Starting phenix.real_space_refine on Thu Nov 20 08:13:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg5_52128/11_2025/9hg5_52128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg5_52128/11_2025/9hg5_52128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hg5_52128/11_2025/9hg5_52128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg5_52128/11_2025/9hg5_52128.map" model { file = "/net/cci-nas-00/data/ceres_data/9hg5_52128/11_2025/9hg5_52128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg5_52128/11_2025/9hg5_52128.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 10153 2.51 5 N 2816 2.21 5 O 3204 1.98 5 H 15755 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31980 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12200 Classifications: {'peptide': 790} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 760} Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 4747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 4747 Classifications: {'peptide': 318} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 301} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1363 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 4675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4675 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.18 Number of scatterers: 31980 At special positions: 0 Unit cell: (111.69, 123.37, 183.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 3204 8.00 N 2816 7.00 C 10153 6.00 H 15755 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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: 3.04 Conformation dependent library (CDL) restraints added in 943.6 milliseconds 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3834 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 24 sheets defined 31.5% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.543A pdb=" N SER A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.069A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.753A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.637A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.907A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.611A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.677A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.619A pdb=" N LYS C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.512A pdb=" N TYR C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.504A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.917A pdb=" N LYS C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 224 Processing helix chain 'C' and resid 247 through 262 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 284 through 291 Processing helix chain 'C' and resid 327 through 336 removed outlier: 3.919A pdb=" N ALA C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.611A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.226A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.630A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.767A pdb=" N GLN F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 60 Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 111 through 118 Processing helix chain 'F' and resid 125 through 149 removed outlier: 4.093A pdb=" N ARG F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.889A pdb=" N GLN F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 208 Processing helix chain 'F' and resid 211 through 220 Processing helix chain 'F' and resid 222 through 228 removed outlier: 4.253A pdb=" N LEU F 226 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 239 Processing helix chain 'F' and resid 240 through 247 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 393 through 421 removed outlier: 3.566A pdb=" N ARG F 418 " --> pdb=" O MET F 414 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.682A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG A 79 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N GLU A 73 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ALA F 29 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 75 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS F 27 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.682A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG A 79 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N GLU A 73 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ALA F 29 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 75 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS F 27 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 5.880A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 183 removed outlier: 6.910A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.103A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.378A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.103A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.378A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.603A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 426 removed outlier: 3.659A pdb=" N THR A 467 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP A 493 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 673 removed outlier: 5.274A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 46 removed outlier: 4.429A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.808A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.213A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.502A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.403A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.779A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.960A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.927A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.480A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR C 157 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN C 147 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY C 159 " --> pdb=" O TRP C 145 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP C 145 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 133 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP C 144 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 131 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AC3, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 269 removed outlier: 4.009A pdb=" N ASP C 268 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR C 303 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 304 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'F' and resid 230 through 234 removed outlier: 6.151A pdb=" N LEU F 176 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP F 233 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU F 174 " --> pdb=" O TRP F 233 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 272 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER F 177 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL F 270 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE F 179 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU F 268 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE F 181 " --> pdb=" O HIS F 266 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS F 266 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG F 260 " --> pdb=" O GLY F 264 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU F 268 " --> pdb=" O VAL F 256 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2085 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: 8.29 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15754 1.03 - 1.23: 11 1.23 - 1.42: 7040 1.42 - 1.62: 9390 1.62 - 1.81: 101 Bond restraints: 32296 Sorted by residual: bond pdb=" N ALA A 21 " pdb=" H1 ALA A 21 " ideal model delta sigma weight residual 0.960 0.888 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N CYS C 25 " pdb=" H1 CYS C 25 " ideal model delta sigma weight residual 0.960 0.890 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N VAL F 157 " pdb=" CA VAL F 157 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.81e+00 bond pdb=" N ARG D 61 " pdb=" H ARG D 61 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.28e+00 bond pdb=" N PHE D 64 " pdb=" H PHE D 64 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.68e+00 ... (remaining 32291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 57928 2.94 - 5.88: 193 5.88 - 8.82: 12 8.82 - 11.76: 3 11.76 - 14.70: 1 Bond angle restraints: 58137 Sorted by residual: angle pdb=" C SER C 294 " pdb=" N ASP C 295 " pdb=" CA ASP C 295 " ideal model delta sigma weight residual 121.17 135.87 -14.70 1.62e+00 3.81e-01 8.23e+01 angle pdb=" N LEU F 426 " pdb=" CA LEU F 426 " pdb=" C LEU F 426 " ideal model delta sigma weight residual 112.94 105.89 7.05 1.41e+00 5.03e-01 2.50e+01 angle pdb=" N MET F 414 " pdb=" CA MET F 414 " pdb=" C MET F 414 " ideal model delta sigma weight residual 112.89 107.60 5.29 1.24e+00 6.50e-01 1.82e+01 angle pdb=" N GLN F 415 " pdb=" CA GLN F 415 " pdb=" C GLN F 415 " ideal model delta sigma weight residual 113.97 108.58 5.39 1.28e+00 6.10e-01 1.77e+01 angle pdb=" N GLN F 155 " pdb=" CA GLN F 155 " pdb=" C GLN F 155 " ideal model delta sigma weight residual 111.33 106.54 4.79 1.21e+00 6.83e-01 1.57e+01 ... (remaining 58132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13464 17.93 - 35.87: 1217 35.87 - 53.80: 396 53.80 - 71.74: 146 71.74 - 89.67: 42 Dihedral angle restraints: 15265 sinusoidal: 8315 harmonic: 6950 Sorted by residual: dihedral pdb=" CA ASP B 363 " pdb=" CB ASP B 363 " pdb=" CG ASP B 363 " pdb=" OD1 ASP B 363 " ideal model delta sinusoidal sigma weight residual -30.00 -86.80 56.80 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA GLU B 370 " pdb=" C GLU B 370 " pdb=" N PRO B 371 " pdb=" CA PRO B 371 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CG ARG C 83 " pdb=" CD ARG C 83 " pdb=" NE ARG C 83 " pdb=" CZ ARG C 83 " ideal model delta sinusoidal sigma weight residual 90.00 134.41 -44.41 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 15262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2061 0.052 - 0.104: 320 0.104 - 0.156: 87 0.156 - 0.209: 4 0.209 - 0.261: 1 Chirality restraints: 2473 Sorted by residual: chirality pdb=" CA GLN F 98 " pdb=" N GLN F 98 " pdb=" C GLN F 98 " pdb=" CB GLN F 98 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA GLN B 225 " pdb=" N GLN B 225 " pdb=" C GLN B 225 " pdb=" CB GLN B 225 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA VAL F 256 " pdb=" N VAL F 256 " pdb=" C VAL F 256 " pdb=" CB VAL F 256 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 2470 not shown) Planarity restraints: 4974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 61 " 0.490 9.50e-02 1.11e+02 2.13e-01 4.52e+02 pdb=" NE ARG D 61 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG D 61 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 61 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 61 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG D 61 " -0.260 2.00e-02 2.50e+03 pdb="HH12 ARG D 61 " 0.276 2.00e-02 2.50e+03 pdb="HH21 ARG D 61 " 0.036 2.00e-02 2.50e+03 pdb="HH22 ARG D 61 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 155 " -0.033 2.00e-02 2.50e+03 3.51e-02 1.84e+01 pdb=" CD GLN F 155 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN F 155 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 GLN F 155 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN F 155 " 0.050 2.00e-02 2.50e+03 pdb="HE22 GLN F 155 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 226 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C MET B 226 " 0.060 2.00e-02 2.50e+03 pdb=" O MET B 226 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 227 " -0.021 2.00e-02 2.50e+03 ... (remaining 4971 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 615 2.10 - 2.73: 54814 2.73 - 3.35: 90906 3.35 - 3.98: 116609 3.98 - 4.60: 182222 Nonbonded interactions: 445166 Sorted by model distance: nonbonded pdb=" O LEU C 310 " pdb=" H ASN C 312 " model vdw 1.475 2.450 nonbonded pdb=" OE1 GLN E 53 " pdb=" H GLN E 53 " model vdw 1.484 2.450 nonbonded pdb=" HZ1 LYS C 32 " pdb=" O GLN D 44 " model vdw 1.503 2.450 nonbonded pdb="HH12 ARG A 526 " pdb=" OG1 THR A 577 " model vdw 1.580 2.450 nonbonded pdb=" O LEU A 66 " pdb=" HG1 THR A 69 " model vdw 1.581 2.450 ... (remaining 445161 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.270 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 0.039 16542 Z= 0.167 Angle : 0.591 14.701 22463 Z= 0.335 Chirality : 0.043 0.261 2473 Planarity : 0.005 0.150 2977 Dihedral : 16.430 89.544 6051 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % Rotamer: Outliers : 1.21 % Allowed : 18.85 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 2071 helix: 1.92 (0.22), residues: 577 sheet: -0.36 (0.21), residues: 563 loop : -0.62 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 355 TYR 0.012 0.001 TYR D 184 PHE 0.019 0.001 PHE D 64 TRP 0.017 0.001 TRP C 288 HIS 0.006 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00337 (16541) covalent geometry : angle 0.59125 (22461) SS BOND : bond 0.00179 ( 1) SS BOND : angle 0.49373 ( 2) hydrogen bonds : bond 0.14322 ( 746) hydrogen bonds : angle 6.33564 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8125 (tt0) cc_final: 0.7690 (tm-30) REVERT: A 87 GLN cc_start: 0.7197 (mt0) cc_final: 0.6986 (tm-30) REVERT: A 121 VAL cc_start: 0.8572 (t) cc_final: 0.8083 (t) REVERT: A 514 THR cc_start: 0.8415 (m) cc_final: 0.8067 (p) REVERT: A 534 ASN cc_start: 0.8764 (m110) cc_final: 0.8073 (m110) REVERT: B 355 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7811 (ptt-90) REVERT: B 364 SER cc_start: 0.8915 (m) cc_final: 0.8541 (p) REVERT: C 127 LYS cc_start: 0.9375 (mmtt) cc_final: 0.8980 (mmmm) REVERT: C 153 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7774 (mt-10) REVERT: D 34 GLU cc_start: 0.7871 (mp0) cc_final: 0.7638 (tm-30) REVERT: D 40 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7508 (mm110) REVERT: D 121 ASP cc_start: 0.8424 (t0) cc_final: 0.8115 (t0) REVERT: D 232 GLU cc_start: 0.7977 (tp30) cc_final: 0.7723 (mm-30) REVERT: E 107 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8237 (mttp) REVERT: F 231 MET cc_start: 0.1611 (tmt) cc_final: 0.0140 (mpp) outliers start: 21 outliers final: 7 residues processed: 238 average time/residue: 1.3063 time to fit residues: 347.0460 Evaluate side-chains 145 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 39 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.132105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.080736 restraints weight = 86671.944| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.00 r_work: 0.3005 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16542 Z= 0.200 Angle : 0.550 7.803 22463 Z= 0.290 Chirality : 0.042 0.164 2473 Planarity : 0.004 0.054 2977 Dihedral : 4.613 88.668 2284 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 1.84 % Allowed : 19.02 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 2071 helix: 1.96 (0.21), residues: 583 sheet: -0.46 (0.21), residues: 556 loop : -0.64 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 355 TYR 0.016 0.001 TYR C 197 PHE 0.012 0.001 PHE E 95 TRP 0.012 0.001 TRP B 143 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00451 (16541) covalent geometry : angle 0.54998 (22461) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.87973 ( 2) hydrogen bonds : bond 0.04175 ( 746) hydrogen bonds : angle 5.03449 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8372 (tt0) cc_final: 0.8099 (mt-10) REVERT: A 76 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7379 (ttm110) REVERT: A 91 ARG cc_start: 0.8481 (ptp-170) cc_final: 0.8274 (ptp-170) REVERT: A 121 VAL cc_start: 0.8397 (t) cc_final: 0.7974 (m) REVERT: A 123 GLU cc_start: 0.7321 (mp0) cc_final: 0.6902 (mp0) REVERT: A 321 ARG cc_start: 0.7726 (ptt90) cc_final: 0.7473 (ptt90) REVERT: A 401 ASP cc_start: 0.8428 (t0) cc_final: 0.7562 (t0) REVERT: A 766 ILE cc_start: 0.9016 (mt) cc_final: 0.8775 (mp) REVERT: B 355 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.8090 (pmm-80) REVERT: B 388 TYR cc_start: 0.8109 (m-80) cc_final: 0.7871 (m-80) REVERT: C 127 LYS cc_start: 0.9494 (mmtt) cc_final: 0.9191 (mmmm) REVERT: C 153 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7928 (mt-10) REVERT: C 155 GLU cc_start: 0.7090 (tp30) cc_final: 0.6853 (tp30) REVERT: C 194 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.8004 (mpp) REVERT: C 261 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8446 (mppt) REVERT: D 34 GLU cc_start: 0.8245 (mp0) cc_final: 0.7811 (tm-30) REVERT: D 121 ASP cc_start: 0.8418 (t0) cc_final: 0.8127 (t0) REVERT: F 58 GLN cc_start: 0.8496 (mp10) cc_final: 0.8092 (pm20) outliers start: 32 outliers final: 9 residues processed: 158 average time/residue: 1.5238 time to fit residues: 264.9760 Evaluate side-chains 126 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 114 optimal weight: 0.0770 chunk 119 optimal weight: 0.0970 chunk 165 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 127 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 44 GLN D 230 GLN F 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.132780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.081984 restraints weight = 85759.129| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.97 r_work: 0.3024 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 0.038 16542 Z= 0.103 Angle : 0.479 5.249 22463 Z= 0.250 Chirality : 0.041 0.143 2473 Planarity : 0.003 0.058 2977 Dihedral : 4.262 89.450 2280 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 1.26 % Allowed : 19.54 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2071 helix: 2.26 (0.21), residues: 583 sheet: -0.33 (0.21), residues: 553 loop : -0.51 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.016 0.001 TYR C 197 PHE 0.015 0.001 PHE A 67 TRP 0.009 0.001 TRP B 143 HIS 0.013 0.001 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00227 (16541) covalent geometry : angle 0.47943 (22461) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.42139 ( 2) hydrogen bonds : bond 0.03796 ( 746) hydrogen bonds : angle 4.74132 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8406 (tt0) cc_final: 0.8092 (mt-10) REVERT: A 91 ARG cc_start: 0.8540 (ptp-170) cc_final: 0.8339 (ptp-170) REVERT: A 121 VAL cc_start: 0.8211 (t) cc_final: 0.7927 (t) REVERT: A 123 GLU cc_start: 0.7325 (mp0) cc_final: 0.6953 (mp0) REVERT: A 321 ARG cc_start: 0.7694 (ptt90) cc_final: 0.7434 (ptt90) REVERT: A 401 ASP cc_start: 0.8409 (t0) cc_final: 0.7593 (t0) REVERT: A 465 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6866 (m-80) REVERT: A 472 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8778 (p) REVERT: A 766 ILE cc_start: 0.9155 (mt) cc_final: 0.8888 (mp) REVERT: B 355 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.8082 (pmm-80) REVERT: B 388 TYR cc_start: 0.7960 (m-80) cc_final: 0.7714 (m-80) REVERT: C 127 LYS cc_start: 0.9476 (mmtt) cc_final: 0.9119 (mmmm) REVERT: C 194 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8042 (mpp) REVERT: C 261 LYS cc_start: 0.8676 (mmmm) cc_final: 0.8363 (mmtm) REVERT: C 281 LYS cc_start: 0.8163 (tttt) cc_final: 0.7854 (tmtt) REVERT: D 121 ASP cc_start: 0.8459 (t0) cc_final: 0.8167 (t0) REVERT: F 58 GLN cc_start: 0.8474 (mp10) cc_final: 0.8101 (pm20) outliers start: 22 outliers final: 6 residues processed: 134 average time/residue: 1.4464 time to fit residues: 214.3199 Evaluate side-chains 116 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 187 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.128231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.076229 restraints weight = 86073.828| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.94 r_work: 0.2901 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16542 Z= 0.246 Angle : 0.534 5.486 22463 Z= 0.285 Chirality : 0.042 0.148 2473 Planarity : 0.004 0.068 2977 Dihedral : 4.406 85.480 2278 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 1.67 % Allowed : 18.56 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 2071 helix: 2.05 (0.21), residues: 585 sheet: -0.47 (0.21), residues: 566 loop : -0.65 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 76 TYR 0.017 0.002 TYR D 77 PHE 0.012 0.001 PHE A 67 TRP 0.012 0.001 TRP B 143 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00564 (16541) covalent geometry : angle 0.53405 (22461) SS BOND : bond 0.00357 ( 1) SS BOND : angle 0.95691 ( 2) hydrogen bonds : bond 0.04220 ( 746) hydrogen bonds : angle 4.80424 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6094 (mp0) cc_final: 0.5798 (mp0) REVERT: A 73 GLU cc_start: 0.8506 (tt0) cc_final: 0.7700 (tm-30) REVERT: A 121 VAL cc_start: 0.8292 (t) cc_final: 0.7935 (t) REVERT: A 123 GLU cc_start: 0.7257 (mp0) cc_final: 0.6881 (mp0) REVERT: A 321 ARG cc_start: 0.7886 (ptt90) cc_final: 0.7588 (ptt90) REVERT: A 401 ASP cc_start: 0.8445 (t0) cc_final: 0.7585 (t0) REVERT: A 472 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8858 (p) REVERT: C 194 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7988 (mpp) REVERT: D 121 ASP cc_start: 0.8470 (t0) cc_final: 0.8043 (m-30) REVERT: F 58 GLN cc_start: 0.8518 (mp10) cc_final: 0.8148 (pm20) outliers start: 29 outliers final: 13 residues processed: 132 average time/residue: 1.3961 time to fit residues: 204.9709 Evaluate side-chains 111 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 13 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 127 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN C 128 ASN D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.135962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078990 restraints weight = 87065.559| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.07 r_work: 0.2928 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16542 Z= 0.122 Angle : 0.474 4.821 22463 Z= 0.248 Chirality : 0.041 0.141 2473 Planarity : 0.003 0.049 2977 Dihedral : 4.188 82.619 2277 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 1.32 % Allowed : 18.74 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 2071 helix: 2.32 (0.21), residues: 587 sheet: -0.39 (0.21), residues: 562 loop : -0.61 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.017 0.001 TYR C 197 PHE 0.015 0.001 PHE A 67 TRP 0.010 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00272 (16541) covalent geometry : angle 0.47436 (22461) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.25170 ( 2) hydrogen bonds : bond 0.03680 ( 746) hydrogen bonds : angle 4.58596 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.5995 (mp0) cc_final: 0.5736 (mp0) REVERT: A 73 GLU cc_start: 0.8609 (tt0) cc_final: 0.7728 (tm-30) REVERT: A 121 VAL cc_start: 0.8321 (t) cc_final: 0.7922 (t) REVERT: A 123 GLU cc_start: 0.7347 (mp0) cc_final: 0.6905 (mp0) REVERT: A 321 ARG cc_start: 0.7875 (ptt90) cc_final: 0.7591 (ptt90) REVERT: A 401 ASP cc_start: 0.8441 (t0) cc_final: 0.7626 (t0) REVERT: A 472 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 534 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8631 (m110) REVERT: B 90 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8780 (mttp) REVERT: B 355 ARG cc_start: 0.8557 (ptt-90) cc_final: 0.8186 (pmm-80) REVERT: C 194 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8030 (mpp) REVERT: D 121 ASP cc_start: 0.8501 (t0) cc_final: 0.8163 (m-30) REVERT: F 58 GLN cc_start: 0.8504 (mp10) cc_final: 0.8147 (pm20) REVERT: F 136 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7964 (mtp) outliers start: 23 outliers final: 11 residues processed: 120 average time/residue: 1.4460 time to fit residues: 192.7211 Evaluate side-chains 115 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 136 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 116 optimal weight: 0.8980 chunk 190 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 195 optimal weight: 50.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.132982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.076775 restraints weight = 87000.145| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.01 r_work: 0.2901 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16542 Z= 0.180 Angle : 0.491 5.737 22463 Z= 0.259 Chirality : 0.041 0.144 2473 Planarity : 0.003 0.045 2977 Dihedral : 4.175 77.946 2277 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 1.55 % Allowed : 18.62 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 2071 helix: 2.29 (0.21), residues: 587 sheet: -0.45 (0.22), residues: 556 loop : -0.66 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.017 0.001 TYR C 197 PHE 0.014 0.001 PHE A 67 TRP 0.011 0.001 TRP B 143 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00408 (16541) covalent geometry : angle 0.49057 (22461) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.47245 ( 2) hydrogen bonds : bond 0.03818 ( 746) hydrogen bonds : angle 4.58694 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6177 (mp0) cc_final: 0.5892 (mp0) REVERT: A 73 GLU cc_start: 0.8690 (tt0) cc_final: 0.7782 (tm-30) REVERT: A 76 ARG cc_start: 0.7313 (mtp-110) cc_final: 0.7109 (ttm110) REVERT: A 108 ASP cc_start: 0.9094 (p0) cc_final: 0.8792 (p0) REVERT: A 121 VAL cc_start: 0.8362 (t) cc_final: 0.7854 (t) REVERT: A 123 GLU cc_start: 0.7382 (mp0) cc_final: 0.6872 (mp0) REVERT: A 321 ARG cc_start: 0.7952 (ptt90) cc_final: 0.7654 (ptt90) REVERT: A 472 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8919 (p) REVERT: B 355 ARG cc_start: 0.8562 (ptt-90) cc_final: 0.8204 (pmm-80) REVERT: C 194 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8029 (mpp) REVERT: D 121 ASP cc_start: 0.8481 (t0) cc_final: 0.8249 (m-30) REVERT: F 58 GLN cc_start: 0.8565 (mp10) cc_final: 0.8192 (pm20) REVERT: F 69 GLN cc_start: 0.9538 (tt0) cc_final: 0.9267 (tm-30) outliers start: 27 outliers final: 15 residues processed: 123 average time/residue: 1.4584 time to fit residues: 198.7800 Evaluate side-chains 114 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 172 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN E 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.126055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071917 restraints weight = 86916.433| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.03 r_work: 0.2828 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16542 Z= 0.189 Angle : 0.493 5.062 22463 Z= 0.261 Chirality : 0.041 0.167 2473 Planarity : 0.003 0.043 2977 Dihedral : 4.171 71.417 2277 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.61 % Allowed : 18.85 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 2071 helix: 2.29 (0.21), residues: 587 sheet: -0.53 (0.22), residues: 561 loop : -0.69 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.018 0.001 TYR C 197 PHE 0.013 0.001 PHE A 67 TRP 0.011 0.001 TRP B 143 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00427 (16541) covalent geometry : angle 0.49273 (22461) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.38845 ( 2) hydrogen bonds : bond 0.03828 ( 746) hydrogen bonds : angle 4.55450 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8714 (tt0) cc_final: 0.7902 (tm-30) REVERT: A 108 ASP cc_start: 0.9096 (p0) cc_final: 0.8782 (p0) REVERT: A 123 GLU cc_start: 0.7451 (mp0) cc_final: 0.6887 (mp0) REVERT: A 321 ARG cc_start: 0.7932 (ptt90) cc_final: 0.7615 (ptt90) REVERT: B 223 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8842 (tp-100) REVERT: C 194 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8070 (mpp) REVERT: D 121 ASP cc_start: 0.8438 (t0) cc_final: 0.8209 (m-30) REVERT: E 50 MET cc_start: 0.9004 (ttt) cc_final: 0.8663 (mtp) REVERT: F 58 GLN cc_start: 0.8622 (mp10) cc_final: 0.8230 (pm20) REVERT: F 69 GLN cc_start: 0.9566 (tt0) cc_final: 0.9303 (tm-30) outliers start: 28 outliers final: 17 residues processed: 121 average time/residue: 1.4273 time to fit residues: 191.5022 Evaluate side-chains 113 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.126271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072017 restraints weight = 86914.353| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.04 r_work: 0.2831 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16542 Z= 0.165 Angle : 0.489 7.609 22463 Z= 0.257 Chirality : 0.041 0.142 2473 Planarity : 0.004 0.094 2977 Dihedral : 4.125 70.522 2277 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Rotamer: Outliers : 1.21 % Allowed : 19.37 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 2071 helix: 2.36 (0.21), residues: 587 sheet: -0.52 (0.21), residues: 570 loop : -0.65 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG A 76 TYR 0.017 0.001 TYR C 197 PHE 0.012 0.001 PHE A 67 TRP 0.011 0.001 TRP B 143 HIS 0.002 0.000 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00373 (16541) covalent geometry : angle 0.48937 (22461) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.29487 ( 2) hydrogen bonds : bond 0.03723 ( 746) hydrogen bonds : angle 4.51150 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8808 (tt0) cc_final: 0.7890 (tm-30) REVERT: A 108 ASP cc_start: 0.9122 (p0) cc_final: 0.8826 (p0) REVERT: A 123 GLU cc_start: 0.7427 (mp0) cc_final: 0.6878 (mp0) REVERT: A 321 ARG cc_start: 0.7948 (ptt90) cc_final: 0.7634 (ptt90) REVERT: A 534 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8531 (m110) REVERT: B 31 LYS cc_start: 0.8167 (tptt) cc_final: 0.7605 (tptp) REVERT: B 223 GLN cc_start: 0.9091 (tp-100) cc_final: 0.8818 (tp-100) REVERT: B 355 ARG cc_start: 0.8476 (ptt-90) cc_final: 0.8146 (pmm-80) REVERT: C 194 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8052 (mpp) REVERT: C 228 MET cc_start: 0.4414 (ptp) cc_final: 0.4063 (ttp) REVERT: D 121 ASP cc_start: 0.8434 (t0) cc_final: 0.8088 (m-30) REVERT: E 50 MET cc_start: 0.8989 (ttt) cc_final: 0.8654 (mtp) REVERT: F 58 GLN cc_start: 0.8573 (mp10) cc_final: 0.8188 (pm20) REVERT: F 69 GLN cc_start: 0.9561 (tt0) cc_final: 0.9300 (tm-30) outliers start: 21 outliers final: 12 residues processed: 112 average time/residue: 1.4802 time to fit residues: 183.6364 Evaluate side-chains 108 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 200 optimal weight: 50.0000 chunk 24 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.125962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.072473 restraints weight = 86551.842| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.97 r_work: 0.2821 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16542 Z= 0.204 Angle : 0.502 7.855 22463 Z= 0.265 Chirality : 0.041 0.146 2473 Planarity : 0.004 0.044 2977 Dihedral : 4.168 69.663 2277 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 1.44 % Allowed : 19.02 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 2071 helix: 2.31 (0.21), residues: 587 sheet: -0.58 (0.21), residues: 575 loop : -0.66 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.017 0.001 TYR C 197 PHE 0.010 0.001 PHE A 791 TRP 0.011 0.001 TRP B 143 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00463 (16541) covalent geometry : angle 0.50238 (22461) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.46442 ( 2) hydrogen bonds : bond 0.03874 ( 746) hydrogen bonds : angle 4.56033 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8770 (tt0) cc_final: 0.8159 (tm-30) REVERT: A 108 ASP cc_start: 0.9124 (p0) cc_final: 0.8838 (p0) REVERT: A 123 GLU cc_start: 0.7432 (mp0) cc_final: 0.6883 (mp0) REVERT: A 321 ARG cc_start: 0.8032 (ptt90) cc_final: 0.7686 (ptt90) REVERT: A 534 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8509 (m110) REVERT: B 31 LYS cc_start: 0.8179 (tptt) cc_final: 0.7662 (tptp) REVERT: B 223 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8802 (tp-100) REVERT: B 355 ARG cc_start: 0.8529 (ptt-90) cc_final: 0.8198 (pmm-80) REVERT: C 194 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8019 (mpp) REVERT: D 121 ASP cc_start: 0.8435 (t0) cc_final: 0.8217 (m-30) REVERT: E 50 MET cc_start: 0.9032 (ttt) cc_final: 0.8703 (mtp) REVERT: F 58 GLN cc_start: 0.8530 (mp10) cc_final: 0.8166 (pm20) REVERT: F 69 GLN cc_start: 0.9557 (tt0) cc_final: 0.9292 (tm-30) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 1.4243 time to fit residues: 180.8110 Evaluate side-chains 113 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 4 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.125126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.071215 restraints weight = 87342.391| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.03 r_work: 0.2813 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16542 Z= 0.199 Angle : 0.502 8.136 22463 Z= 0.264 Chirality : 0.041 0.144 2473 Planarity : 0.004 0.045 2977 Dihedral : 4.166 69.147 2277 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 1.26 % Allowed : 19.25 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 2071 helix: 2.32 (0.21), residues: 588 sheet: -0.59 (0.21), residues: 575 loop : -0.67 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.017 0.001 TYR C 197 PHE 0.009 0.001 PHE A 67 TRP 0.011 0.001 TRP B 143 HIS 0.002 0.000 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00449 (16541) covalent geometry : angle 0.50186 (22461) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.35991 ( 2) hydrogen bonds : bond 0.03812 ( 746) hydrogen bonds : angle 4.54709 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8761 (tt0) cc_final: 0.8095 (tm-30) REVERT: A 108 ASP cc_start: 0.9133 (p0) cc_final: 0.8856 (p0) REVERT: A 123 GLU cc_start: 0.7448 (mp0) cc_final: 0.6901 (mp0) REVERT: A 321 ARG cc_start: 0.8036 (ptt90) cc_final: 0.7698 (ptt90) REVERT: B 31 LYS cc_start: 0.8212 (tptt) cc_final: 0.7711 (tptp) REVERT: B 223 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8799 (tp-100) REVERT: B 355 ARG cc_start: 0.8543 (ptt-90) cc_final: 0.8209 (pmm-80) REVERT: C 194 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8007 (mpp) REVERT: C 228 MET cc_start: 0.4581 (ptp) cc_final: 0.4247 (ttp) REVERT: C 276 MET cc_start: 0.5806 (ttp) cc_final: 0.5067 (ptm) REVERT: D 121 ASP cc_start: 0.8428 (t0) cc_final: 0.8019 (m-30) REVERT: E 50 MET cc_start: 0.9025 (ttt) cc_final: 0.8692 (mtp) REVERT: F 69 GLN cc_start: 0.9560 (tt0) cc_final: 0.9292 (tm-30) outliers start: 22 outliers final: 18 residues processed: 114 average time/residue: 1.5485 time to fit residues: 194.7721 Evaluate side-chains 113 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 136 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 198 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 199 optimal weight: 50.0000 chunk 96 optimal weight: 0.0270 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.125813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.071947 restraints weight = 87029.661| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.02 r_work: 0.2830 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16542 Z= 0.143 Angle : 0.489 8.863 22463 Z= 0.255 Chirality : 0.041 0.145 2473 Planarity : 0.004 0.083 2977 Dihedral : 4.098 68.693 2277 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 1.09 % Allowed : 19.60 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 2071 helix: 2.41 (0.21), residues: 587 sheet: -0.54 (0.21), residues: 576 loop : -0.61 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 64 TYR 0.017 0.001 TYR C 197 PHE 0.008 0.001 PHE A 478 TRP 0.011 0.001 TRP B 143 HIS 0.001 0.000 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00321 (16541) covalent geometry : angle 0.48952 (22461) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.23260 ( 2) hydrogen bonds : bond 0.03627 ( 746) hydrogen bonds : angle 4.47698 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15613.51 seconds wall clock time: 263 minutes 41.52 seconds (15821.52 seconds total)