Starting phenix.real_space_refine on Thu May 29 12:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg5_52128/05_2025/9hg5_52128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg5_52128/05_2025/9hg5_52128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hg5_52128/05_2025/9hg5_52128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg5_52128/05_2025/9hg5_52128.map" model { file = "/net/cci-nas-00/data/ceres_data/9hg5_52128/05_2025/9hg5_52128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg5_52128/05_2025/9hg5_52128.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 10153 2.51 5 N 2816 2.21 5 O 3204 1.98 5 H 15755 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.76, per 1000 atoms: 0.46 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: 8.55 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.543A pdb=" N SER A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.069A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.753A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.637A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.907A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.611A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.677A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.619A pdb=" N LYS C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.512A pdb=" N TYR C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.504A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.917A pdb=" N LYS C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 224 Processing helix chain 'C' and resid 247 through 262 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 284 through 291 Processing helix chain 'C' and resid 327 through 336 removed outlier: 3.919A pdb=" N ALA C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.611A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.226A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.630A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.767A pdb=" N GLN F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 60 Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 111 through 118 Processing helix chain 'F' and resid 125 through 149 removed outlier: 4.093A pdb=" N ARG F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.889A pdb=" N GLN F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 208 Processing helix chain 'F' and resid 211 through 220 Processing helix chain 'F' and resid 222 through 228 removed outlier: 4.253A pdb=" N LEU F 226 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 239 Processing helix chain 'F' and resid 240 through 247 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 393 through 421 removed outlier: 3.566A pdb=" N ARG F 418 " --> pdb=" O MET F 414 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.682A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG A 79 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N GLU A 73 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ALA F 29 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 75 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS F 27 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.682A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG A 79 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N GLU A 73 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ALA F 29 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 75 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS F 27 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 5.880A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 183 removed outlier: 6.910A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.103A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.378A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.103A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.378A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.603A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 426 removed outlier: 3.659A pdb=" N THR A 467 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP A 493 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 673 removed outlier: 5.274A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 46 removed outlier: 4.429A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.808A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.213A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.502A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.403A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.779A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.960A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.927A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.480A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR C 157 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN C 147 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY C 159 " --> pdb=" O TRP C 145 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP C 145 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 133 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP C 144 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 131 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AC3, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 269 removed outlier: 4.009A pdb=" N ASP C 268 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR C 303 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 304 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'F' and resid 230 through 234 removed outlier: 6.151A pdb=" N LEU F 176 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP F 233 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU F 174 " --> pdb=" O TRP F 233 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 272 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER F 177 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL F 270 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE F 179 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU F 268 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE F 181 " --> pdb=" O HIS F 266 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS F 266 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG F 260 " --> pdb=" O GLY F 264 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU F 268 " --> pdb=" O VAL F 256 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.47 Time building geometry restraints manager: 10.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15754 1.03 - 1.23: 11 1.23 - 1.42: 7040 1.42 - 1.62: 9390 1.62 - 1.81: 101 Bond restraints: 32296 Sorted by residual: bond pdb=" N ALA A 21 " pdb=" H1 ALA A 21 " ideal model delta sigma weight residual 0.960 0.888 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N CYS C 25 " pdb=" H1 CYS C 25 " ideal model delta sigma weight residual 0.960 0.890 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N VAL F 157 " pdb=" CA VAL F 157 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.81e+00 bond pdb=" N ARG D 61 " pdb=" H ARG D 61 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.28e+00 bond pdb=" N PHE D 64 " pdb=" H PHE D 64 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.68e+00 ... (remaining 32291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 57928 2.94 - 5.88: 193 5.88 - 8.82: 12 8.82 - 11.76: 3 11.76 - 14.70: 1 Bond angle restraints: 58137 Sorted by residual: angle pdb=" C SER C 294 " pdb=" N ASP C 295 " pdb=" CA ASP C 295 " ideal model delta sigma weight residual 121.17 135.87 -14.70 1.62e+00 3.81e-01 8.23e+01 angle pdb=" N LEU F 426 " pdb=" CA LEU F 426 " pdb=" C LEU F 426 " ideal model delta sigma weight residual 112.94 105.89 7.05 1.41e+00 5.03e-01 2.50e+01 angle pdb=" N MET F 414 " pdb=" CA MET F 414 " pdb=" C MET F 414 " ideal model delta sigma weight residual 112.89 107.60 5.29 1.24e+00 6.50e-01 1.82e+01 angle pdb=" N GLN F 415 " pdb=" CA GLN F 415 " pdb=" C GLN F 415 " ideal model delta sigma weight residual 113.97 108.58 5.39 1.28e+00 6.10e-01 1.77e+01 angle pdb=" N GLN F 155 " pdb=" CA GLN F 155 " pdb=" C GLN F 155 " ideal model delta sigma weight residual 111.33 106.54 4.79 1.21e+00 6.83e-01 1.57e+01 ... (remaining 58132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13464 17.93 - 35.87: 1217 35.87 - 53.80: 396 53.80 - 71.74: 146 71.74 - 89.67: 42 Dihedral angle restraints: 15265 sinusoidal: 8315 harmonic: 6950 Sorted by residual: dihedral pdb=" CA ASP B 363 " pdb=" CB ASP B 363 " pdb=" CG ASP B 363 " pdb=" OD1 ASP B 363 " ideal model delta sinusoidal sigma weight residual -30.00 -86.80 56.80 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA GLU B 370 " pdb=" C GLU B 370 " pdb=" N PRO B 371 " pdb=" CA PRO B 371 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CG ARG C 83 " pdb=" CD ARG C 83 " pdb=" NE ARG C 83 " pdb=" CZ ARG C 83 " ideal model delta sinusoidal sigma weight residual 90.00 134.41 -44.41 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 15262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2061 0.052 - 0.104: 320 0.104 - 0.156: 87 0.156 - 0.209: 4 0.209 - 0.261: 1 Chirality restraints: 2473 Sorted by residual: chirality pdb=" CA GLN F 98 " pdb=" N GLN F 98 " pdb=" C GLN F 98 " pdb=" CB GLN F 98 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA GLN B 225 " pdb=" N GLN B 225 " pdb=" C GLN B 225 " pdb=" CB GLN B 225 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA VAL F 256 " pdb=" N VAL F 256 " pdb=" C VAL F 256 " pdb=" CB VAL F 256 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 2470 not shown) Planarity restraints: 4974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 61 " 0.490 9.50e-02 1.11e+02 2.13e-01 4.52e+02 pdb=" NE ARG D 61 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG D 61 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 61 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 61 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG D 61 " -0.260 2.00e-02 2.50e+03 pdb="HH12 ARG D 61 " 0.276 2.00e-02 2.50e+03 pdb="HH21 ARG D 61 " 0.036 2.00e-02 2.50e+03 pdb="HH22 ARG D 61 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 155 " -0.033 2.00e-02 2.50e+03 3.51e-02 1.84e+01 pdb=" CD GLN F 155 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN F 155 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 GLN F 155 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN F 155 " 0.050 2.00e-02 2.50e+03 pdb="HE22 GLN F 155 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 226 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C MET B 226 " 0.060 2.00e-02 2.50e+03 pdb=" O MET B 226 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 227 " -0.021 2.00e-02 2.50e+03 ... (remaining 4971 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 615 2.10 - 2.73: 54814 2.73 - 3.35: 90906 3.35 - 3.98: 116609 3.98 - 4.60: 182222 Nonbonded interactions: 445166 Sorted by model distance: nonbonded pdb=" O LEU C 310 " pdb=" H ASN C 312 " model vdw 1.475 2.450 nonbonded pdb=" OE1 GLN E 53 " pdb=" H GLN E 53 " model vdw 1.484 2.450 nonbonded pdb=" HZ1 LYS C 32 " pdb=" O GLN D 44 " model vdw 1.503 2.450 nonbonded pdb="HH12 ARG A 526 " pdb=" OG1 THR A 577 " model vdw 1.580 2.450 nonbonded pdb=" O LEU A 66 " pdb=" HG1 THR A 69 " model vdw 1.581 2.450 ... (remaining 445161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 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: 0.530 Extract box with map and model: 1.380 Check model and map are aligned: 0.260 Set scattering table: 0.350 Process input model: 65.510 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16542 Z= 0.167 Angle : 0.591 14.701 22463 Z= 0.335 Chirality : 0.043 0.261 2473 Planarity : 0.005 0.150 2977 Dihedral : 16.430 89.544 6051 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % Rotamer: Outliers : 1.21 % Allowed : 18.85 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.001 TRP C 288 HIS 0.006 0.001 HIS A 30 PHE 0.019 0.001 PHE D 64 TYR 0.012 0.001 TYR D 184 ARG 0.015 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.14322 ( 746) hydrogen bonds : angle 6.33564 ( 2085) SS BOND : bond 0.00179 ( 1) SS BOND : angle 0.49373 ( 2) covalent geometry : bond 0.00337 (16541) covalent geometry : angle 0.59125 (22461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8125 (tt0) cc_final: 0.7690 (tm-30) REVERT: A 87 GLN cc_start: 0.7197 (mt0) cc_final: 0.6986 (tm-30) REVERT: A 121 VAL cc_start: 0.8572 (t) cc_final: 0.8083 (t) REVERT: A 514 THR cc_start: 0.8415 (m) cc_final: 0.8067 (p) REVERT: A 534 ASN cc_start: 0.8764 (m110) cc_final: 0.8073 (m110) REVERT: B 364 SER cc_start: 0.8915 (m) cc_final: 0.8541 (p) REVERT: C 127 LYS cc_start: 0.9375 (mmtt) cc_final: 0.8980 (mmmm) REVERT: C 153 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7774 (mt-10) REVERT: D 34 GLU cc_start: 0.7871 (mp0) cc_final: 0.7638 (tm-30) REVERT: D 40 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7508 (mm110) REVERT: D 121 ASP cc_start: 0.8424 (t0) cc_final: 0.8115 (t0) REVERT: D 232 GLU cc_start: 0.7977 (tp30) cc_final: 0.7723 (mm-30) REVERT: E 50 MET cc_start: 0.6819 (ttm) cc_final: 0.6600 (ttt) REVERT: E 107 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8237 (mttp) REVERT: F 231 MET cc_start: 0.1611 (tmt) cc_final: 0.0140 (mpp) outliers start: 21 outliers final: 7 residues processed: 238 average time/residue: 2.3989 time to fit residues: 642.2318 Evaluate side-chains 143 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 39 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.138764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082881 restraints weight = 86059.451| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.06 r_work: 0.2992 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16542 Z= 0.223 Angle : 0.557 7.455 22463 Z= 0.296 Chirality : 0.043 0.157 2473 Planarity : 0.004 0.056 2977 Dihedral : 4.637 89.173 2284 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 1.72 % Allowed : 19.25 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2071 helix: 1.93 (0.21), residues: 584 sheet: -0.47 (0.21), residues: 558 loop : -0.64 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.003 0.001 HIS A 555 PHE 0.011 0.001 PHE E 95 TYR 0.017 0.001 TYR A 255 ARG 0.008 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 746) hydrogen bonds : angle 5.08554 ( 2085) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.04044 ( 2) covalent geometry : bond 0.00502 (16541) covalent geometry : angle 0.55718 (22461) *********************** 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 160 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8366 (tt0) cc_final: 0.8094 (mt-10) REVERT: A 76 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7365 (ttm110) REVERT: A 91 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8358 (ptp-170) REVERT: A 121 VAL cc_start: 0.8424 (t) cc_final: 0.7997 (m) REVERT: A 123 GLU cc_start: 0.7378 (mp0) cc_final: 0.6949 (mp0) REVERT: A 321 ARG cc_start: 0.7763 (ptt90) cc_final: 0.7539 (ptt90) REVERT: A 401 ASP cc_start: 0.8443 (t0) cc_final: 0.7600 (t0) REVERT: B 355 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.8110 (pmm-80) REVERT: B 388 TYR cc_start: 0.8203 (m-80) cc_final: 0.7970 (m-80) REVERT: C 127 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9180 (mmmm) REVERT: C 153 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7968 (mt-10) REVERT: C 194 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8055 (mpp) REVERT: D 34 GLU cc_start: 0.8241 (mp0) cc_final: 0.7838 (tm-30) REVERT: D 121 ASP cc_start: 0.8480 (t0) cc_final: 0.8184 (t0) REVERT: F 58 GLN cc_start: 0.8489 (mp10) cc_final: 0.8087 (pm20) outliers start: 30 outliers final: 10 residues processed: 154 average time/residue: 2.8122 time to fit residues: 479.0268 Evaluate side-chains 123 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 169 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 80 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 230 GLN F 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.133943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.083067 restraints weight = 86252.019| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.97 r_work: 0.3007 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16542 Z= 0.112 Angle : 0.479 5.248 22463 Z= 0.251 Chirality : 0.041 0.144 2473 Planarity : 0.003 0.056 2977 Dihedral : 4.313 89.842 2280 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 1.61 % Allowed : 19.60 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2071 helix: 2.21 (0.21), residues: 584 sheet: -0.35 (0.21), residues: 558 loop : -0.52 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.013 0.001 HIS F 68 PHE 0.013 0.001 PHE A 67 TYR 0.015 0.001 TYR C 197 ARG 0.005 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 746) hydrogen bonds : angle 4.77429 ( 2085) SS BOND : bond 0.00179 ( 1) SS BOND : angle 0.46031 ( 2) covalent geometry : bond 0.00245 (16541) covalent geometry : angle 0.47914 (22461) *********************** 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 140 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 2.413 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: A 73 GLU cc_start: 0.8428 (tt0) cc_final: 0.8089 (mt-10) REVERT: A 91 ARG cc_start: 0.8505 (ptp-170) cc_final: 0.8294 (ptp-170) REVERT: A 121 VAL cc_start: 0.8210 (t) cc_final: 0.7942 (t) REVERT: A 123 GLU cc_start: 0.7274 (mp0) cc_final: 0.6912 (mp0) REVERT: A 321 ARG cc_start: 0.7742 (ptt90) cc_final: 0.7483 (ptt90) REVERT: A 401 ASP cc_start: 0.8380 (t0) cc_final: 0.7543 (t0) REVERT: A 472 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8793 (p) REVERT: A 768 MET cc_start: 0.8658 (mtt) cc_final: 0.8206 (mtt) REVERT: B 388 TYR cc_start: 0.8053 (m-80) cc_final: 0.7798 (m-80) REVERT: C 127 LYS cc_start: 0.9475 (mmtt) cc_final: 0.9124 (mmmm) REVERT: C 153 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7982 (mt-10) REVERT: C 194 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (mpp) REVERT: D 121 ASP cc_start: 0.8474 (t0) cc_final: 0.8176 (t0) REVERT: F 58 GLN cc_start: 0.8481 (mp10) cc_final: 0.8106 (pm20) outliers start: 28 outliers final: 10 residues processed: 129 average time/residue: 2.7655 time to fit residues: 396.9121 Evaluate side-chains 113 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 203 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 185 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 230 GLN E 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.128398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076253 restraints weight = 86305.385| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.95 r_work: 0.2907 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16542 Z= 0.207 Angle : 0.521 5.314 22463 Z= 0.277 Chirality : 0.042 0.159 2473 Planarity : 0.004 0.065 2977 Dihedral : 4.386 84.263 2280 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 1.67 % Allowed : 18.62 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 2071 helix: 2.13 (0.21), residues: 586 sheet: -0.50 (0.21), residues: 568 loop : -0.63 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.003 0.001 HIS B 165 PHE 0.017 0.001 PHE A 67 TYR 0.017 0.001 TYR C 197 ARG 0.013 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 746) hydrogen bonds : angle 4.73206 ( 2085) SS BOND : bond 0.00365 ( 1) SS BOND : angle 0.93500 ( 2) covalent geometry : bond 0.00472 (16541) covalent geometry : angle 0.52047 (22461) *********************** 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 137 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6102 (mp0) cc_final: 0.5816 (mp0) REVERT: A 73 GLU cc_start: 0.8482 (tt0) cc_final: 0.7702 (tm-30) REVERT: A 121 VAL cc_start: 0.8334 (t) cc_final: 0.7951 (t) REVERT: A 123 GLU cc_start: 0.7333 (mp0) cc_final: 0.6874 (mp0) REVERT: A 321 ARG cc_start: 0.7894 (ptt90) cc_final: 0.7593 (ptt90) REVERT: A 401 ASP cc_start: 0.8416 (t0) cc_final: 0.7575 (t0) REVERT: A 472 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8850 (p) REVERT: B 355 ARG cc_start: 0.8586 (ptt-90) cc_final: 0.8272 (pmm-80) REVERT: B 388 TYR cc_start: 0.8365 (m-80) cc_final: 0.8161 (m-80) REVERT: C 194 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7981 (mpp) REVERT: D 121 ASP cc_start: 0.8456 (t0) cc_final: 0.8019 (m-30) REVERT: E 50 MET cc_start: 0.9031 (ttm) cc_final: 0.8713 (ttt) REVERT: F 58 GLN cc_start: 0.8510 (mp10) cc_final: 0.8147 (pm20) outliers start: 29 outliers final: 12 residues processed: 130 average time/residue: 2.6427 time to fit residues: 384.5861 Evaluate side-chains 110 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 204 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 147 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 331 ASN D 44 GLN D 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.133826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076768 restraints weight = 87243.715| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.09 r_work: 0.2944 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16542 Z= 0.100 Angle : 0.464 4.942 22463 Z= 0.242 Chirality : 0.041 0.141 2473 Planarity : 0.003 0.041 2977 Dihedral : 4.136 81.392 2279 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 1.26 % Allowed : 18.91 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 2071 helix: 2.41 (0.21), residues: 588 sheet: -0.42 (0.21), residues: 562 loop : -0.56 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 PHE 0.016 0.001 PHE A 67 TYR 0.017 0.001 TYR C 197 ARG 0.004 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 746) hydrogen bonds : angle 4.51078 ( 2085) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.10957 ( 2) covalent geometry : bond 0.00223 (16541) covalent geometry : angle 0.46358 (22461) *********************** 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 130 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.5983 (mp0) cc_final: 0.5735 (mp0) REVERT: A 73 GLU cc_start: 0.8628 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 76 ARG cc_start: 0.7325 (mtp-110) cc_final: 0.7039 (ttm110) REVERT: A 121 VAL cc_start: 0.8283 (t) cc_final: 0.7885 (t) REVERT: A 123 GLU cc_start: 0.7304 (mp0) cc_final: 0.6879 (mp0) REVERT: A 321 ARG cc_start: 0.7851 (ptt90) cc_final: 0.7564 (ptt90) REVERT: A 401 ASP cc_start: 0.8398 (t0) cc_final: 0.7589 (t0) REVERT: B 355 ARG cc_start: 0.8541 (ptt-90) cc_final: 0.8236 (pmm-80) REVERT: B 388 TYR cc_start: 0.8338 (m-80) cc_final: 0.8051 (m-80) REVERT: C 194 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8012 (mpp) REVERT: D 121 ASP cc_start: 0.8431 (t0) cc_final: 0.8113 (m-30) REVERT: E 50 MET cc_start: 0.8926 (ttm) cc_final: 0.8638 (ttt) REVERT: F 58 GLN cc_start: 0.8525 (mp10) cc_final: 0.8148 (pm20) REVERT: F 69 GLN cc_start: 0.9542 (tt0) cc_final: 0.9294 (tm-30) REVERT: F 96 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7522 (mt) REVERT: F 136 MET cc_start: 0.8185 (mmm) cc_final: 0.7976 (mtp) outliers start: 22 outliers final: 8 residues processed: 126 average time/residue: 2.8152 time to fit residues: 399.9154 Evaluate side-chains 110 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 180 optimal weight: 0.1980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.137528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080487 restraints weight = 87026.791| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.07 r_work: 0.2915 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16542 Z= 0.151 Angle : 0.475 5.430 22463 Z= 0.249 Chirality : 0.041 0.139 2473 Planarity : 0.003 0.041 2977 Dihedral : 4.075 77.452 2277 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % Rotamer: Outliers : 1.21 % Allowed : 19.48 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2071 helix: 2.44 (0.21), residues: 588 sheet: -0.44 (0.21), residues: 568 loop : -0.55 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.000 HIS D 139 PHE 0.015 0.001 PHE A 67 TYR 0.016 0.001 TYR C 197 ARG 0.003 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 746) hydrogen bonds : angle 4.48366 ( 2085) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.38950 ( 2) covalent geometry : bond 0.00341 (16541) covalent geometry : angle 0.47467 (22461) *********************** 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 123 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 2.430 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: A 32 GLU cc_start: 0.6043 (mp0) cc_final: 0.5770 (mp0) REVERT: A 73 GLU cc_start: 0.8672 (tt0) cc_final: 0.7734 (tm-30) REVERT: A 76 ARG cc_start: 0.7378 (mtp-110) cc_final: 0.7083 (ttm110) REVERT: A 121 VAL cc_start: 0.8266 (t) cc_final: 0.7782 (t) REVERT: A 123 GLU cc_start: 0.7338 (mp0) cc_final: 0.6862 (mp0) REVERT: A 321 ARG cc_start: 0.7922 (ptt90) cc_final: 0.7609 (ptt90) REVERT: B 355 ARG cc_start: 0.8557 (ptt-90) cc_final: 0.8257 (pmm-80) REVERT: B 388 TYR cc_start: 0.8451 (m-80) cc_final: 0.8242 (m-80) REVERT: C 194 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7996 (mpp) REVERT: D 121 ASP cc_start: 0.8422 (t0) cc_final: 0.8094 (m-30) REVERT: E 50 MET cc_start: 0.9020 (ttm) cc_final: 0.8727 (ttt) REVERT: F 58 GLN cc_start: 0.8538 (mp10) cc_final: 0.8171 (pm20) REVERT: F 69 GLN cc_start: 0.9523 (tt0) cc_final: 0.9248 (tm-30) REVERT: F 96 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7610 (mt) REVERT: F 136 MET cc_start: 0.8211 (mmm) cc_final: 0.7999 (mtp) outliers start: 21 outliers final: 11 residues processed: 117 average time/residue: 2.7664 time to fit residues: 360.2815 Evaluate side-chains 111 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 44 optimal weight: 6.9990 chunk 198 optimal weight: 50.0000 chunk 158 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 94 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 150 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 230 GLN F 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.135943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079015 restraints weight = 87306.507| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.07 r_work: 0.2922 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16542 Z= 0.125 Angle : 0.465 6.738 22463 Z= 0.242 Chirality : 0.041 0.143 2473 Planarity : 0.003 0.040 2977 Dihedral : 3.987 73.339 2277 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 19.66 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2071 helix: 2.55 (0.21), residues: 588 sheet: -0.38 (0.21), residues: 565 loop : -0.51 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.001 0.000 HIS D 139 PHE 0.013 0.001 PHE A 67 TYR 0.017 0.001 TYR C 197 ARG 0.003 0.000 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 746) hydrogen bonds : angle 4.40148 ( 2085) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.16496 ( 2) covalent geometry : bond 0.00282 (16541) covalent geometry : angle 0.46460 (22461) *********************** 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 124 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6124 (mp0) cc_final: 0.5893 (mp0) REVERT: A 73 GLU cc_start: 0.8737 (tt0) cc_final: 0.7801 (tm-30) REVERT: A 76 ARG cc_start: 0.7493 (mtp-110) cc_final: 0.7183 (ttm110) REVERT: A 108 ASP cc_start: 0.9081 (p0) cc_final: 0.8769 (p0) REVERT: A 121 VAL cc_start: 0.8427 (t) cc_final: 0.7905 (t) REVERT: A 123 GLU cc_start: 0.7469 (mp0) cc_final: 0.6895 (mp0) REVERT: A 321 ARG cc_start: 0.7938 (ptt90) cc_final: 0.7632 (ptt90) REVERT: B 355 ARG cc_start: 0.8570 (ptt-90) cc_final: 0.8285 (pmm-80) REVERT: B 388 TYR cc_start: 0.8455 (m-80) cc_final: 0.8209 (m-80) REVERT: C 194 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8022 (mpp) REVERT: D 121 ASP cc_start: 0.8420 (t0) cc_final: 0.8087 (m-30) REVERT: E 50 MET cc_start: 0.9053 (ttm) cc_final: 0.8746 (ttt) REVERT: F 58 GLN cc_start: 0.8553 (mp10) cc_final: 0.8182 (pm20) REVERT: F 69 GLN cc_start: 0.9545 (tt0) cc_final: 0.9281 (tm-30) REVERT: F 96 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7526 (mt) REVERT: F 136 MET cc_start: 0.8208 (mmm) cc_final: 0.7958 (mtp) outliers start: 20 outliers final: 12 residues processed: 120 average time/residue: 2.7189 time to fit residues: 364.3193 Evaluate side-chains 114 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 18 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.136128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.079157 restraints weight = 87496.530| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.07 r_work: 0.2929 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16542 Z= 0.110 Angle : 0.457 6.104 22463 Z= 0.238 Chirality : 0.040 0.158 2473 Planarity : 0.003 0.039 2977 Dihedral : 3.916 71.343 2277 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % Rotamer: Outliers : 1.26 % Allowed : 19.43 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 2071 helix: 2.62 (0.21), residues: 588 sheet: -0.34 (0.21), residues: 564 loop : -0.48 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.001 0.000 HIS D 139 PHE 0.007 0.001 PHE A 67 TYR 0.016 0.001 TYR C 197 ARG 0.006 0.000 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 746) hydrogen bonds : angle 4.34425 ( 2085) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.14042 ( 2) covalent geometry : bond 0.00248 (16541) covalent geometry : angle 0.45724 (22461) *********************** 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 124 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 2.459 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: A 32 GLU cc_start: 0.6156 (mp0) cc_final: 0.5894 (mp0) REVERT: A 73 GLU cc_start: 0.8762 (tt0) cc_final: 0.7819 (tm-30) REVERT: A 76 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.7142 (ttm110) REVERT: A 108 ASP cc_start: 0.9096 (p0) cc_final: 0.8794 (p0) REVERT: A 123 GLU cc_start: 0.7438 (mp0) cc_final: 0.6898 (mp0) REVERT: A 321 ARG cc_start: 0.7940 (ptt90) cc_final: 0.7638 (ptt90) REVERT: B 355 ARG cc_start: 0.8575 (ptt-90) cc_final: 0.8231 (pmm-80) REVERT: B 388 TYR cc_start: 0.8453 (m-80) cc_final: 0.8223 (m-80) REVERT: C 194 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8013 (mpp) REVERT: D 121 ASP cc_start: 0.8381 (t0) cc_final: 0.8047 (m-30) REVERT: E 50 MET cc_start: 0.9009 (ttm) cc_final: 0.8712 (mtp) REVERT: F 58 GLN cc_start: 0.8540 (mp10) cc_final: 0.8172 (pm20) REVERT: F 69 GLN cc_start: 0.9542 (tt0) cc_final: 0.9278 (tm-30) REVERT: F 96 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7478 (mt) REVERT: F 136 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7966 (mtp) outliers start: 22 outliers final: 15 residues processed: 118 average time/residue: 2.8912 time to fit residues: 383.8572 Evaluate side-chains 116 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 136 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 127 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.125851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071491 restraints weight = 87193.822| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.04 r_work: 0.2820 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16542 Z= 0.217 Angle : 0.507 6.879 22463 Z= 0.269 Chirality : 0.042 0.149 2473 Planarity : 0.003 0.049 2977 Dihedral : 4.116 70.591 2277 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 1.49 % Allowed : 19.20 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2071 helix: 2.36 (0.21), residues: 588 sheet: -0.41 (0.21), residues: 567 loop : -0.62 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.004 0.001 HIS B 165 PHE 0.011 0.001 PHE A 791 TYR 0.018 0.001 TYR D 77 ARG 0.004 0.000 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 746) hydrogen bonds : angle 4.51769 ( 2085) SS BOND : bond 0.00203 ( 1) SS BOND : angle 0.60274 ( 2) covalent geometry : bond 0.00494 (16541) covalent geometry : angle 0.50738 (22461) *********************** 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 123 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8745 (tt0) cc_final: 0.7819 (tm-30) REVERT: A 76 ARG cc_start: 0.7344 (mtp-110) cc_final: 0.7059 (ttm110) REVERT: A 108 ASP cc_start: 0.9106 (p0) cc_final: 0.8821 (p0) REVERT: A 123 GLU cc_start: 0.7454 (mp0) cc_final: 0.6904 (mp0) REVERT: A 321 ARG cc_start: 0.7966 (ptt90) cc_final: 0.7651 (ptt90) REVERT: B 223 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8818 (tp-100) REVERT: C 194 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: D 121 ASP cc_start: 0.8415 (t0) cc_final: 0.8198 (m-30) REVERT: E 50 MET cc_start: 0.9018 (ttm) cc_final: 0.8753 (mtp) REVERT: F 58 GLN cc_start: 0.8530 (mp10) cc_final: 0.8144 (pm20) REVERT: F 69 GLN cc_start: 0.9549 (tt0) cc_final: 0.9282 (tm-30) outliers start: 26 outliers final: 17 residues processed: 116 average time/residue: 2.7850 time to fit residues: 361.4940 Evaluate side-chains 111 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 3 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 173 optimal weight: 0.0270 chunk 119 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.128168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.074689 restraints weight = 86492.705| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.06 r_work: 0.2865 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16542 Z= 0.100 Angle : 0.474 9.196 22463 Z= 0.246 Chirality : 0.041 0.148 2473 Planarity : 0.003 0.070 2977 Dihedral : 3.978 69.621 2277 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 0.92 % Allowed : 19.77 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2071 helix: 2.57 (0.21), residues: 588 sheet: -0.41 (0.21), residues: 568 loop : -0.51 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.001 0.000 HIS D 139 PHE 0.007 0.001 PHE A 478 TYR 0.016 0.001 TYR C 197 ARG 0.010 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 746) hydrogen bonds : angle 4.36019 ( 2085) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.09263 ( 2) covalent geometry : bond 0.00224 (16541) covalent geometry : angle 0.47431 (22461) ********************** 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 115 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8757 (tt0) cc_final: 0.7832 (tm-30) REVERT: A 76 ARG cc_start: 0.7465 (mtp-110) cc_final: 0.7159 (ttm110) REVERT: A 108 ASP cc_start: 0.9103 (p0) cc_final: 0.8805 (p0) REVERT: A 123 GLU cc_start: 0.7485 (mp0) cc_final: 0.6911 (mp0) REVERT: A 321 ARG cc_start: 0.7903 (ptt90) cc_final: 0.7595 (ptt90) REVERT: B 223 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8768 (tp-100) REVERT: B 355 ARG cc_start: 0.8486 (ptt-90) cc_final: 0.8140 (pmm-80) REVERT: C 194 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8012 (mpp) REVERT: D 121 ASP cc_start: 0.8370 (t0) cc_final: 0.8054 (m-30) REVERT: E 50 MET cc_start: 0.8986 (ttm) cc_final: 0.8679 (mtp) REVERT: F 58 GLN cc_start: 0.8574 (mp10) cc_final: 0.8197 (pm20) REVERT: F 69 GLN cc_start: 0.9557 (tt0) cc_final: 0.9295 (tm-30) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 2.7900 time to fit residues: 345.3713 Evaluate side-chains 112 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 202 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 92 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.126787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.073062 restraints weight = 86829.501| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.01 r_work: 0.2854 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4600 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= 0.137 Angle : 0.486 10.580 22463 Z= 0.252 Chirality : 0.041 0.145 2473 Planarity : 0.003 0.060 2977 Dihedral : 3.963 69.273 2277 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 0.92 % Allowed : 19.94 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 2071 helix: 2.56 (0.21), residues: 588 sheet: -0.40 (0.21), residues: 569 loop : -0.49 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.001 0.000 HIS D 139 PHE 0.009 0.001 PHE A 67 TYR 0.016 0.001 TYR C 197 ARG 0.009 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 746) hydrogen bonds : angle 4.35798 ( 2085) SS BOND : bond 0.00109 ( 1) SS BOND : angle 0.27955 ( 2) covalent geometry : bond 0.00311 (16541) covalent geometry : angle 0.48613 (22461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28410.26 seconds wall clock time: 484 minutes 25.75 seconds (29065.75 seconds total)