Starting phenix.real_space_refine on Fri Jun 27 17:44:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg5_52128/06_2025/9hg5_52128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg5_52128/06_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_52128/06_2025/9hg5_52128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg5_52128/06_2025/9hg5_52128.map" model { file = "/net/cci-nas-00/data/ceres_data/9hg5_52128/06_2025/9hg5_52128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg5_52128/06_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-5710/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: 16.40, per 1000 atoms: 0.51 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: 9.15 Conformation dependent library (CDL) restraints added in 2.8 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: 3.21 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: 13.54 Time building geometry restraints manager: 10.96 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: 0.010 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.600 Extract box with map and model: 1.480 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 72.800 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 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:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.790 ------------------------------------------------------------------------------- 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 : 2.720 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: 2.7309 time to fit residues: 734.6385 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 : 3.144 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082885 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: 0.2863 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 2.412 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: 0.8367 (tt0) cc_final: 0.8101 (mt-10) REVERT: A 76 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7378 (ttm110) REVERT: A 91 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.8370 (ptp-170) REVERT: A 121 VAL cc_start: 0.8433 (t) cc_final: 0.8006 (m) REVERT: A 123 GLU cc_start: 0.7390 (mp0) cc_final: 0.6961 (mp0) REVERT: A 321 ARG cc_start: 0.7772 (ptt90) cc_final: 0.7549 (ptt90) REVERT: A 401 ASP cc_start: 0.8444 (t0) cc_final: 0.7601 (t0) REVERT: B 355 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.8113 (pmm-80) REVERT: B 388 TYR cc_start: 0.8206 (m-80) cc_final: 0.7973 (m-80) REVERT: C 127 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9180 (mmmm) REVERT: C 153 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7963 (mt-10) REVERT: C 194 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8054 (mpp) REVERT: D 34 GLU cc_start: 0.8240 (mp0) cc_final: 0.7836 (tm-30) REVERT: D 121 ASP cc_start: 0.8481 (t0) cc_final: 0.8185 (t0) REVERT: F 58 GLN cc_start: 0.8498 (mp10) cc_final: 0.8093 (pm20) outliers start: 30 outliers final: 10 residues processed: 154 average time/residue: 2.8803 time to fit residues: 491.7529 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 : 2.690 ------------------------------------------------------------------------------- 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: 0.5980 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: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.132145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.080858 restraints weight = 86220.984| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.99 r_work: 0.3004 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16542 Z= 0.111 Angle : 0.481 5.234 22463 Z= 0.252 Chirality : 0.041 0.144 2473 Planarity : 0.003 0.054 2977 Dihedral : 4.309 89.813 2280 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 1.67 % Allowed : 19.43 % Favored : 78.91 % 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: 0.42 (0.19), residues: 2071 helix: 2.18 (0.21), residues: 586 sheet: -0.35 (0.22), residues: 553 loop : -0.50 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.014 0.001 HIS F 68 PHE 0.014 0.001 PHE A 67 TYR 0.016 0.001 TYR C 197 ARG 0.007 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 746) hydrogen bonds : angle 4.76046 ( 2085) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.45480 ( 2) covalent geometry : bond 0.00247 (16541) covalent geometry : angle 0.48075 (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 141 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 2.756 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: 0.8424 (tt0) cc_final: 0.8075 (mt-10) REVERT: A 91 ARG cc_start: 0.8464 (ptp-170) cc_final: 0.8246 (ptp-170) REVERT: A 121 VAL cc_start: 0.8165 (t) cc_final: 0.7898 (t) REVERT: A 123 GLU cc_start: 0.7254 (mp0) cc_final: 0.6900 (mp0) REVERT: A 321 ARG cc_start: 0.7744 (ptt90) cc_final: 0.7486 (ptt90) REVERT: A 401 ASP cc_start: 0.8379 (t0) cc_final: 0.7543 (t0) REVERT: A 472 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8793 (p) REVERT: B 388 TYR cc_start: 0.8026 (m-80) cc_final: 0.7775 (m-80) REVERT: C 127 LYS cc_start: 0.9475 (mmtt) cc_final: 0.9120 (mmmm) REVERT: C 153 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8016 (mt-10) REVERT: C 194 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8051 (mpp) REVERT: C 202 MET cc_start: 0.8390 (tpp) cc_final: 0.8189 (tpp) REVERT: D 34 GLU cc_start: 0.8286 (mp0) cc_final: 0.8083 (tm-30) REVERT: D 121 ASP cc_start: 0.8463 (t0) cc_final: 0.8157 (t0) REVERT: F 58 GLN cc_start: 0.8481 (mp10) cc_final: 0.8106 (pm20) outliers start: 29 outliers final: 10 residues processed: 129 average time/residue: 2.8485 time to fit residues: 410.0942 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 : 3.763 ------------------------------------------------------------------------------- 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 183 GLN 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 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 203 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 D 44 GLN D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.127990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075809 restraints weight = 86438.049| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.95 r_work: 0.2895 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16542 Z= 0.230 Angle : 0.532 5.456 22463 Z= 0.284 Chirality : 0.042 0.160 2473 Planarity : 0.004 0.072 2977 Dihedral : 4.449 83.854 2280 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 1.78 % Allowed : 18.74 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.19), residues: 2071 helix: 2.00 (0.21), residues: 586 sheet: -0.48 (0.21), residues: 566 loop : -0.63 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.014 0.001 HIS F 68 PHE 0.013 0.001 PHE A 67 TYR 0.016 0.001 TYR D 77 ARG 0.021 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 746) hydrogen bonds : angle 4.79126 ( 2085) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.98245 ( 2) covalent geometry : bond 0.00522 (16541) covalent geometry : angle 0.53206 (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 140 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 2.593 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: 0.6094 (mp0) cc_final: 0.5794 (mp0) REVERT: A 73 GLU cc_start: 0.8496 (tt0) cc_final: 0.7736 (tm-30) REVERT: A 121 VAL cc_start: 0.8386 (t) cc_final: 0.7993 (t) REVERT: A 123 GLU cc_start: 0.7380 (mp0) cc_final: 0.6922 (mp0) REVERT: A 321 ARG cc_start: 0.7918 (ptt90) cc_final: 0.7623 (ptt90) REVERT: A 472 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8857 (p) REVERT: B 355 ARG cc_start: 0.8609 (ptt-90) cc_final: 0.8306 (pmm-80) REVERT: C 194 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7996 (mpp) REVERT: D 34 GLU cc_start: 0.8359 (mp0) cc_final: 0.8093 (tm-30) REVERT: D 121 ASP cc_start: 0.8472 (t0) cc_final: 0.8037 (m-30) REVERT: E 50 MET cc_start: 0.9032 (ttm) cc_final: 0.8725 (ttt) REVERT: F 58 GLN cc_start: 0.8548 (mp10) cc_final: 0.8171 (pm20) outliers start: 31 outliers final: 16 residues processed: 133 average time/residue: 2.7274 time to fit residues: 406.5423 Evaluate side-chains 114 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE 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 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 Chi-restraints excluded: chain F residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 204 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 147 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** D 44 GLN D 230 GLN ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.131694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074924 restraints weight = 87033.532| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.06 r_work: 0.2923 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16542 Z= 0.126 Angle : 0.477 5.674 22463 Z= 0.251 Chirality : 0.041 0.142 2473 Planarity : 0.003 0.043 2977 Dihedral : 4.225 80.700 2279 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 1.55 % Allowed : 19.14 % 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: 0.36 (0.19), residues: 2071 helix: 2.27 (0.21), residues: 588 sheet: -0.43 (0.21), residues: 562 loop : -0.61 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.016 0.001 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 0.03730 ( 746) hydrogen bonds : angle 4.60234 ( 2085) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.27481 ( 2) covalent geometry : bond 0.00281 (16541) covalent geometry : angle 0.47751 (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 129 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 2.568 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 32 GLU cc_start: 0.6005 (mp0) cc_final: 0.5742 (mp0) REVERT: A 73 GLU cc_start: 0.8660 (tt0) cc_final: 0.7729 (tm-30) REVERT: A 76 ARG cc_start: 0.7361 (mtp-110) cc_final: 0.7095 (ttm110) REVERT: A 121 VAL cc_start: 0.8395 (t) cc_final: 0.7984 (t) REVERT: A 123 GLU cc_start: 0.7397 (mp0) cc_final: 0.6934 (mp0) REVERT: A 321 ARG cc_start: 0.7926 (ptt90) cc_final: 0.7631 (ptt90) REVERT: A 534 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8621 (m110) REVERT: B 355 ARG cc_start: 0.8547 (ptt-90) cc_final: 0.8236 (pmm-80) REVERT: B 388 TYR cc_start: 0.8439 (m-80) cc_final: 0.8229 (m-80) REVERT: C 194 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8025 (mpp) REVERT: D 34 GLU cc_start: 0.8382 (mp0) cc_final: 0.8153 (tm-30) REVERT: D 121 ASP cc_start: 0.8491 (t0) cc_final: 0.8149 (m-30) REVERT: E 50 MET cc_start: 0.9003 (ttm) cc_final: 0.8714 (ttt) REVERT: F 58 GLN cc_start: 0.8552 (mp10) cc_final: 0.8179 (pm20) outliers start: 27 outliers final: 10 residues processed: 121 average time/residue: 3.4273 time to fit residues: 472.2170 Evaluate side-chains 109 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 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: 0.9980 chunk 180 optimal weight: 7.9990 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 128 ASN D 44 GLN D 230 GLN E 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.132872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075531 restraints weight = 87435.046| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.08 r_work: 0.2886 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16542 Z= 0.196 Angle : 0.495 5.172 22463 Z= 0.263 Chirality : 0.041 0.144 2473 Planarity : 0.003 0.048 2977 Dihedral : 4.230 75.899 2279 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 1.38 % Allowed : 19.31 % 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: 0.27 (0.19), residues: 2071 helix: 2.22 (0.21), residues: 588 sheet: -0.50 (0.21), residues: 561 loop : -0.68 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.002 0.001 HIS B 165 PHE 0.015 0.001 PHE A 67 TYR 0.018 0.001 TYR C 197 ARG 0.007 0.000 ARG F 129 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 746) hydrogen bonds : angle 4.63768 ( 2085) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.49214 ( 2) covalent geometry : bond 0.00447 (16541) covalent geometry : angle 0.49482 (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 125 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 2.591 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 32 GLU cc_start: 0.6091 (mp0) cc_final: 0.5825 (mp0) REVERT: A 73 GLU cc_start: 0.8715 (tt0) cc_final: 0.7796 (tm-30) REVERT: A 76 ARG cc_start: 0.7343 (mtp-110) cc_final: 0.7070 (ttm110) REVERT: A 108 ASP cc_start: 0.9043 (p0) cc_final: 0.8729 (p0) REVERT: A 121 VAL cc_start: 0.8421 (t) cc_final: 0.7916 (t) REVERT: A 123 GLU cc_start: 0.7420 (mp0) cc_final: 0.6903 (mp0) REVERT: A 321 ARG cc_start: 0.8001 (ptt90) cc_final: 0.7701 (ptt90) REVERT: B 223 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8842 (tp-100) REVERT: B 355 ARG cc_start: 0.8580 (ptt-90) cc_final: 0.8310 (pmm-80) REVERT: C 194 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8015 (mpp) REVERT: D 34 GLU cc_start: 0.8335 (mp0) cc_final: 0.8090 (tm-30) REVERT: D 121 ASP cc_start: 0.8484 (t0) cc_final: 0.8045 (m-30) REVERT: E 50 MET cc_start: 0.9063 (ttm) cc_final: 0.8772 (mtp) REVERT: F 58 GLN cc_start: 0.8577 (mp10) cc_final: 0.8200 (pm20) outliers start: 24 outliers final: 16 residues processed: 119 average time/residue: 2.7406 time to fit residues: 364.5445 Evaluate side-chains 113 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 465 TYR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 44 optimal weight: 5.9990 chunk 198 optimal weight: 50.0000 chunk 158 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 chunk 126 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.126006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.071832 restraints weight = 87162.787| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.04 r_work: 0.2827 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16542 Z= 0.188 Angle : 0.490 6.515 22463 Z= 0.259 Chirality : 0.041 0.139 2473 Planarity : 0.003 0.043 2977 Dihedral : 4.198 72.051 2279 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 1.49 % Allowed : 19.31 % 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: 0.24 (0.19), residues: 2071 helix: 2.23 (0.21), residues: 588 sheet: -0.54 (0.21), residues: 565 loop : -0.70 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.004 0.001 HIS F 68 PHE 0.009 0.001 PHE A 67 TYR 0.019 0.001 TYR C 197 ARG 0.003 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 746) hydrogen bonds : angle 4.58098 ( 2085) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.33784 ( 2) covalent geometry : bond 0.00425 (16541) covalent geometry : angle 0.48998 (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 127 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 3.009 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: 0.8730 (tt0) cc_final: 0.7823 (tm-30) REVERT: A 76 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.7074 (ttm110) REVERT: A 108 ASP cc_start: 0.9076 (p0) cc_final: 0.8776 (p0) REVERT: A 121 VAL cc_start: 0.8410 (t) cc_final: 0.7919 (t) REVERT: A 123 GLU cc_start: 0.7426 (mp0) cc_final: 0.6912 (mp0) REVERT: A 321 ARG cc_start: 0.7926 (ptt90) cc_final: 0.7615 (ptt90) REVERT: A 534 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8561 (m110) REVERT: B 223 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8811 (tp-100) REVERT: C 194 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8110 (mpp) REVERT: D 34 GLU cc_start: 0.8308 (mp0) cc_final: 0.8049 (tm-30) REVERT: D 121 ASP cc_start: 0.8453 (t0) cc_final: 0.8224 (m-30) REVERT: E 50 MET cc_start: 0.8976 (ttm) cc_final: 0.8775 (ttt) REVERT: F 58 GLN cc_start: 0.8540 (mp10) cc_final: 0.8167 (pm20) REVERT: F 69 GLN cc_start: 0.9556 (tt0) cc_final: 0.9278 (tm-30) outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 2.9009 time to fit residues: 392.1198 Evaluate side-chains 117 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 306 MET 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 Chi-restraints excluded: chain F residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 18 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 2 optimal weight: 0.0060 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.126997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072997 restraints weight = 87253.789| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.05 r_work: 0.2853 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16542 Z= 0.117 Angle : 0.468 6.298 22463 Z= 0.245 Chirality : 0.041 0.141 2473 Planarity : 0.003 0.057 2977 Dihedral : 4.070 70.750 2279 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % 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: 0.40 (0.19), residues: 2071 helix: 2.43 (0.21), residues: 588 sheet: -0.49 (0.21), residues: 560 loop : -0.62 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.003 0.000 HIS F 68 PHE 0.012 0.001 PHE A 67 TYR 0.017 0.001 TYR C 197 ARG 0.008 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 746) hydrogen bonds : angle 4.46483 ( 2085) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.14375 ( 2) covalent geometry : bond 0.00260 (16541) covalent geometry : angle 0.46823 (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 119 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 2.897 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 73 GLU cc_start: 0.8757 (tt0) cc_final: 0.7827 (tm-30) REVERT: A 76 ARG cc_start: 0.7386 (mtp-110) cc_final: 0.7096 (ttm110) REVERT: A 108 ASP cc_start: 0.9071 (p0) cc_final: 0.8762 (p0) REVERT: A 123 GLU cc_start: 0.7427 (mp0) cc_final: 0.6861 (mp0) REVERT: A 321 ARG cc_start: 0.7902 (ptt90) cc_final: 0.7601 (ptt90) REVERT: A 545 MET cc_start: 0.8592 (mtp) cc_final: 0.8231 (ttm) REVERT: B 223 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8794 (tp-100) REVERT: C 194 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8048 (mpp) REVERT: C 228 MET cc_start: 0.4269 (ptp) cc_final: 0.3931 (ttp) REVERT: D 34 GLU cc_start: 0.8249 (mp0) cc_final: 0.7956 (tm-30) REVERT: D 121 ASP cc_start: 0.8415 (t0) cc_final: 0.8101 (m-30) REVERT: E 50 MET cc_start: 0.8979 (ttm) cc_final: 0.8754 (ttt) REVERT: F 58 GLN cc_start: 0.8573 (mp10) cc_final: 0.8180 (pm20) REVERT: F 69 GLN cc_start: 0.9566 (tt0) cc_final: 0.9302 (tm-30) outliers start: 20 outliers final: 14 residues processed: 115 average time/residue: 2.8049 time to fit residues: 363.2503 Evaluate side-chains 110 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 2.586 ------------------------------------------------------------------------------- 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 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 217 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 261 LYS Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 127 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 18 optimal weight: 0.0270 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.126249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072134 restraints weight = 86999.135| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.03 r_work: 0.2835 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.004 0.035 16542 Z= 0.162 Angle : 0.488 9.993 22463 Z= 0.255 Chirality : 0.041 0.139 2473 Planarity : 0.003 0.042 2977 Dihedral : 4.066 70.035 2277 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 1.38 % Allowed : 19.43 % 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: 0.37 (0.19), residues: 2071 helix: 2.40 (0.21), residues: 588 sheet: -0.55 (0.21), residues: 570 loop : -0.61 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.004 0.000 HIS F 68 PHE 0.008 0.001 PHE A 791 TYR 0.017 0.001 TYR C 197 ARG 0.007 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 746) hydrogen bonds : angle 4.48560 ( 2085) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.31695 ( 2) covalent geometry : bond 0.00367 (16541) covalent geometry : angle 0.48816 (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 120 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 2.523 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: 0.8804 (tt0) cc_final: 0.7878 (tm-30) REVERT: A 76 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.7204 (ttm110) REVERT: A 108 ASP cc_start: 0.9076 (p0) cc_final: 0.8759 (p0) REVERT: A 123 GLU cc_start: 0.7488 (mp0) cc_final: 0.6924 (mp0) REVERT: A 321 ARG cc_start: 0.7939 (ptt90) cc_final: 0.7626 (ptt90) REVERT: B 223 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8801 (tp-100) REVERT: C 194 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8019 (mpp) REVERT: C 228 MET cc_start: 0.4311 (ptp) cc_final: 0.3981 (ttp) REVERT: D 34 GLU cc_start: 0.8255 (mp0) cc_final: 0.7964 (tm-30) REVERT: D 121 ASP cc_start: 0.8425 (t0) cc_final: 0.8109 (m-30) REVERT: E 50 MET cc_start: 0.9006 (ttm) cc_final: 0.8733 (mtp) REVERT: F 58 GLN cc_start: 0.8598 (mp10) cc_final: 0.8190 (pm20) REVERT: F 69 GLN cc_start: 0.9567 (tt0) cc_final: 0.9294 (tm-30) outliers start: 24 outliers final: 18 residues processed: 114 average time/residue: 2.7593 time to fit residues: 352.4259 Evaluate side-chains 111 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 2.829 ------------------------------------------------------------------------------- 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 539 MET Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain 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 261 LYS Chi-restraints excluded: chain C residue 311 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 3 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.127444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073883 restraints weight = 86679.606| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.06 r_work: 0.2851 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16542 Z= 0.125 Angle : 0.479 9.662 22463 Z= 0.248 Chirality : 0.041 0.159 2473 Planarity : 0.003 0.045 2977 Dihedral : 3.996 69.236 2277 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 1.38 % Allowed : 19.37 % Favored : 79.25 % 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: 0.45 (0.19), residues: 2071 helix: 2.51 (0.21), residues: 588 sheet: -0.53 (0.21), residues: 567 loop : -0.57 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.004 0.000 HIS F 68 PHE 0.013 0.001 PHE A 67 TYR 0.017 0.001 TYR C 197 ARG 0.007 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 746) hydrogen bonds : angle 4.42174 ( 2085) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.16510 ( 2) covalent geometry : bond 0.00280 (16541) covalent geometry : angle 0.47867 (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 121 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 2.482 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: 0.8811 (tt0) cc_final: 0.7828 (tm-30) REVERT: A 76 ARG cc_start: 0.7505 (mtp-110) cc_final: 0.7198 (ttm110) REVERT: A 108 ASP cc_start: 0.9086 (p0) cc_final: 0.8780 (p0) REVERT: A 123 GLU cc_start: 0.7451 (mp0) cc_final: 0.6899 (mp0) REVERT: A 321 ARG cc_start: 0.7902 (ptt90) cc_final: 0.7598 (ptt90) REVERT: B 223 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8772 (tp-100) REVERT: B 355 ARG cc_start: 0.8466 (ptt-90) cc_final: 0.8146 (pmm-80) REVERT: C 194 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8013 (mpp) REVERT: C 228 MET cc_start: 0.4409 (ptp) cc_final: 0.4071 (ttp) REVERT: D 34 GLU cc_start: 0.8261 (mp0) cc_final: 0.7949 (tm-30) REVERT: D 121 ASP cc_start: 0.8387 (t0) cc_final: 0.8072 (m-30) REVERT: E 50 MET cc_start: 0.8983 (ttm) cc_final: 0.8717 (mtp) REVERT: F 58 GLN cc_start: 0.8575 (mp10) cc_final: 0.8174 (pm20) REVERT: F 69 GLN cc_start: 0.9562 (tt0) cc_final: 0.9291 (tm-30) outliers start: 24 outliers final: 21 residues processed: 115 average time/residue: 2.7482 time to fit residues: 353.0360 Evaluate side-chains 116 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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 539 MET Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain 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 261 LYS 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 E residue 98 SER Chi-restraints excluded: chain F residue 66 LEU 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: 0.9990 chunk 112 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 132 optimal weight: 0.0370 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 ASN D 44 GLN D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.127854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074224 restraints weight = 86961.351| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.04 r_work: 0.2883 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16542 Z= 0.090 Angle : 0.463 8.531 22463 Z= 0.239 Chirality : 0.040 0.141 2473 Planarity : 0.003 0.044 2977 Dihedral : 3.844 68.053 2277 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.30 % 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: 0.65 (0.19), residues: 2071 helix: 2.71 (0.21), residues: 588 sheet: -0.44 (0.21), residues: 568 loop : -0.45 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.004 0.000 HIS F 68 PHE 0.006 0.001 PHE A 354 TYR 0.016 0.001 TYR C 197 ARG 0.007 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 746) hydrogen bonds : angle 4.28628 ( 2085) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.04520 ( 2) covalent geometry : bond 0.00204 (16541) covalent geometry : angle 0.46351 (22461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29185.06 seconds wall clock time: 499 minutes 1.83 seconds (29941.83 seconds total)