Starting phenix.real_space_refine on Thu Nov 20 08:12:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg6_52127/11_2025/9hg6_52127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg6_52127/11_2025/9hg6_52127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hg6_52127/11_2025/9hg6_52127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg6_52127/11_2025/9hg6_52127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hg6_52127/11_2025/9hg6_52127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg6_52127/11_2025/9hg6_52127.map" } resolution = 2.73 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= 0.008 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: 5.39, per 1000 atoms: 0.17 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: 2.87 Conformation dependent library (CDL) restraints added in 894.3 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: 0.95 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: 3.542A 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: 4.068A 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: 3.618A pdb=" N LYS C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.511A pdb=" N TYR C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.505A 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: 3.920A 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: 3.768A pdb=" N GLN F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 4.054A 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: 4.094A pdb=" N ARG F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.890A pdb=" N GLN F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 4.603A 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: 7.555A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.000A 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: 4.310A 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: 6.599A 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: 7.147A 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: 7.555A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.000A 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: 4.310A 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: 6.599A 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: 7.147A 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: 7.602A 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: 7.194A 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: 4.352A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.320A 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: 3.660A 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: 5.284A 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: 5.275A 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: 6.214A 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: 6.802A 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: 4.494A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.816A 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: 6.961A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.850A 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: 6.484A 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: 7.769A 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: 6.634A 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: 6.233A 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: 4.010A pdb=" N ASP C 268 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.599A 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: 5.370A 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: 8.27 Time building geometry restraints manager: 4.01 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: 12 1.23 - 1.42: 7039 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 0.889 0.071 2.00e-02 2.50e+03 1.27e+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 8.97e+00 bond pdb=" N ARG D 61 " pdb=" H ARG D 61 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" N TYR D 62 " pdb=" H TYR D 62 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.64e+00 ... (remaining 32291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 57924 2.94 - 5.87: 197 5.87 - 8.81: 12 8.81 - 11.75: 3 11.75 - 14.69: 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 121.17 135.86 -14.69 1.62e+00 3.81e-01 8.22e+01 angle pdb=" N LEU F 426 " pdb=" CA LEU F 426 " pdb=" C LEU F 426 " ideal model delta sigma weight residual 112.94 105.88 7.06 1.41e+00 5.03e-01 2.51e+01 angle pdb=" N MET F 414 " pdb=" CA MET F 414 " pdb=" C MET F 414 " ideal model delta sigma weight residual 112.89 107.57 5.32 1.24e+00 6.50e-01 1.84e+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 1.78e+01 angle pdb=" N GLN F 155 " pdb=" CA GLN F 155 " pdb=" C GLN F 155 " ideal model delta sigma weight residual 111.33 106.51 4.82 1.21e+00 6.83e-01 1.59e+01 ... (remaining 58132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13462 17.94 - 35.89: 1219 35.89 - 53.83: 397 53.83 - 71.77: 145 71.77 - 89.71: 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 -86.82 56.82 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 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+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 90.00 134.40 -44.40 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 15262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2073 0.053 - 0.105: 310 0.105 - 0.158: 85 0.158 - 0.211: 4 0.211 - 0.264: 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 1.74e+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 1.01e+00 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 8.66e-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 4.51e+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 3.50e-02 1.83e+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 " 0.002 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 3.48e-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: 54813 2.73 - 3.35: 90912 3.35 - 3.98: 116602 3.98 - 4.60: 182223 Nonbonded interactions: 445165 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 1.483 2.450 nonbonded pdb=" HZ1 LYS C 32 " pdb=" O GLN D 44 " model vdw 1.502 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 445160 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.450 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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= 0.165 Angle : 0.591 14.686 22463 Z= 0.334 Chirality : 0.043 0.264 2473 Planarity : 0.005 0.150 2977 Dihedral : 16.430 89.543 6051 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % 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 0.00334 (16541) covalent geometry : angle 0.59076 (22461) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.49399 ( 2) hydrogen bonds : bond 0.14319 ( 746) hydrogen bonds : angle 6.33592 ( 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 145 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.885 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: A 321 ARG cc_start: 0.7705 (ptt90) cc_final: 0.7411 (ptt90) REVERT: A 777 MET cc_start: 0.9206 (mmt) cc_final: 0.8763 (mmt) REVERT: C 31 TYR cc_start: 0.8060 (p90) cc_final: 0.7741 (p90) REVERT: C 229 ASP cc_start: 0.8014 (m-30) cc_final: 0.7417 (t0) REVERT: D 232 GLU cc_start: 0.8639 (tp30) cc_final: 0.8419 (mm-30) REVERT: F 87 MET cc_start: 0.8740 (mtm) cc_final: 0.8536 (mtm) REVERT: F 128 TYR cc_start: 0.8273 (t80) cc_final: 0.7818 (t80) REVERT: F 136 MET cc_start: 0.8238 (mmt) cc_final: 0.7958 (mmt) outliers start: 21 outliers final: 13 residues processed: 142 average time/residue: 1.4488 time to fit residues: 227.0170 Evaluate side-chains 117 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 582 ASP 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 C residue 69 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain F residue 102 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 50.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.131856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.075663 restraints weight = 89280.541| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.21 r_work: 0.2809 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16542 Z= 0.182 Angle : 0.516 6.519 22463 Z= 0.273 Chirality : 0.041 0.159 2473 Planarity : 0.004 0.067 2977 Dihedral : 5.322 116.659 2293 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 1.38 % Allowed : 18.74 % Favored : 79.89 % 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: 0.32 (0.19), residues: 2071 helix: 2.04 (0.21), residues: 586 sheet: -0.30 (0.21), residues: 557 loop : -0.60 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 355 TYR 0.014 0.001 TYR A 255 PHE 0.012 0.001 PHE A 428 TRP 0.010 0.001 TRP F 413 HIS 0.004 0.001 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00405 (16541) covalent geometry : angle 0.51553 (22461) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.64843 ( 2) hydrogen bonds : bond 0.04265 ( 746) hydrogen bonds : angle 5.06020 ( 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 133 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.896 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 30 HIS cc_start: 0.8104 (m170) cc_final: 0.7822 (m-70) REVERT: A 582 ASP cc_start: 0.9133 (t0) cc_final: 0.8911 (OUTLIER) REVERT: A 777 MET cc_start: 0.9220 (mmt) cc_final: 0.8805 (mmt) REVERT: C 201 MET cc_start: 0.8838 (mmm) cc_final: 0.8531 (mmt) REVERT: C 311 ASP cc_start: 0.8408 (p0) cc_final: 0.8075 (p0) REVERT: C 312 ASN cc_start: 0.8804 (m110) cc_final: 0.8372 (t0) REVERT: D 56 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8484 (mt-10) REVERT: F 128 TYR cc_start: 0.8298 (t80) cc_final: 0.7938 (t80) REVERT: F 136 MET cc_start: 0.8368 (mmt) cc_final: 0.8039 (mmt) outliers start: 24 outliers final: 11 residues processed: 130 average time/residue: 1.3108 time to fit residues: 191.3367 Evaluate side-chains 117 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 205 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 114 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 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 = 0.4017 r_free = 0.4017 target = 0.131991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.075819 restraints weight = 89023.058| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.22 r_work: 0.2825 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16542 Z= 0.144 Angle : 0.482 6.305 22463 Z= 0.253 Chirality : 0.041 0.145 2473 Planarity : 0.003 0.060 2977 Dihedral : 4.415 86.596 2283 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.15 % Allowed : 18.97 % Favored : 79.89 % 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: 0.42 (0.19), residues: 2071 helix: 2.18 (0.21), residues: 590 sheet: -0.28 (0.21), residues: 558 loop : -0.58 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 49 TYR 0.017 0.001 TYR C 197 PHE 0.008 0.001 PHE C 318 TRP 0.009 0.001 TRP B 143 HIS 0.003 0.001 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00320 (16541) covalent geometry : angle 0.48159 (22461) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.50704 ( 2) hydrogen bonds : bond 0.03968 ( 746) hydrogen bonds : angle 4.77685 ( 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 133 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.919 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 30 HIS cc_start: 0.8050 (m170) cc_final: 0.7753 (m-70) REVERT: A 582 ASP cc_start: 0.8933 (t0) cc_final: 0.8716 (OUTLIER) REVERT: A 777 MET cc_start: 0.9142 (mmt) cc_final: 0.8715 (mmt) REVERT: C 311 ASP cc_start: 0.8406 (p0) cc_final: 0.7907 (p0) REVERT: C 312 ASN cc_start: 0.8870 (m110) cc_final: 0.8396 (t0) REVERT: D 232 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8386 (mm-30) REVERT: F 128 TYR cc_start: 0.8290 (t80) cc_final: 0.7905 (t80) REVERT: F 136 MET cc_start: 0.8412 (mmt) cc_final: 0.8145 (mmt) outliers start: 20 outliers final: 9 residues processed: 127 average time/residue: 1.3405 time to fit residues: 190.7523 Evaluate side-chains 115 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 187 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 123 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN F 78 GLN F 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.129788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073738 restraints weight = 89348.482| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.21 r_work: 0.2748 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16542 Z= 0.254 Angle : 0.521 5.995 22463 Z= 0.277 Chirality : 0.042 0.145 2473 Planarity : 0.004 0.060 2977 Dihedral : 4.445 77.800 2280 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.78 % Allowed : 18.33 % Favored : 79.89 % 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: 2.14 (0.21), residues: 588 sheet: -0.35 (0.22), residues: 562 loop : -0.72 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 49 TYR 0.018 0.001 TYR C 197 PHE 0.012 0.001 PHE A 428 TRP 0.010 0.001 TRP B 143 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00577 (16541) covalent geometry : angle 0.52100 (22461) SS BOND : bond 0.00360 ( 1) SS BOND : angle 0.79304 ( 2) hydrogen bonds : bond 0.04187 ( 746) hydrogen bonds : angle 4.79612 ( 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 140 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.913 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 30 HIS cc_start: 0.8062 (m170) cc_final: 0.7738 (m-70) REVERT: A 292 PRO cc_start: 0.8402 (Cg_exo) cc_final: 0.8071 (Cg_endo) REVERT: A 582 ASP cc_start: 0.9024 (t0) cc_final: 0.8820 (t0) REVERT: C 311 ASP cc_start: 0.8493 (p0) cc_final: 0.7950 (p0) REVERT: C 312 ASN cc_start: 0.8896 (m110) cc_final: 0.8398 (t0) REVERT: D 44 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8794 (mt0) REVERT: D 56 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8258 (mt-10) REVERT: D 232 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8391 (mm-30) REVERT: F 128 TYR cc_start: 0.8308 (t80) cc_final: 0.7933 (t80) REVERT: F 136 MET cc_start: 0.8431 (mmt) cc_final: 0.8163 (mmt) outliers start: 31 outliers final: 11 residues processed: 134 average time/residue: 1.3738 time to fit residues: 205.7366 Evaluate side-chains 123 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 127 optimal weight: 40.0000 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 0.0570 chunk 201 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.130958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075055 restraints weight = 89334.608| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.22 r_work: 0.2777 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16542 Z= 0.143 Angle : 0.479 6.332 22463 Z= 0.252 Chirality : 0.041 0.144 2473 Planarity : 0.003 0.051 2977 Dihedral : 4.288 72.809 2280 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 1.32 % Allowed : 18.33 % Favored : 80.34 % 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: 0.39 (0.19), residues: 2071 helix: 2.30 (0.21), residues: 589 sheet: -0.31 (0.22), residues: 563 loop : -0.68 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 355 TYR 0.019 0.001 TYR C 197 PHE 0.008 0.001 PHE A 791 TRP 0.010 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00314 (16541) covalent geometry : angle 0.47879 (22461) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.37215 ( 2) hydrogen bonds : bond 0.03767 ( 746) hydrogen bonds : angle 4.61075 ( 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 140 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.926 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 30 HIS cc_start: 0.8042 (m170) cc_final: 0.7715 (m-70) REVERT: A 292 PRO cc_start: 0.8431 (Cg_exo) cc_final: 0.8106 (Cg_endo) REVERT: A 582 ASP cc_start: 0.8976 (t0) cc_final: 0.8764 (OUTLIER) REVERT: C 112 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7602 (mtp85) REVERT: C 271 ARG cc_start: 0.6758 (ttp-170) cc_final: 0.6168 (ttp80) REVERT: C 311 ASP cc_start: 0.8493 (p0) cc_final: 0.7913 (p0) REVERT: C 312 ASN cc_start: 0.8933 (m110) cc_final: 0.8429 (t0) REVERT: D 232 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: E 51 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8418 (p) REVERT: F 128 TYR cc_start: 0.8289 (t80) cc_final: 0.7903 (t80) outliers start: 23 outliers final: 14 residues processed: 134 average time/residue: 1.4968 time to fit residues: 222.3915 Evaluate side-chains 126 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 116 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 165 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 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 = 0.4027 r_free = 0.4027 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.085049 restraints weight = 88947.195| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.12 r_work: 0.2838 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16542 Z= 0.111 Angle : 0.468 6.195 22463 Z= 0.244 Chirality : 0.040 0.144 2473 Planarity : 0.003 0.057 2977 Dihedral : 4.149 70.878 2280 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Rotamer: Outliers : 1.21 % Allowed : 18.56 % Favored : 80.23 % 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: 0.52 (0.19), residues: 2071 helix: 2.43 (0.21), residues: 589 sheet: -0.26 (0.21), residues: 570 loop : -0.61 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 355 TYR 0.017 0.001 TYR C 197 PHE 0.012 0.001 PHE A 428 TRP 0.009 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00245 (16541) covalent geometry : angle 0.46794 (22461) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.23956 ( 2) hydrogen bonds : bond 0.03518 ( 746) hydrogen bonds : angle 4.46292 ( 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 137 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.947 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 30 HIS cc_start: 0.8113 (m170) cc_final: 0.7783 (m-70) REVERT: A 292 PRO cc_start: 0.8448 (Cg_exo) cc_final: 0.8118 (Cg_endo) REVERT: A 582 ASP cc_start: 0.9083 (t0) cc_final: 0.8871 (OUTLIER) REVERT: C 271 ARG cc_start: 0.6903 (ttp-170) cc_final: 0.6247 (ttp80) REVERT: C 312 ASN cc_start: 0.8944 (m110) cc_final: 0.8550 (t0) REVERT: D 232 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8437 (mm-30) REVERT: F 109 MET cc_start: 0.2516 (mtt) cc_final: 0.1887 (mtp) REVERT: F 128 TYR cc_start: 0.8286 (t80) cc_final: 0.7881 (t80) outliers start: 21 outliers final: 17 residues processed: 131 average time/residue: 1.4927 time to fit residues: 216.3913 Evaluate side-chains 127 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 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: 2.9990 chunk 162 optimal weight: 1.9990 chunk 146 optimal weight: 50.0000 chunk 139 optimal weight: 10.0000 chunk 119 optimal weight: 0.0570 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 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 = 0.4016 r_free = 0.4016 target = 0.138523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082594 restraints weight = 86467.221| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.46 r_work: 0.2788 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1873 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= 0.178 Angle : 0.487 6.465 22463 Z= 0.256 Chirality : 0.041 0.142 2473 Planarity : 0.004 0.064 2977 Dihedral : 4.165 69.007 2279 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 1.61 % Allowed : 18.51 % Favored : 79.89 % 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: 0.45 (0.19), residues: 2071 helix: 2.38 (0.21), residues: 588 sheet: -0.28 (0.22), residues: 570 loop : -0.66 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 355 TYR 0.016 0.001 TYR C 197 PHE 0.009 0.001 PHE A 791 TRP 0.009 0.001 TRP B 143 HIS 0.002 0.000 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00401 (16541) covalent geometry : angle 0.48737 (22461) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.38386 ( 2) hydrogen bonds : bond 0.03734 ( 746) hydrogen bonds : angle 4.50678 ( 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 140 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.147 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 30 HIS cc_start: 0.8099 (m170) cc_final: 0.7788 (m-70) REVERT: A 292 PRO cc_start: 0.8480 (Cg_exo) cc_final: 0.8161 (Cg_endo) REVERT: A 582 ASP cc_start: 0.8971 (t0) cc_final: 0.8760 (OUTLIER) REVERT: C 229 ASP cc_start: 0.7241 (m-30) cc_final: 0.6823 (t0) REVERT: C 312 ASN cc_start: 0.8949 (m110) cc_final: 0.8531 (t0) REVERT: D 44 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8685 (mt0) REVERT: D 232 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8403 (mm-30) REVERT: E 51 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8435 (p) REVERT: F 109 MET cc_start: 0.2524 (mtt) cc_final: 0.1855 (mtp) REVERT: F 128 TYR cc_start: 0.8337 (t80) cc_final: 0.7932 (t80) outliers start: 28 outliers final: 20 residues processed: 134 average time/residue: 1.4835 time to fit residues: 220.0141 Evaluate side-chains 131 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 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 = 0.4006 r_free = 0.4006 target = 0.131018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.075556 restraints weight = 89139.147| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.16 r_work: 0.2793 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16542 Z= 0.159 Angle : 0.484 6.408 22463 Z= 0.253 Chirality : 0.041 0.143 2473 Planarity : 0.004 0.062 2977 Dihedral : 4.165 68.986 2279 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 1.55 % Allowed : 18.56 % Favored : 79.89 % 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: 0.47 (0.19), residues: 2071 helix: 2.42 (0.21), residues: 588 sheet: -0.25 (0.22), residues: 570 loop : -0.68 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 355 TYR 0.018 0.001 TYR C 197 PHE 0.011 0.001 PHE A 428 TRP 0.010 0.001 TRP B 143 HIS 0.002 0.000 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00356 (16541) covalent geometry : angle 0.48376 (22461) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.32245 ( 2) hydrogen bonds : bond 0.03664 ( 746) hydrogen bonds : angle 4.46475 ( 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 140 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.954 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 30 HIS cc_start: 0.8120 (m170) cc_final: 0.7798 (m-70) REVERT: A 292 PRO cc_start: 0.8473 (Cg_exo) cc_final: 0.8155 (Cg_endo) REVERT: A 582 ASP cc_start: 0.9104 (t0) cc_final: 0.8891 (OUTLIER) REVERT: C 229 ASP cc_start: 0.7424 (m-30) cc_final: 0.6945 (t0) REVERT: C 264 MET cc_start: 0.5071 (mmm) cc_final: 0.4769 (mmm) REVERT: C 271 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6316 (ttp80) REVERT: C 312 ASN cc_start: 0.8933 (m110) cc_final: 0.8541 (t0) REVERT: D 232 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8481 (mm-30) REVERT: E 51 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8429 (p) REVERT: F 109 MET cc_start: 0.2700 (mtt) cc_final: 0.1960 (mtp) REVERT: F 128 TYR cc_start: 0.8310 (t80) cc_final: 0.7865 (t80) outliers start: 27 outliers final: 20 residues processed: 136 average time/residue: 1.4489 time to fit residues: 218.5023 Evaluate side-chains 133 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 200 optimal weight: 40.0000 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 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 = 0.4023 r_free = 0.4023 target = 0.131406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.076410 restraints weight = 88091.968| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.51 r_work: 0.2788 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16542 Z= 0.130 Angle : 0.477 6.716 22463 Z= 0.249 Chirality : 0.041 0.143 2473 Planarity : 0.004 0.080 2977 Dihedral : 4.112 69.432 2279 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 1.26 % Allowed : 19.08 % Favored : 79.66 % 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: 0.54 (0.19), residues: 2071 helix: 2.47 (0.21), residues: 589 sheet: -0.23 (0.22), residues: 570 loop : -0.63 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 355 TYR 0.018 0.001 TYR C 197 PHE 0.007 0.001 PHE C 318 TRP 0.009 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00291 (16541) covalent geometry : angle 0.47691 (22461) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.23956 ( 2) hydrogen bonds : bond 0.03540 ( 746) hydrogen bonds : angle 4.40416 ( 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 137 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.914 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 30 HIS cc_start: 0.8112 (m170) cc_final: 0.7799 (m-70) REVERT: A 292 PRO cc_start: 0.8462 (Cg_exo) cc_final: 0.8155 (Cg_endo) REVERT: A 582 ASP cc_start: 0.8973 (t0) cc_final: 0.8770 (OUTLIER) REVERT: C 229 ASP cc_start: 0.7323 (m-30) cc_final: 0.6874 (t0) REVERT: C 312 ASN cc_start: 0.8963 (m110) cc_final: 0.8542 (t0) REVERT: D 232 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8393 (mm-30) REVERT: E 51 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8453 (p) REVERT: F 109 MET cc_start: 0.2748 (mtt) cc_final: 0.2043 (mtp) REVERT: F 128 TYR cc_start: 0.8273 (t80) cc_final: 0.7887 (t80) outliers start: 22 outliers final: 20 residues processed: 134 average time/residue: 1.5179 time to fit residues: 225.2568 Evaluate side-chains 132 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 658 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 4 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.131511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.075245 restraints weight = 88739.916| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.43 r_work: 0.2817 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16542 Z= 0.119 Angle : 0.489 10.408 22463 Z= 0.253 Chirality : 0.041 0.143 2473 Planarity : 0.004 0.081 2977 Dihedral : 4.069 69.457 2279 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 1.15 % Allowed : 19.20 % Favored : 79.66 % 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: 0.59 (0.19), residues: 2071 helix: 2.51 (0.21), residues: 589 sheet: -0.19 (0.22), residues: 570 loop : -0.60 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 355 TYR 0.018 0.001 TYR C 197 PHE 0.010 0.001 PHE A 428 TRP 0.010 0.001 TRP B 183 HIS 0.005 0.000 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00268 (16541) covalent geometry : angle 0.48891 (22461) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.21429 ( 2) hydrogen bonds : bond 0.03477 ( 746) hydrogen bonds : angle 4.36893 ( 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 132 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.927 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 30 HIS cc_start: 0.8114 (m170) cc_final: 0.7801 (m-70) REVERT: A 292 PRO cc_start: 0.8504 (Cg_exo) cc_final: 0.8200 (Cg_endo) REVERT: C 229 ASP cc_start: 0.7435 (m-30) cc_final: 0.6954 (t0) REVERT: C 312 ASN cc_start: 0.8952 (m110) cc_final: 0.8548 (t0) REVERT: D 232 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8388 (mm-30) REVERT: E 51 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8394 (p) REVERT: F 109 MET cc_start: 0.2470 (mtt) cc_final: 0.1778 (mtp) REVERT: F 128 TYR cc_start: 0.8299 (t80) cc_final: 0.7847 (t80) outliers start: 20 outliers final: 19 residues processed: 130 average time/residue: 1.5169 time to fit residues: 218.1710 Evaluate side-chains 131 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 136 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 160 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 198 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN C 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.130457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074927 restraints weight = 88387.871| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.33 r_work: 0.2806 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2184 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= 0.180 Angle : 0.504 10.093 22463 Z= 0.261 Chirality : 0.041 0.142 2473 Planarity : 0.004 0.080 2977 Dihedral : 4.105 68.903 2279 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Rotamer: Outliers : 1.38 % Allowed : 19.02 % Favored : 79.60 % 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: 0.50 (0.19), residues: 2071 helix: 2.46 (0.21), residues: 588 sheet: -0.24 (0.22), residues: 582 loop : -0.67 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 355 TYR 0.017 0.001 TYR C 197 PHE 0.009 0.001 PHE A 791 TRP 0.009 0.001 TRP B 143 HIS 0.003 0.000 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00405 (16541) covalent geometry : angle 0.50353 (22461) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.33146 ( 2) hydrogen bonds : bond 0.03633 ( 746) hydrogen bonds : angle 4.42706 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14360.79 seconds wall clock time: 242 minutes 49.97 seconds (14569.97 seconds total)