Starting phenix.real_space_refine on Thu May 29 11:57:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg6_52127/05_2025/9hg6_52127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg6_52127/05_2025/9hg6_52127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hg6_52127/05_2025/9hg6_52127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg6_52127/05_2025/9hg6_52127.map" model { file = "/net/cci-nas-00/data/ceres_data/9hg6_52127/05_2025/9hg6_52127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg6_52127/05_2025/9hg6_52127.cif" } resolution = 2.73 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 10153 2.51 5 N 2816 2.21 5 O 3204 1.98 5 H 15755 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31980 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12200 Classifications: {'peptide': 790} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 760} Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 4747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 4747 Classifications: {'peptide': 318} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 301} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1363 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 4675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4675 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 1 Time building chain proxies: 15.66, per 1000 atoms: 0.49 Number of scatterers: 31980 At special positions: 0 Unit cell: (111.69, 123.37, 183.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 3204 8.00 N 2816 7.00 C 10153 6.00 H 15755 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3834 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 24 sheets defined 31.5% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.542A pdb=" N SER A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.068A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.753A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.637A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.907A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.611A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.677A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.618A pdb=" N LYS C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.511A pdb=" N TYR C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.505A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.917A pdb=" N LYS C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 224 Processing helix chain 'C' and resid 247 through 262 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 284 through 291 Processing helix chain 'C' and resid 327 through 336 removed outlier: 3.920A pdb=" N ALA C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.611A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.226A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.630A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.768A pdb=" N GLN F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 60 Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 111 through 118 Processing helix chain 'F' and resid 125 through 149 removed outlier: 4.094A pdb=" N ARG F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.890A pdb=" N GLN F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 208 Processing helix chain 'F' and resid 211 through 220 Processing helix chain 'F' and resid 222 through 228 removed outlier: 4.253A pdb=" N LEU F 226 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 239 Processing helix chain 'F' and resid 240 through 247 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 393 through 421 removed outlier: 3.566A pdb=" N ARG F 418 " --> pdb=" O MET F 414 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.682A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG A 79 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N GLU A 73 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ALA F 29 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 75 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS F 27 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.682A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG A 79 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N GLU A 73 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ALA F 29 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 75 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS F 27 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 5.880A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 183 removed outlier: 6.910A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.103A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.378A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.103A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.378A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.602A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 426 removed outlier: 3.660A pdb=" N THR A 467 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP A 493 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 673 removed outlier: 5.275A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 46 removed outlier: 4.429A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.808A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.214A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.502A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.403A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.779A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.961A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.927A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.480A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TYR C 157 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN C 147 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY C 159 " --> pdb=" O TRP C 145 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP C 145 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 133 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP C 144 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 131 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AC3, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 269 removed outlier: 4.010A pdb=" N ASP C 268 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 303 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 304 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'F' and resid 230 through 234 removed outlier: 6.151A pdb=" N LEU F 176 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP F 233 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU F 174 " --> pdb=" O TRP F 233 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 272 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER F 177 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL F 270 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE F 179 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU F 268 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE F 181 " --> pdb=" O HIS F 266 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS F 266 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG F 260 " --> pdb=" O GLY F 264 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU F 268 " --> pdb=" O VAL F 256 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.68 Time building geometry restraints manager: 10.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15754 1.03 - 1.23: 12 1.23 - 1.42: 7039 1.42 - 1.62: 9390 1.62 - 1.81: 101 Bond restraints: 32296 Sorted by residual: bond pdb=" N ALA A 21 " pdb=" H1 ALA A 21 " ideal model delta sigma weight residual 0.960 0.889 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" N CYS C 25 " pdb=" H1 CYS C 25 " ideal model delta sigma weight residual 0.960 0.890 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N VAL F 157 " pdb=" CA VAL F 157 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.97e+00 bond pdb=" N ARG D 61 " pdb=" H ARG D 61 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" N TYR D 62 " pdb=" H TYR D 62 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.64e+00 ... (remaining 32291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 57924 2.94 - 5.87: 197 5.87 - 8.81: 12 8.81 - 11.75: 3 11.75 - 14.69: 1 Bond angle restraints: 58137 Sorted by residual: angle pdb=" C SER C 294 " pdb=" N ASP C 295 " pdb=" CA ASP C 295 " ideal model delta sigma weight residual 121.17 135.86 -14.69 1.62e+00 3.81e-01 8.22e+01 angle pdb=" N LEU F 426 " pdb=" CA LEU F 426 " pdb=" C LEU F 426 " ideal model delta sigma weight residual 112.94 105.88 7.06 1.41e+00 5.03e-01 2.51e+01 angle pdb=" N MET F 414 " pdb=" CA MET F 414 " pdb=" C MET F 414 " ideal model delta sigma weight residual 112.89 107.57 5.32 1.24e+00 6.50e-01 1.84e+01 angle pdb=" N GLN F 415 " pdb=" CA GLN F 415 " pdb=" C GLN F 415 " ideal model delta sigma weight residual 113.97 108.58 5.39 1.28e+00 6.10e-01 1.78e+01 angle pdb=" N GLN F 155 " pdb=" CA GLN F 155 " pdb=" C GLN F 155 " ideal model delta sigma weight residual 111.33 106.51 4.82 1.21e+00 6.83e-01 1.59e+01 ... (remaining 58132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13462 17.94 - 35.89: 1219 35.89 - 53.83: 397 53.83 - 71.77: 145 71.77 - 89.71: 42 Dihedral angle restraints: 15265 sinusoidal: 8315 harmonic: 6950 Sorted by residual: dihedral pdb=" CA ASP B 363 " pdb=" CB ASP B 363 " pdb=" CG ASP B 363 " pdb=" OD1 ASP B 363 " ideal model delta sinusoidal sigma weight residual -30.00 -86.82 56.82 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA GLU B 370 " pdb=" C GLU B 370 " pdb=" N PRO B 371 " pdb=" CA PRO B 371 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG C 83 " pdb=" CD ARG C 83 " pdb=" NE ARG C 83 " pdb=" CZ ARG C 83 " ideal model delta sinusoidal sigma weight residual 90.00 134.40 -44.40 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 15262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2073 0.053 - 0.105: 310 0.105 - 0.158: 85 0.158 - 0.211: 4 0.211 - 0.264: 1 Chirality restraints: 2473 Sorted by residual: chirality pdb=" CA GLN F 98 " pdb=" N GLN F 98 " pdb=" C GLN F 98 " pdb=" CB GLN F 98 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA GLN B 225 " pdb=" N GLN B 225 " pdb=" C GLN B 225 " pdb=" CB GLN B 225 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL F 256 " pdb=" N VAL F 256 " pdb=" C VAL F 256 " pdb=" CB VAL F 256 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2470 not shown) Planarity restraints: 4974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 61 " 0.490 9.50e-02 1.11e+02 2.13e-01 4.51e+02 pdb=" NE ARG D 61 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG D 61 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 61 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 61 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG D 61 " -0.260 2.00e-02 2.50e+03 pdb="HH12 ARG D 61 " 0.276 2.00e-02 2.50e+03 pdb="HH21 ARG D 61 " 0.036 2.00e-02 2.50e+03 pdb="HH22 ARG D 61 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 155 " -0.033 2.00e-02 2.50e+03 3.50e-02 1.83e+01 pdb=" CD GLN F 155 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN F 155 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 GLN F 155 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN F 155 " 0.050 2.00e-02 2.50e+03 pdb="HE22 GLN F 155 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 226 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C MET B 226 " 0.060 2.00e-02 2.50e+03 pdb=" O MET B 226 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 227 " -0.021 2.00e-02 2.50e+03 ... (remaining 4971 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 615 2.10 - 2.73: 54813 2.73 - 3.35: 90912 3.35 - 3.98: 116602 3.98 - 4.60: 182223 Nonbonded interactions: 445165 Sorted by model distance: nonbonded pdb=" O LEU C 310 " pdb=" H ASN C 312 " model vdw 1.475 2.450 nonbonded pdb=" OE1 GLN E 53 " pdb=" H GLN E 53 " model vdw 1.483 2.450 nonbonded pdb=" HZ1 LYS C 32 " pdb=" O GLN D 44 " model vdw 1.502 2.450 nonbonded pdb="HH12 ARG A 526 " pdb=" OG1 THR A 577 " model vdw 1.580 2.450 nonbonded pdb=" O LEU A 66 " pdb=" HG1 THR A 69 " model vdw 1.581 2.450 ... (remaining 445160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.590 Extract box with map and model: 1.380 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 67.430 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16542 Z= 0.165 Angle : 0.591 14.686 22463 Z= 0.334 Chirality : 0.043 0.264 2473 Planarity : 0.005 0.150 2977 Dihedral : 16.430 89.543 6051 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 1.21 % Allowed : 18.85 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.14319 ( 746) hydrogen bonds : angle 6.33592 ( 2085) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.49399 ( 2) covalent geometry : bond 0.00334 (16541) covalent geometry : angle 0.59076 (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 145 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 2.500 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: A 321 ARG cc_start: 0.7705 (ptt90) cc_final: 0.7411 (ptt90) REVERT: A 777 MET cc_start: 0.9206 (mmt) cc_final: 0.8763 (mmt) REVERT: C 31 TYR cc_start: 0.8060 (p90) cc_final: 0.7741 (p90) REVERT: C 229 ASP cc_start: 0.8014 (m-30) cc_final: 0.7417 (t0) REVERT: D 232 GLU cc_start: 0.8639 (tp30) cc_final: 0.8419 (mm-30) REVERT: F 87 MET cc_start: 0.8740 (mtm) cc_final: 0.8536 (mtm) REVERT: F 128 TYR cc_start: 0.8273 (t80) cc_final: 0.7819 (t80) REVERT: F 136 MET cc_start: 0.8238 (mmt) cc_final: 0.7986 (mmt) outliers start: 21 outliers final: 13 residues processed: 142 average time/residue: 2.7513 time to fit residues: 435.8586 Evaluate side-chains 118 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain F residue 102 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 187 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.133354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.077466 restraints weight = 88433.300| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.21 r_work: 0.2845 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16542 Z= 0.115 Angle : 0.492 6.468 22463 Z= 0.260 Chirality : 0.041 0.156 2473 Planarity : 0.004 0.054 2977 Dihedral : 5.223 118.173 2293 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 0.92 % Allowed : 19.20 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.19), residues: 2071 helix: 2.13 (0.22), residues: 586 sheet: -0.23 (0.21), residues: 557 loop : -0.53 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 413 HIS 0.004 0.001 HIS F 68 PHE 0.012 0.001 PHE A 428 TYR 0.013 0.001 TYR D 184 ARG 0.008 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 746) hydrogen bonds : angle 5.06135 ( 2085) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.50451 ( 2) covalent geometry : bond 0.00246 (16541) covalent geometry : angle 0.49192 (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 125 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.8081 (m170) cc_final: 0.7806 (m-70) REVERT: A 582 ASP cc_start: 0.9069 (t0) cc_final: 0.8860 (OUTLIER) REVERT: C 201 MET cc_start: 0.8841 (mmm) cc_final: 0.8539 (mmt) REVERT: C 229 ASP cc_start: 0.8013 (m-30) cc_final: 0.7462 (t0) REVERT: C 311 ASP cc_start: 0.8414 (p0) cc_final: 0.8095 (p0) REVERT: C 312 ASN cc_start: 0.8785 (m110) cc_final: 0.8340 (t0) REVERT: D 56 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8385 (mt-10) REVERT: D 232 GLU cc_start: 0.8680 (tp30) cc_final: 0.8464 (mm-30) REVERT: F 128 TYR cc_start: 0.8278 (t80) cc_final: 0.7988 (t80) outliers start: 16 outliers final: 8 residues processed: 121 average time/residue: 2.4489 time to fit residues: 334.0279 Evaluate side-chains 113 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 169 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.130459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.073998 restraints weight = 89578.718| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.21 r_work: 0.2788 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16542 Z= 0.236 Angle : 0.524 6.222 22463 Z= 0.278 Chirality : 0.042 0.145 2473 Planarity : 0.004 0.069 2977 Dihedral : 4.562 86.328 2283 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 1.38 % Allowed : 18.62 % Favored : 80.00 % 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: 0.31 (0.19), residues: 2071 helix: 2.08 (0.21), residues: 589 sheet: -0.31 (0.22), residues: 560 loop : -0.64 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.003 0.001 HIS D 139 PHE 0.012 0.001 PHE A 791 TYR 0.017 0.001 TYR A 255 ARG 0.009 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 746) hydrogen bonds : angle 4.88400 ( 2085) SS BOND : bond 0.00395 ( 1) SS BOND : angle 0.88071 ( 2) covalent geometry : bond 0.00535 (16541) covalent geometry : angle 0.52347 (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 136 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.8101 (m170) cc_final: 0.7796 (m-70) REVERT: A 292 PRO cc_start: 0.8357 (Cg_exo) cc_final: 0.8018 (Cg_endo) REVERT: A 321 ARG cc_start: 0.8014 (ptt90) cc_final: 0.7755 (ptt90) REVERT: C 229 ASP cc_start: 0.8086 (m-30) cc_final: 0.7569 (t0) REVERT: C 311 ASP cc_start: 0.8451 (p0) cc_final: 0.7985 (p0) REVERT: C 312 ASN cc_start: 0.8875 (m110) cc_final: 0.8374 (t0) REVERT: D 56 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8573 (mt-10) REVERT: D 232 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8488 (mm-30) REVERT: F 128 TYR cc_start: 0.8327 (t80) cc_final: 0.7951 (t80) outliers start: 24 outliers final: 11 residues processed: 133 average time/residue: 2.3467 time to fit residues: 353.4138 Evaluate side-chains 120 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 203 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 143 optimal weight: 40.0000 chunk 188 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 185 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.131610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075760 restraints weight = 89217.679| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.22 r_work: 0.2821 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16542 Z= 0.127 Angle : 0.474 6.549 22463 Z= 0.249 Chirality : 0.041 0.144 2473 Planarity : 0.003 0.081 2977 Dihedral : 4.332 81.179 2281 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 1.03 % Allowed : 18.51 % Favored : 80.46 % 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: 2.27 (0.21), residues: 590 sheet: -0.27 (0.22), residues: 556 loop : -0.60 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.003 0.000 HIS F 68 PHE 0.011 0.001 PHE A 428 TYR 0.020 0.001 TYR C 197 ARG 0.009 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 746) hydrogen bonds : angle 4.64282 ( 2085) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.38948 ( 2) covalent geometry : bond 0.00278 (16541) covalent geometry : angle 0.47392 (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 132 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.8111 (m170) cc_final: 0.7808 (m-70) REVERT: A 292 PRO cc_start: 0.8434 (Cg_exo) cc_final: 0.8152 (Cg_endo) REVERT: A 321 ARG cc_start: 0.7895 (ptt90) cc_final: 0.7688 (ptt90) REVERT: C 229 ASP cc_start: 0.8146 (m-30) cc_final: 0.7598 (t0) REVERT: C 311 ASP cc_start: 0.8372 (p0) cc_final: 0.7800 (p0) REVERT: C 312 ASN cc_start: 0.8810 (m110) cc_final: 0.8388 (t0) REVERT: D 232 GLU cc_start: 0.8607 (tp30) cc_final: 0.8388 (mm-30) REVERT: F 128 TYR cc_start: 0.8334 (t80) cc_final: 0.7924 (t80) outliers start: 18 outliers final: 8 residues processed: 127 average time/residue: 2.5134 time to fit residues: 360.9409 Evaluate side-chains 121 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 204 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 146 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.131261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.075524 restraints weight = 89086.948| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.20 r_work: 0.2789 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1576 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= 0.148 Angle : 0.477 6.661 22463 Z= 0.251 Chirality : 0.041 0.144 2473 Planarity : 0.003 0.049 2977 Dihedral : 4.241 75.847 2280 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.32 % Allowed : 18.28 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2071 helix: 2.32 (0.21), residues: 590 sheet: -0.27 (0.21), residues: 563 loop : -0.60 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 PHE 0.007 0.001 PHE A 791 TYR 0.016 0.001 TYR C 197 ARG 0.009 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 746) hydrogen bonds : angle 4.57171 ( 2085) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.41069 ( 2) covalent geometry : bond 0.00330 (16541) covalent geometry : angle 0.47705 (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 137 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.8112 (m170) cc_final: 0.7808 (m-70) REVERT: A 108 ASP cc_start: 0.9037 (t0) cc_final: 0.8765 (t0) REVERT: A 112 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8740 (mm110) REVERT: A 292 PRO cc_start: 0.8479 (Cg_exo) cc_final: 0.8151 (Cg_endo) REVERT: A 321 ARG cc_start: 0.7899 (ptt90) cc_final: 0.7606 (ptt90) REVERT: C 31 TYR cc_start: 0.7998 (p90) cc_final: 0.7741 (p90) REVERT: C 229 ASP cc_start: 0.8040 (m-30) cc_final: 0.7547 (t0) REVERT: C 271 ARG cc_start: 0.6725 (ttp-170) cc_final: 0.6154 (ttp80) REVERT: C 311 ASP cc_start: 0.8507 (p0) cc_final: 0.7951 (p0) REVERT: C 312 ASN cc_start: 0.8930 (m110) cc_final: 0.8426 (t0) REVERT: D 232 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8378 (mm-30) REVERT: F 128 TYR cc_start: 0.8287 (t80) cc_final: 0.7891 (t80) outliers start: 23 outliers final: 14 residues processed: 132 average time/residue: 2.8126 time to fit residues: 412.7294 Evaluate side-chains 129 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.131245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075749 restraints weight = 89689.041| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.16 r_work: 0.2810 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16542 Z= 0.172 Angle : 0.484 6.336 22463 Z= 0.255 Chirality : 0.041 0.143 2473 Planarity : 0.004 0.055 2977 Dihedral : 4.206 71.035 2279 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.61 % Allowed : 18.05 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 2071 helix: 2.33 (0.21), residues: 589 sheet: -0.28 (0.21), residues: 568 loop : -0.61 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 PHE 0.012 0.001 PHE A 428 TYR 0.017 0.001 TYR C 197 ARG 0.011 0.000 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 746) hydrogen bonds : angle 4.55115 ( 2085) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.43730 ( 2) covalent geometry : bond 0.00385 (16541) covalent geometry : angle 0.48394 (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 141 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.8169 (m170) cc_final: 0.7849 (m-70) REVERT: A 292 PRO cc_start: 0.8435 (Cg_exo) cc_final: 0.8125 (Cg_endo) REVERT: A 321 ARG cc_start: 0.8030 (ptt90) cc_final: 0.7747 (ptt90) REVERT: C 229 ASP cc_start: 0.8080 (m-30) cc_final: 0.7574 (t0) REVERT: C 271 ARG cc_start: 0.6885 (ttp-170) cc_final: 0.6219 (ttp80) REVERT: C 312 ASN cc_start: 0.8935 (m110) cc_final: 0.8555 (t0) REVERT: D 232 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8445 (mm-30) REVERT: E 51 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8381 (p) REVERT: F 109 MET cc_start: 0.2616 (mtt) cc_final: 0.1913 (mtp) REVERT: F 128 TYR cc_start: 0.8313 (t80) cc_final: 0.7920 (t80) outliers start: 28 outliers final: 16 residues processed: 135 average time/residue: 2.9348 time to fit residues: 439.2667 Evaluate side-chains 132 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 44 optimal weight: 6.9990 chunk 198 optimal weight: 40.0000 chunk 158 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 191 optimal weight: 40.0000 chunk 150 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN C 149 ASN D 230 GLN F 78 GLN F 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.129543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074388 restraints weight = 89444.717| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.48 r_work: 0.2733 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16542 Z= 0.255 Angle : 0.522 6.168 22463 Z= 0.278 Chirality : 0.042 0.143 2473 Planarity : 0.004 0.070 2977 Dihedral : 4.355 67.634 2279 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.51 % Rotamer: Outliers : 1.90 % Allowed : 17.70 % Favored : 80.40 % 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: 2.18 (0.21), residues: 588 sheet: -0.44 (0.21), residues: 574 loop : -0.75 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 183 HIS 0.003 0.001 HIS B 165 PHE 0.013 0.001 PHE A 791 TYR 0.018 0.001 TYR C 197 ARG 0.012 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 746) hydrogen bonds : angle 4.67180 ( 2085) SS BOND : bond 0.00291 ( 1) SS BOND : angle 0.64858 ( 2) covalent geometry : bond 0.00577 (16541) covalent geometry : angle 0.52209 (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 146 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 2.558 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: A 30 HIS cc_start: 0.8047 (m170) cc_final: 0.7724 (m-70) REVERT: A 292 PRO cc_start: 0.8488 (Cg_exo) cc_final: 0.8173 (Cg_endo) REVERT: A 321 ARG cc_start: 0.7997 (ptt90) cc_final: 0.7600 (ptt90) REVERT: C 229 ASP cc_start: 0.7990 (m-30) cc_final: 0.7517 (t0) REVERT: C 264 MET cc_start: 0.5141 (mmm) cc_final: 0.4916 (mmm) REVERT: C 311 ASP cc_start: 0.8475 (p0) cc_final: 0.7900 (p0) REVERT: C 312 ASN cc_start: 0.8956 (m110) cc_final: 0.8435 (t0) REVERT: D 232 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8390 (mm-30) REVERT: E 51 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8447 (p) REVERT: F 109 MET cc_start: 0.2867 (mtt) cc_final: 0.2217 (mtp) REVERT: F 128 TYR cc_start: 0.8293 (t80) cc_final: 0.7862 (t80) outliers start: 33 outliers final: 20 residues processed: 140 average time/residue: 2.6866 time to fit residues: 423.5081 Evaluate side-chains 131 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 18 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 138 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 67 optimal weight: 0.0670 chunk 139 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.139756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083453 restraints weight = 87234.900| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.54 r_work: 0.2812 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16542 Z= 0.099 Angle : 0.474 6.616 22463 Z= 0.249 Chirality : 0.041 0.147 2473 Planarity : 0.003 0.065 2977 Dihedral : 4.193 69.339 2279 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 1.03 % Allowed : 18.79 % Favored : 80.17 % 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: 2.39 (0.21), residues: 589 sheet: -0.32 (0.21), residues: 573 loop : -0.65 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 PHE 0.012 0.001 PHE A 428 TYR 0.018 0.001 TYR C 197 ARG 0.013 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 746) hydrogen bonds : angle 4.46633 ( 2085) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.15177 ( 2) covalent geometry : bond 0.00217 (16541) covalent geometry : angle 0.47384 (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 133 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 2.651 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: A 30 HIS cc_start: 0.8033 (m170) cc_final: 0.7707 (m-70) REVERT: A 292 PRO cc_start: 0.8492 (Cg_exo) cc_final: 0.8181 (Cg_endo) REVERT: A 321 ARG cc_start: 0.7916 (ptt90) cc_final: 0.7599 (ptt90) REVERT: C 201 MET cc_start: 0.8683 (tmm) cc_final: 0.8465 (tmm) REVERT: C 229 ASP cc_start: 0.7915 (m-30) cc_final: 0.7482 (t0) REVERT: C 311 ASP cc_start: 0.8455 (p0) cc_final: 0.7906 (p0) REVERT: C 312 ASN cc_start: 0.8969 (m110) cc_final: 0.8435 (t0) REVERT: D 232 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8337 (mm-30) REVERT: E 51 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8376 (p) REVERT: F 109 MET cc_start: 0.2754 (mtt) cc_final: 0.2072 (mtp) REVERT: F 128 TYR cc_start: 0.8252 (t80) cc_final: 0.7831 (t80) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 2.7902 time to fit residues: 403.2086 Evaluate side-chains 130 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 127 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 157 optimal weight: 0.7980 chunk 193 optimal weight: 50.0000 chunk 29 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN C 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.130015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073679 restraints weight = 89235.187| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.41 r_work: 0.2757 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16542 Z= 0.223 Angle : 0.517 9.615 22463 Z= 0.272 Chirality : 0.041 0.143 2473 Planarity : 0.004 0.078 2977 Dihedral : 4.257 68.716 2279 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 1.21 % Allowed : 18.79 % Favored : 80.00 % 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: 0.35 (0.19), residues: 2071 helix: 2.29 (0.21), residues: 588 sheet: -0.35 (0.21), residues: 574 loop : -0.71 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.000 HIS D 139 PHE 0.010 0.001 PHE A 791 TYR 0.019 0.001 TYR C 197 ARG 0.016 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 746) hydrogen bonds : angle 4.56217 ( 2085) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.46857 ( 2) covalent geometry : bond 0.00504 (16541) covalent geometry : angle 0.51674 (22461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.8078 (m170) cc_final: 0.7749 (m-70) REVERT: A 292 PRO cc_start: 0.8491 (Cg_exo) cc_final: 0.8178 (Cg_endo) REVERT: A 321 ARG cc_start: 0.8107 (ptt90) cc_final: 0.7725 (ptt90) REVERT: C 229 ASP cc_start: 0.8025 (m-30) cc_final: 0.7544 (OUTLIER) REVERT: C 311 ASP cc_start: 0.8592 (p0) cc_final: 0.7990 (p0) REVERT: C 312 ASN cc_start: 0.8954 (m110) cc_final: 0.8421 (t0) REVERT: D 232 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8511 (mm-30) REVERT: E 51 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8430 (p) REVERT: F 109 MET cc_start: 0.2831 (mtt) cc_final: 0.2147 (mtp) REVERT: F 128 TYR cc_start: 0.8297 (t80) cc_final: 0.7852 (t80) outliers start: 21 outliers final: 16 residues processed: 122 average time/residue: 2.9501 time to fit residues: 398.0657 Evaluate side-chains 117 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 3 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 176 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 81 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.131762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.075836 restraints weight = 88701.305| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.39 r_work: 0.2815 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16542 Z= 0.098 Angle : 0.480 9.947 22463 Z= 0.249 Chirality : 0.041 0.147 2473 Planarity : 0.004 0.081 2977 Dihedral : 4.112 69.897 2279 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.03 % Allowed : 18.97 % Favored : 80.00 % 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: 0.55 (0.19), residues: 2071 helix: 2.49 (0.21), residues: 589 sheet: -0.26 (0.21), residues: 573 loop : -0.60 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 PHE 0.010 0.001 PHE A 428 TYR 0.018 0.001 TYR C 197 ARG 0.016 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 746) hydrogen bonds : angle 4.38362 ( 2085) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.03153 ( 2) covalent geometry : bond 0.00217 (16541) covalent geometry : angle 0.48037 (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 125 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 2.565 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: A 30 HIS cc_start: 0.8049 (m170) cc_final: 0.7724 (m-70) REVERT: A 292 PRO cc_start: 0.8494 (Cg_exo) cc_final: 0.8187 (Cg_endo) REVERT: A 321 ARG cc_start: 0.7916 (ptt90) cc_final: 0.7600 (ptt90) REVERT: C 229 ASP cc_start: 0.8042 (m-30) cc_final: 0.7556 (OUTLIER) REVERT: C 311 ASP cc_start: 0.8596 (p0) cc_final: 0.7892 (p0) REVERT: C 312 ASN cc_start: 0.8970 (m110) cc_final: 0.8408 (t0) REVERT: D 232 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8389 (mm-30) REVERT: E 51 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8360 (p) REVERT: F 109 MET cc_start: 0.2696 (mtt) cc_final: 0.2046 (mtp) REVERT: F 128 TYR cc_start: 0.8262 (t80) cc_final: 0.7845 (t80) outliers start: 18 outliers final: 16 residues processed: 123 average time/residue: 2.9919 time to fit residues: 412.3197 Evaluate side-chains 123 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 202 optimal weight: 10.0000 chunk 81 optimal weight: 0.0470 chunk 112 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.131974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077409 restraints weight = 89566.454| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.41 r_work: 0.2816 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16542 Z= 0.103 Angle : 0.482 9.639 22463 Z= 0.249 Chirality : 0.040 0.144 2473 Planarity : 0.004 0.082 2977 Dihedral : 4.062 70.015 2279 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % Rotamer: Outliers : 0.80 % Allowed : 19.37 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 2071 helix: 2.55 (0.21), residues: 589 sheet: -0.20 (0.22), residues: 566 loop : -0.58 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.002 0.000 HIS F 68 PHE 0.006 0.001 PHE C 318 TYR 0.019 0.001 TYR C 197 ARG 0.016 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 746) hydrogen bonds : angle 4.34292 ( 2085) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.14494 ( 2) covalent geometry : bond 0.00230 (16541) covalent geometry : angle 0.48222 (22461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25813.01 seconds wall clock time: 440 minutes 34.14 seconds (26434.14 seconds total)