00 angle pdb=" N THR F 14 " pdb=" CA THR F 14 " pdb=" C THR F 14 " ideal model delta sigma weight residual 111.71 109.21 2.50 1.34e+00 5.57e-01 3.49e+00 ... (remaining 13103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 5361 17.17 - 34.33: 353 34.33 - 51.50: 50 51.50 - 68.67: 16 68.67 - 85.84: 3 Dihedral angle restraints: 5783 sinusoidal: 2261 harmonic: 3522 Sorted by residual: dihedral pdb=" CA THR F 14 " pdb=" C THR F 14 " pdb=" N LEU F 15 " pdb=" CA LEU F 15 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LEU F 12 " pdb=" C LEU F 12 " pdb=" N GLN F 13 " pdb=" CA GLN F 13 " ideal model delta harmonic sigma weight residual 180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA GLN F 13 " pdb=" C GLN F 13 " pdb=" N THR F 14 " pdb=" CA THR F 14 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 5780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 990 0.029 - 0.059: 327 0.059 - 0.088: 102 0.088 - 0.117: 67 0.117 - 0.147: 19 Chirality restraints: 1505 Sorted by residual: chirality pdb=" CA ILE C 9 " pdb=" N ILE C 9 " pdb=" C ILE C 9 " pdb=" CB ILE C 9 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA VAL E 36 " pdb=" N VAL E 36 " pdb=" C VAL E 36 " pdb=" CB VAL E 36 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1502 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO C 49 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 265 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO E 266 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 266 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 266 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 310 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO E 311 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " -0.020 5.00e-02 4.00e+02 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4229 2.94 - 3.43: 9501 3.43 - 3.92: 14338 3.92 - 4.41: 16329 4.41 - 4.90: 28045 Nonbonded interactions: 72442 Sorted by model distance: nonbonded pdb=" O ASP B 118 " pdb=" OD1 ASP B 118 " model vdw 2.452 3.040 nonbonded pdb=" O ASP D 90 " pdb=" OD1 ASP D 90 " model vdw 2.452 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.452 3.040 nonbonded pdb=" O ASP A 337 " pdb=" OG1 THR A 340 " model vdw 2.456 3.040 nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 2.479 3.040 ... (remaining 72437 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: 2.870 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: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 0.041 9686 Z= 0.124 Angle : 0.483 6.034 13122 Z= 0.268 Chirality : 0.039 0.147 1505 Planarity : 0.004 0.050 1651 Dihedral : 11.796 85.836 3490 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.33 (0.25), residues: 1197 helix: 1.85 (0.27), residues: 387 sheet: -0.36 (0.31), residues: 279 loop : -0.63 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 129 TYR 0.011 0.001 TYR E 128 PHE 0.015 0.001 PHE B 235 TRP 0.020 0.001 TRP E 154 HIS 0.004 0.001 HIS F 19 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9679) covalent geometry : angle 0.48272 (13108) SS BOND : bond 0.00321 ( 7) SS BOND : angle 0.77930 ( 14) hydrogen bonds : bond 0.17959 ( 425) hydrogen bonds : angle 7.12005 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6747 (ttp80) REVERT: B 44 GLN cc_start: 0.7134 (pm20) cc_final: 0.6848 (pm20) REVERT: B 188 MET cc_start: 0.7562 (mtp) cc_final: 0.7222 (mtp) REVERT: B 217 MET cc_start: 0.6264 (ttm) cc_final: 0.5896 (ttm) REVERT: C 58 GLU cc_start: 0.7505 (tt0) cc_final: 0.6996 (tm-30) REVERT: E 76 ARG cc_start: 0.7292 (ptt180) cc_final: 0.7016 (ptm160) REVERT: F 3 VAL cc_start: 0.8438 (t) cc_final: 0.8199 (m) REVERT: A 53 MET cc_start: 0.0688 (ttt) cc_final: -0.0194 (ttp) REVERT: A 243 MET cc_start: 0.1185 (mpp) cc_final: 0.0863 (mpp) REVERT: A 247 MET cc_start: 0.4285 (ttp) cc_final: 0.3902 (ptt) REVERT: D 157 ASN cc_start: 0.7487 (p0) cc_final: 0.7218 (p0) REVERT: D 189 ASP cc_start: 0.8025 (t0) cc_final: 0.7514 (t0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.6636 time to fit residues: 88.9296 Evaluate side-chains 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS B 340 ASN E 92 ASN E 268 HIS E 293 ASN A 331 ASN D 3 GLN D 130 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.109185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.094369 restraints weight = 26250.489| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.10 r_work: 0.3789 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9686 Z= 0.177 Angle : 0.606 9.000 13122 Z= 0.321 Chirality : 0.044 0.172 1505 Planarity : 0.004 0.045 1651 Dihedral : 4.735 31.647 1319 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.63 % Allowed : 7.46 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.32 (0.25), residues: 1197 helix: 1.61 (0.27), residues: 396 sheet: -0.08 (0.31), residues: 295 loop : -0.66 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 246 TYR 0.015 0.001 TYR E 128 PHE 0.020 0.002 PHE E 107 TRP 0.013 0.001 TRP E 154 HIS 0.005 0.001 HIS F 19 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9679) covalent geometry : angle 0.60606 (13108) SS BOND : bond 0.00558 ( 7) SS BOND : angle 0.87152 ( 14) hydrogen bonds : bond 0.04927 ( 425) hydrogen bonds : angle 5.39686 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6938 (tpp80) REVERT: B 44 GLN cc_start: 0.7190 (pm20) cc_final: 0.6845 (pm20) REVERT: B 134 ARG cc_start: 0.7112 (ptm160) cc_final: 0.6502 (mtm-85) REVERT: B 188 MET cc_start: 0.7686 (mtp) cc_final: 0.7334 (mtp) REVERT: B 217 MET cc_start: 0.6433 (ttm) cc_final: 0.5976 (ttm) REVERT: C 58 GLU cc_start: 0.7619 (tt0) cc_final: 0.7066 (tm-30) REVERT: E 76 ARG cc_start: 0.7461 (ptt180) cc_final: 0.7171 (ptm160) REVERT: E 181 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7264 (mtm180) REVERT: E 221 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.7012 (mp) REVERT: E 270 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6595 (mp) REVERT: E 324 ARG cc_start: 0.7702 (mpt-90) cc_final: 0.6244 (tpm170) REVERT: E 326 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5628 (t80) REVERT: F 3 VAL cc_start: 0.8555 (t) cc_final: 0.8323 (m) REVERT: F 37 GLN cc_start: 0.7163 (mp10) cc_final: 0.6921 (mp10) REVERT: A 243 MET cc_start: 0.0801 (mpp) cc_final: 0.0495 (mpp) REVERT: A 247 MET cc_start: 0.4158 (ttp) cc_final: 0.3838 (ptt) REVERT: D 83 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7769 (mtm) REVERT: D 93 MET cc_start: 0.7310 (ttm) cc_final: 0.7035 (ttp) REVERT: D 148 ARG cc_start: 0.7319 (ttp80) cc_final: 0.6869 (ttp80) REVERT: D 177 ILE cc_start: 0.8405 (mm) cc_final: 0.8181 (mt) REVERT: D 189 ASP cc_start: 0.8132 (t0) cc_final: 0.7597 (t0) outliers start: 17 outliers final: 2 residues processed: 121 average time/residue: 0.6366 time to fit residues: 81.3604 Evaluate side-chains 118 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain D residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN D 130 GLN D 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.109340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.094746 restraints weight = 26359.093| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.08 r_work: 0.3796 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9686 Z= 0.136 Angle : 0.560 8.611 13122 Z= 0.296 Chirality : 0.042 0.174 1505 Planarity : 0.004 0.041 1651 Dihedral : 4.590 24.143 1319 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.53 % Allowed : 9.85 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.40 (0.25), residues: 1197 helix: 1.70 (0.27), residues: 391 sheet: 0.13 (0.32), residues: 291 loop : -0.74 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 48 TYR 0.016 0.001 TYR D 178 PHE 0.014 0.002 PHE A 259 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9679) covalent geometry : angle 0.55959 (13108) SS BOND : bond 0.00516 ( 7) SS BOND : angle 0.77432 ( 14) hydrogen bonds : bond 0.04295 ( 425) hydrogen bonds : angle 5.01759 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.435 Fit side-chains REVERT: B 42 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6957 (tpp80) REVERT: B 44 GLN cc_start: 0.7162 (pm20) cc_final: 0.6789 (pm20) REVERT: B 134 ARG cc_start: 0.7127 (ptm160) cc_final: 0.6564 (mtp85) REVERT: B 137 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7336 (mmp-170) REVERT: B 188 MET cc_start: 0.7668 (mtp) cc_final: 0.7389 (mtp) REVERT: B 217 MET cc_start: 0.6430 (ttm) cc_final: 0.5964 (ttm) REVERT: B 268 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7088 (t0) REVERT: C 21 MET cc_start: 0.6916 (mmp) cc_final: 0.6398 (mmp) REVERT: C 58 GLU cc_start: 0.7599 (tt0) cc_final: 0.7089 (tm-30) REVERT: E 76 ARG cc_start: 0.7357 (ptt180) cc_final: 0.6970 (ptm160) REVERT: E 198 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7186 (pp20) REVERT: E 270 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6657 (mp) REVERT: E 324 ARG cc_start: 0.7646 (mpt-90) cc_final: 0.6227 (tpm170) REVERT: E 326 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5598 (t80) REVERT: F 3 VAL cc_start: 0.8565 (t) cc_final: 0.8344 (m) REVERT: A 53 MET cc_start: 0.0786 (ttt) cc_final: 0.0100 (ttp) REVERT: A 243 MET cc_start: 0.0738 (mpp) cc_final: 0.0479 (mpp) REVERT: A 247 MET cc_start: 0.4171 (ttp) cc_final: 0.3862 (ptt) REVERT: D 34 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7790 (mtp) REVERT: D 42 GLU cc_start: 0.7528 (mp0) cc_final: 0.7303 (mp0) REVERT: D 93 MET cc_start: 0.7360 (ttm) cc_final: 0.7093 (ttp) REVERT: D 128 MET cc_start: 0.8498 (mmm) cc_final: 0.7836 (mtm) REVERT: D 148 ARG cc_start: 0.7314 (ttp80) cc_final: 0.6887 (ttp80) REVERT: D 189 ASP cc_start: 0.8179 (t0) cc_final: 0.7632 (t0) REVERT: D 206 ARG cc_start: 0.7152 (mtt-85) cc_final: 0.6909 (mtt-85) outliers start: 16 outliers final: 4 residues processed: 119 average time/residue: 0.6974 time to fit residues: 87.6696 Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 157 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 340 ASN E 182 HIS D 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.107809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.093056 restraints weight = 26423.947| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.08 r_work: 0.3759 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9686 Z= 0.210 Angle : 0.614 9.596 13122 Z= 0.326 Chirality : 0.044 0.165 1505 Planarity : 0.004 0.044 1651 Dihedral : 4.913 26.117 1319 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.58 % Allowed : 12.05 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.24 (0.25), residues: 1197 helix: 1.45 (0.27), residues: 393 sheet: 0.32 (0.33), residues: 279 loop : -0.92 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 48 TYR 0.018 0.002 TYR D 178 PHE 0.025 0.002 PHE E 107 TRP 0.014 0.001 TRP B 211 HIS 0.007 0.001 HIS F 19 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 9679) covalent geometry : angle 0.61303 (13108) SS BOND : bond 0.00650 ( 7) SS BOND : angle 0.96929 ( 14) hydrogen bonds : bond 0.04779 ( 425) hydrogen bonds : angle 5.09622 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7234 (ttm-80) cc_final: 0.6906 (tpp80) REVERT: B 44 GLN cc_start: 0.7147 (pm20) cc_final: 0.6761 (pm20) REVERT: B 134 ARG cc_start: 0.7134 (ptm160) cc_final: 0.6575 (mtp85) REVERT: B 137 ARG cc_start: 0.7630 (mmm160) cc_final: 0.7319 (mmp-170) REVERT: B 188 MET cc_start: 0.7694 (mtp) cc_final: 0.7335 (mtt) REVERT: B 217 MET cc_start: 0.6404 (ttm) cc_final: 0.5974 (ttm) REVERT: B 268 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7089 (t0) REVERT: B 314 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7615 (mtp-110) REVERT: C 21 MET cc_start: 0.7010 (mmp) cc_final: 0.6502 (mmp) REVERT: C 58 GLU cc_start: 0.7639 (tt0) cc_final: 0.7093 (tm-30) REVERT: E 47 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6180 (t80) REVERT: E 76 ARG cc_start: 0.7416 (ptt180) cc_final: 0.7048 (ptm160) REVERT: E 181 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7498 (mtt180) REVERT: E 198 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7351 (pp20) REVERT: E 296 LEU cc_start: 0.7035 (tt) cc_final: 0.6665 (mt) REVERT: E 324 ARG cc_start: 0.7702 (mpt-90) cc_final: 0.6195 (tpm170) REVERT: E 326 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.5478 (t80) REVERT: F 3 VAL cc_start: 0.8604 (t) cc_final: 0.8392 (m) REVERT: F 37 GLN cc_start: 0.7216 (mp10) cc_final: 0.7016 (OUTLIER) REVERT: A 53 MET cc_start: 0.1032 (ttt) cc_final: 0.0147 (ttp) REVERT: A 247 MET cc_start: 0.4197 (ttp) cc_final: 0.3514 (ppp) REVERT: D 38 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7805 (mtm180) REVERT: D 93 MET cc_start: 0.7361 (ttm) cc_final: 0.7090 (ttp) REVERT: D 128 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7991 (mtm) REVERT: D 148 ARG cc_start: 0.7367 (ttp80) cc_final: 0.7134 (ttp80) REVERT: D 189 ASP cc_start: 0.8147 (t0) cc_final: 0.7609 (t0) outliers start: 27 outliers final: 10 residues processed: 130 average time/residue: 0.7077 time to fit residues: 96.9543 Evaluate side-chains 128 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain D residue 128 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 116 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 3 optimal weight: 0.0060 chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN D 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.108116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.093429 restraints weight = 26645.018| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.10 r_work: 0.3766 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9686 Z= 0.174 Angle : 0.585 8.931 13122 Z= 0.311 Chirality : 0.043 0.188 1505 Planarity : 0.004 0.044 1651 Dihedral : 4.816 25.818 1319 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.39 % Allowed : 12.91 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.23 (0.25), residues: 1197 helix: 1.46 (0.27), residues: 392 sheet: 0.37 (0.33), residues: 277 loop : -0.96 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.018 0.001 TYR D 178 PHE 0.016 0.002 PHE A 259 TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS F 19 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9679) covalent geometry : angle 0.58480 (13108) SS BOND : bond 0.00606 ( 7) SS BOND : angle 0.91202 ( 14) hydrogen bonds : bond 0.04381 ( 425) hydrogen bonds : angle 4.97290 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6905 (tpp80) REVERT: B 44 GLN cc_start: 0.7166 (pm20) cc_final: 0.6777 (pm20) REVERT: B 134 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6583 (mtp85) REVERT: B 137 ARG cc_start: 0.7615 (mmm160) cc_final: 0.7315 (mmp-170) REVERT: B 188 MET cc_start: 0.7714 (mtp) cc_final: 0.7353 (mtt) REVERT: B 217 MET cc_start: 0.6389 (ttm) cc_final: 0.5966 (ttm) REVERT: B 268 ASN cc_start: 0.7417 (p0) cc_final: 0.7075 (t0) REVERT: B 314 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.7583 (mtp-110) REVERT: C 21 MET cc_start: 0.7034 (mmp) cc_final: 0.6484 (mmp) REVERT: C 58 GLU cc_start: 0.7647 (tt0) cc_final: 0.7069 (tm-30) REVERT: E 47 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6233 (t80) REVERT: E 76 ARG cc_start: 0.7405 (ptt180) cc_final: 0.7021 (ptm160) REVERT: E 181 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7439 (mtt180) REVERT: E 198 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7342 (pp20) REVERT: E 199 ASN cc_start: 0.7882 (t0) cc_final: 0.7674 (t0) REVERT: E 296 LEU cc_start: 0.7010 (tt) cc_final: 0.6702 (mt) REVERT: E 324 ARG cc_start: 0.7699 (mpt-90) cc_final: 0.6202 (tpm170) REVERT: E 326 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.5476 (t80) REVERT: F 3 VAL cc_start: 0.8617 (t) cc_final: 0.8413 (m) REVERT: A 53 MET cc_start: 0.1064 (ttt) cc_final: 0.0259 (ttp) REVERT: A 247 MET cc_start: 0.4208 (ttp) cc_final: 0.3516 (ppp) REVERT: D 34 MET cc_start: 0.8093 (mtp) cc_final: 0.7866 (mtp) REVERT: D 38 ARG cc_start: 0.8224 (ptp-170) cc_final: 0.7821 (mtm180) REVERT: D 42 GLU cc_start: 0.7537 (mp0) cc_final: 0.7314 (mp0) REVERT: D 93 MET cc_start: 0.7341 (ttm) cc_final: 0.7061 (ttp) REVERT: D 128 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7936 (mtm) REVERT: D 148 ARG cc_start: 0.7364 (ttp80) cc_final: 0.7157 (ttp80) REVERT: D 189 ASP cc_start: 0.8141 (t0) cc_final: 0.7610 (t0) REVERT: D 206 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6503 (mtt-85) REVERT: D 211 ASP cc_start: 0.7775 (p0) cc_final: 0.7419 (p0) outliers start: 25 outliers final: 14 residues processed: 133 average time/residue: 0.7314 time to fit residues: 102.7442 Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 89 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 85 optimal weight: 30.0000 chunk 102 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN D 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.108860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.094329 restraints weight = 26751.037| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.09 r_work: 0.3788 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9686 Z= 0.123 Angle : 0.557 11.136 13122 Z= 0.296 Chirality : 0.042 0.163 1505 Planarity : 0.004 0.041 1651 Dihedral : 4.559 24.216 1319 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.01 % Allowed : 13.86 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.31 (0.25), residues: 1197 helix: 1.53 (0.27), residues: 397 sheet: 0.40 (0.32), residues: 278 loop : -0.93 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.016 0.001 TYR D 178 PHE 0.026 0.002 PHE E 107 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9679) covalent geometry : angle 0.55656 (13108) SS BOND : bond 0.00547 ( 7) SS BOND : angle 0.82367 ( 14) hydrogen bonds : bond 0.03849 ( 425) hydrogen bonds : angle 4.74072 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7271 (ttm-80) cc_final: 0.6942 (tpp80) REVERT: B 44 GLN cc_start: 0.7102 (pm20) cc_final: 0.6744 (pm20) REVERT: B 59 TYR cc_start: 0.8555 (m-80) cc_final: 0.8334 (m-80) REVERT: B 120 ILE cc_start: 0.8125 (tt) cc_final: 0.7869 (mt) REVERT: B 137 ARG cc_start: 0.7580 (mmm160) cc_final: 0.7306 (mmp-170) REVERT: B 188 MET cc_start: 0.7680 (mtp) cc_final: 0.7416 (mtp) REVERT: B 217 MET cc_start: 0.6382 (ttm) cc_final: 0.5942 (ttm) REVERT: B 268 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7070 (t0) REVERT: C 21 MET cc_start: 0.7024 (mmp) cc_final: 0.6478 (mmp) REVERT: C 58 GLU cc_start: 0.7623 (tt0) cc_final: 0.7095 (tm-30) REVERT: E 47 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6195 (t80) REVERT: E 76 ARG cc_start: 0.7416 (ptt180) cc_final: 0.7147 (ptt180) REVERT: E 296 LEU cc_start: 0.6896 (tt) cc_final: 0.6595 (mt) REVERT: E 324 ARG cc_start: 0.7615 (mpt-90) cc_final: 0.6192 (tpm170) REVERT: E 326 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.5457 (t80) REVERT: F 10 GLN cc_start: 0.7400 (tm-30) cc_final: 0.7032 (tp40) REVERT: A 53 MET cc_start: 0.0964 (ttt) cc_final: 0.0249 (ttp) REVERT: A 247 MET cc_start: 0.4172 (ttp) cc_final: 0.3494 (ppp) REVERT: D 34 MET cc_start: 0.8076 (mtp) cc_final: 0.7871 (mtt) REVERT: D 38 ARG cc_start: 0.8192 (ptp-170) cc_final: 0.7811 (mtm180) REVERT: D 42 GLU cc_start: 0.7507 (mp0) cc_final: 0.7281 (mp0) REVERT: D 93 MET cc_start: 0.7343 (ttm) cc_final: 0.7071 (ttp) REVERT: D 128 MET cc_start: 0.8467 (mmm) cc_final: 0.7898 (mtm) REVERT: D 148 ARG cc_start: 0.7359 (ttp80) cc_final: 0.6994 (ttp80) REVERT: D 189 ASP cc_start: 0.8147 (t0) cc_final: 0.7616 (t0) REVERT: D 206 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6445 (mtt-85) outliers start: 21 outliers final: 8 residues processed: 130 average time/residue: 0.7061 time to fit residues: 96.8929 Evaluate side-chains 125 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 31 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.108859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.094332 restraints weight = 26645.129| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.09 r_work: 0.3787 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9686 Z= 0.130 Angle : 0.556 8.236 13122 Z= 0.295 Chirality : 0.042 0.161 1505 Planarity : 0.004 0.043 1651 Dihedral : 4.495 23.265 1319 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.20 % Allowed : 14.53 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.36 (0.25), residues: 1197 helix: 1.56 (0.27), residues: 397 sheet: 0.47 (0.33), residues: 278 loop : -0.92 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 129 TYR 0.016 0.001 TYR D 178 PHE 0.016 0.001 PHE A 259 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9679) covalent geometry : angle 0.55613 (13108) SS BOND : bond 0.00531 ( 7) SS BOND : angle 0.80606 ( 14) hydrogen bonds : bond 0.03803 ( 425) hydrogen bonds : angle 4.66658 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6922 (tpp80) REVERT: B 44 GLN cc_start: 0.7061 (pm20) cc_final: 0.6706 (pm20) REVERT: B 120 ILE cc_start: 0.8119 (tt) cc_final: 0.7858 (mt) REVERT: B 134 ARG cc_start: 0.7124 (ptm160) cc_final: 0.6605 (mtp85) REVERT: B 137 ARG cc_start: 0.7574 (mmm160) cc_final: 0.7304 (mmp-170) REVERT: B 188 MET cc_start: 0.7697 (mtp) cc_final: 0.7307 (mtt) REVERT: B 217 MET cc_start: 0.6380 (ttm) cc_final: 0.5940 (ttm) REVERT: B 268 ASN cc_start: 0.7379 (p0) cc_final: 0.7052 (t0) REVERT: C 21 MET cc_start: 0.7015 (mmp) cc_final: 0.6481 (mmp) REVERT: C 58 GLU cc_start: 0.7585 (tt0) cc_final: 0.7138 (tm-30) REVERT: E 47 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6198 (t80) REVERT: E 76 ARG cc_start: 0.7403 (ptt180) cc_final: 0.7139 (ptt180) REVERT: E 109 PHE cc_start: 0.7185 (m-80) cc_final: 0.5976 (t80) REVERT: E 296 LEU cc_start: 0.6893 (tt) cc_final: 0.6599 (mt) REVERT: E 324 ARG cc_start: 0.7626 (mpt-90) cc_final: 0.6191 (tpm170) REVERT: E 326 TYR cc_start: 0.6418 (OUTLIER) cc_final: 0.5457 (t80) REVERT: F 6 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6357 (mm-30) REVERT: A 53 MET cc_start: 0.0992 (ttt) cc_final: 0.0336 (ttp) REVERT: A 243 MET cc_start: 0.0664 (mpp) cc_final: 0.0440 (mpt) REVERT: A 247 MET cc_start: 0.4164 (ttp) cc_final: 0.3489 (ppp) REVERT: D 34 MET cc_start: 0.8079 (mtp) cc_final: 0.7759 (mtm) REVERT: D 38 ARG cc_start: 0.8200 (ptp-170) cc_final: 0.7821 (mtm180) REVERT: D 42 GLU cc_start: 0.7495 (mp0) cc_final: 0.7261 (mp0) REVERT: D 93 MET cc_start: 0.7331 (ttm) cc_final: 0.7062 (ttp) REVERT: D 128 MET cc_start: 0.8475 (mmm) cc_final: 0.7925 (mtm) REVERT: D 148 ARG cc_start: 0.7407 (ttp80) cc_final: 0.7041 (ttp80) REVERT: D 206 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6352 (mtt-85) REVERT: D 211 ASP cc_start: 0.7727 (p0) cc_final: 0.7460 (p0) outliers start: 23 outliers final: 13 residues processed: 129 average time/residue: 0.7071 time to fit residues: 96.3634 Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 240 ARG Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 59 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 0.0670 chunk 27 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.108382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.093706 restraints weight = 26747.159| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.12 r_work: 0.3771 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9686 Z= 0.159 Angle : 0.584 9.182 13122 Z= 0.309 Chirality : 0.043 0.167 1505 Planarity : 0.004 0.046 1651 Dihedral : 4.603 24.318 1319 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.39 % Allowed : 14.82 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.26 (0.25), residues: 1197 helix: 1.45 (0.27), residues: 400 sheet: 0.47 (0.33), residues: 277 loop : -1.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.017 0.001 TYR D 178 PHE 0.029 0.002 PHE E 107 TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS F 19 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9679) covalent geometry : angle 0.58371 (13108) SS BOND : bond 0.00620 ( 7) SS BOND : angle 0.95325 ( 14) hydrogen bonds : bond 0.04035 ( 425) hydrogen bonds : angle 4.74028 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7233 (ttm-80) cc_final: 0.6857 (tpp80) REVERT: B 44 GLN cc_start: 0.7076 (pm20) cc_final: 0.6716 (pm20) REVERT: B 120 ILE cc_start: 0.8143 (tt) cc_final: 0.7883 (mt) REVERT: B 134 ARG cc_start: 0.7145 (ptm160) cc_final: 0.6615 (mtp85) REVERT: B 137 ARG cc_start: 0.7585 (mmm160) cc_final: 0.7319 (mmp-170) REVERT: B 188 MET cc_start: 0.7718 (mtp) cc_final: 0.7356 (mtt) REVERT: B 217 MET cc_start: 0.6389 (ttm) cc_final: 0.5943 (ttm) REVERT: B 268 ASN cc_start: 0.7370 (p0) cc_final: 0.7061 (t0) REVERT: B 292 PHE cc_start: 0.4949 (OUTLIER) cc_final: 0.4586 (p90) REVERT: C 21 MET cc_start: 0.7017 (mmp) cc_final: 0.6469 (mmp) REVERT: C 58 GLU cc_start: 0.7576 (tt0) cc_final: 0.7098 (tm-30) REVERT: E 47 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6234 (t80) REVERT: E 76 ARG cc_start: 0.7409 (ptt180) cc_final: 0.7034 (ptm160) REVERT: E 198 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7296 (pp20) REVERT: E 208 ARG cc_start: 0.7606 (tpt-90) cc_final: 0.7339 (tpt-90) REVERT: E 296 LEU cc_start: 0.6962 (tt) cc_final: 0.6681 (mt) REVERT: E 324 ARG cc_start: 0.7661 (mpt-90) cc_final: 0.6176 (tpm170) REVERT: E 326 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.5426 (t80) REVERT: F 10 GLN cc_start: 0.7459 (tm-30) cc_final: 0.6847 (tp40) REVERT: F 29 LYS cc_start: 0.7099 (mmtt) cc_final: 0.6799 (mmmm) REVERT: A 53 MET cc_start: 0.1054 (ttt) cc_final: 0.0306 (ttp) REVERT: A 243 MET cc_start: 0.0582 (mpp) cc_final: 0.0367 (mpt) REVERT: A 247 MET cc_start: 0.4160 (ttp) cc_final: 0.3486 (ppp) REVERT: D 34 MET cc_start: 0.8099 (mtp) cc_final: 0.7806 (mtm) REVERT: D 38 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7833 (mtm180) REVERT: D 93 MET cc_start: 0.7326 (ttm) cc_final: 0.7061 (ttp) REVERT: D 128 MET cc_start: 0.8464 (mmm) cc_final: 0.7927 (mtm) REVERT: D 148 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7040 (ttp80) REVERT: D 206 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6391 (mtt-85) REVERT: D 211 ASP cc_start: 0.7717 (p0) cc_final: 0.7509 (p0) outliers start: 25 outliers final: 13 residues processed: 132 average time/residue: 0.6380 time to fit residues: 88.7850 Evaluate side-chains 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.108851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.094213 restraints weight = 26737.201| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.13 r_work: 0.3781 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9686 Z= 0.133 Angle : 0.574 9.199 13122 Z= 0.303 Chirality : 0.042 0.163 1505 Planarity : 0.004 0.045 1651 Dihedral : 4.531 23.691 1319 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.63 % Allowed : 15.68 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.33 (0.25), residues: 1197 helix: 1.51 (0.27), residues: 400 sheet: 0.44 (0.33), residues: 279 loop : -0.93 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.016 0.001 TYR D 178 PHE 0.020 0.002 PHE A 259 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9679) covalent geometry : angle 0.57340 (13108) SS BOND : bond 0.00551 ( 7) SS BOND : angle 0.83943 ( 14) hydrogen bonds : bond 0.03779 ( 425) hydrogen bonds : angle 4.64001 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7229 (ttm-80) cc_final: 0.6853 (tpp80) REVERT: B 44 GLN cc_start: 0.7054 (pm20) cc_final: 0.6703 (pm20) REVERT: B 120 ILE cc_start: 0.8131 (tt) cc_final: 0.7859 (mt) REVERT: B 134 ARG cc_start: 0.7153 (ptm160) cc_final: 0.6620 (mtp85) REVERT: B 137 ARG cc_start: 0.7580 (mmm160) cc_final: 0.7322 (mmp-170) REVERT: B 188 MET cc_start: 0.7711 (mtp) cc_final: 0.7426 (mtp) REVERT: B 217 MET cc_start: 0.6368 (ttm) cc_final: 0.5916 (ttm) REVERT: B 268 ASN cc_start: 0.7377 (p0) cc_final: 0.7069 (t0) REVERT: C 21 MET cc_start: 0.7012 (mmp) cc_final: 0.6756 (tpp) REVERT: C 58 GLU cc_start: 0.7550 (tt0) cc_final: 0.7102 (tm-30) REVERT: E 47 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6216 (t80) REVERT: E 76 ARG cc_start: 0.7413 (ptt180) cc_final: 0.7045 (ptm160) REVERT: E 109 PHE cc_start: 0.7171 (m-80) cc_final: 0.5975 (t80) REVERT: E 296 LEU cc_start: 0.6885 (tt) cc_final: 0.6599 (mt) REVERT: E 324 ARG cc_start: 0.7636 (mpt-90) cc_final: 0.6153 (tpm170) REVERT: E 326 TYR cc_start: 0.6414 (OUTLIER) cc_final: 0.5424 (t80) REVERT: F 29 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6764 (mmmm) REVERT: A 53 MET cc_start: 0.1049 (ttt) cc_final: 0.0307 (ttp) REVERT: A 243 MET cc_start: 0.0581 (mpp) cc_final: 0.0370 (mpt) REVERT: A 247 MET cc_start: 0.4161 (ttp) cc_final: 0.3487 (ppp) REVERT: D 34 MET cc_start: 0.8081 (mtp) cc_final: 0.7790 (mtm) REVERT: D 38 ARG cc_start: 0.8209 (ptp-170) cc_final: 0.7814 (mtm180) REVERT: D 42 GLU cc_start: 0.7478 (mp0) cc_final: 0.7229 (mp0) REVERT: D 93 MET cc_start: 0.7286 (ttm) cc_final: 0.7017 (ttp) REVERT: D 128 MET cc_start: 0.8463 (mmm) cc_final: 0.7940 (mtm) REVERT: D 148 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7047 (ttp80) REVERT: D 206 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6483 (mtt-85) outliers start: 17 outliers final: 12 residues processed: 125 average time/residue: 0.6491 time to fit residues: 85.5757 Evaluate side-chains 128 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 42 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.109458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.094993 restraints weight = 26579.990| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 3.09 r_work: 0.3801 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9686 Z= 0.113 Angle : 0.551 8.922 13122 Z= 0.291 Chirality : 0.041 0.164 1505 Planarity : 0.004 0.045 1651 Dihedral : 4.378 23.055 1319 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.53 % Allowed : 16.06 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.44 (0.25), residues: 1197 helix: 1.64 (0.27), residues: 399 sheet: 0.52 (0.33), residues: 275 loop : -0.90 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 129 TYR 0.015 0.001 TYR D 178 PHE 0.037 0.001 PHE E 107 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9679) covalent geometry : angle 0.55060 (13108) SS BOND : bond 0.00499 ( 7) SS BOND : angle 0.73696 ( 14) hydrogen bonds : bond 0.03492 ( 425) hydrogen bonds : angle 4.50130 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6799 (tpp80) REVERT: B 44 GLN cc_start: 0.7079 (pm20) cc_final: 0.6726 (pm20) REVERT: B 120 ILE cc_start: 0.8114 (tt) cc_final: 0.7839 (mt) REVERT: B 134 ARG cc_start: 0.7146 (ptm160) cc_final: 0.6628 (mtp85) REVERT: B 137 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7313 (mmp-170) REVERT: B 188 MET cc_start: 0.7689 (mtp) cc_final: 0.7319 (mtt) REVERT: B 217 MET cc_start: 0.6340 (ttm) cc_final: 0.5916 (ttm) REVERT: B 268 ASN cc_start: 0.7363 (p0) cc_final: 0.7041 (t0) REVERT: C 21 MET cc_start: 0.7022 (mmp) cc_final: 0.6606 (tpp) REVERT: C 58 GLU cc_start: 0.7458 (tt0) cc_final: 0.7088 (tm-30) REVERT: E 47 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6142 (t80) REVERT: E 76 ARG cc_start: 0.7341 (ptt180) cc_final: 0.7099 (ptt180) REVERT: E 109 PHE cc_start: 0.7060 (m-80) cc_final: 0.5921 (t80) REVERT: E 324 ARG cc_start: 0.7531 (mpt-90) cc_final: 0.6165 (tpm170) REVERT: E 326 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5451 (t80) REVERT: F 29 LYS cc_start: 0.6968 (mmtt) cc_final: 0.6673 (mmmm) REVERT: A 53 MET cc_start: 0.1028 (ttt) cc_final: 0.0433 (ttp) REVERT: A 243 MET cc_start: 0.0589 (mpp) cc_final: 0.0356 (mpt) REVERT: A 247 MET cc_start: 0.4121 (ttp) cc_final: 0.3430 (ppp) REVERT: D 34 MET cc_start: 0.8027 (mtp) cc_final: 0.7709 (mtm) REVERT: D 38 ARG cc_start: 0.8194 (ptp-170) cc_final: 0.7814 (mtm180) REVERT: D 42 GLU cc_start: 0.7471 (mp0) cc_final: 0.7238 (mp0) REVERT: D 93 MET cc_start: 0.7257 (ttm) cc_final: 0.7018 (ttp) REVERT: D 128 MET cc_start: 0.8447 (mmm) cc_final: 0.7941 (mtm) REVERT: D 148 ARG cc_start: 0.7369 (ttp80) cc_final: 0.7115 (ttp80) REVERT: D 206 ARG cc_start: 0.7205 (mtt-85) cc_final: 0.6701 (mtm-85) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 0.7219 time to fit residues: 95.8445 Evaluate side-chains 122 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 47 TYR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain D residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 37 optimal weight: 0.0670 chunk 80 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 79 optimal weight: 0.0040 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 overall best weight: 1.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.109418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.094880 restraints weight = 26504.382| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.11 r_work: 0.3798 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9686 Z= 0.117 Angle : 0.568 11.249 13122 Z= 0.295 Chirality : 0.041 0.164 1505 Planarity : 0.004 0.046 1651 Dihedral : 4.354 25.010 1319 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.15 % Allowed : 16.92 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.53 (0.25), residues: 1197 helix: 1.74 (0.27), residues: 396 sheet: 0.49 (0.33), residues: 277 loop : -0.81 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 129 TYR 0.015 0.001 TYR D 178 PHE 0.021 0.001 PHE A 259 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9679) covalent geometry : angle 0.56823 (13108) SS BOND : bond 0.00487 ( 7) SS BOND : angle 0.74031 ( 14) hydrogen bonds : bond 0.03477 ( 425) hydrogen bonds : angle 4.46243 ( 1233) =============================================================================== Job complete usr+sys time: 3161.84 seconds wall clock time: 54 minutes 35.73 seconds (3275.73 seconds total)