Starting phenix.real_space_refine on Thu Feb 5 17:34:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hb4_52013/02_2026/9hb4_52013.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hb4_52013/02_2026/9hb4_52013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hb4_52013/02_2026/9hb4_52013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hb4_52013/02_2026/9hb4_52013.map" model { file = "/net/cci-nas-00/data/ceres_data/9hb4_52013/02_2026/9hb4_52013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hb4_52013/02_2026/9hb4_52013.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 P 12 5.49 5 S 84 5.16 5 C 11930 2.51 5 N 3287 2.21 5 O 3693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19006 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3143 Classifications: {'peptide': 408} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 392} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3140 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 14, 'TRANS': 393} Chain breaks: 2 Chain: "C" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3140 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 14, 'TRANS': 393} Chain breaks: 2 Chain: "D" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2574 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 10, 'TRANS': 320} Chain breaks: 4 Chain: "E" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3107 Classifications: {'peptide': 400} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 386} Chain breaks: 5 Chain: "F" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2523 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 10, 'TRANS': 314} Chain breaks: 4 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1028 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "H" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.55, per 1000 atoms: 0.24 Number of scatterers: 19006 At special positions: 0 Unit cell: (153.51, 138.675, 122.55, 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 84 16.00 P 12 15.00 O 3693 8.00 N 3287 7.00 C 11930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 894.8 milliseconds 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 26 sheets defined 49.7% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.784A pdb=" N GLY A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 107 through 118 Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.888A pdb=" N TYR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.861A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'B' and resid 11 through 17 removed outlier: 3.920A pdb=" N ILE B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 240 through 247 removed outlier: 3.643A pdb=" N ASN B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 347 through 350 Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.687A pdb=" N ASP B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.546A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 439 through 449 removed outlier: 3.600A pdb=" N ASP B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 17 removed outlier: 3.865A pdb=" N ILE C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 107 through 118 Processing helix chain 'C' and resid 173 through 184 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.676A pdb=" N TYR C 209 " --> pdb=" O CYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 273 through 290 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.777A pdb=" N TYR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 320 " --> pdb=" O HIS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 367 through 382 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 439 through 449 removed outlier: 4.268A pdb=" N ASP C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.641A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 269 through 286 Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.709A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 378 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 4.199A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 435 through 449 removed outlier: 3.558A pdb=" N MET D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 Processing helix chain 'E' and resid 49 through 65 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 175 through 185 removed outlier: 3.563A pdb=" N LYS E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 257 through 261 removed outlier: 3.877A pdb=" N LEU E 260 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 287 removed outlier: 3.566A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.754A pdb=" N SER E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 317 " --> pdb=" O ASN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.709A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E 416 " --> pdb=" O VAL E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 447 Processing helix chain 'F' and resid 19 through 23 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 244 through 251 Processing helix chain 'F' and resid 271 through 286 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.512A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.699A pdb=" N ILE F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 447 removed outlier: 3.641A pdb=" N MET F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 805 through 816 Processing helix chain 'G' and resid 821 through 830 removed outlier: 4.272A pdb=" N CYS G 825 " --> pdb=" O ASP G 821 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA G 830 " --> pdb=" O ALA G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 836 through 842 Processing helix chain 'G' and resid 846 through 858 Processing helix chain 'G' and resid 866 through 876 Processing helix chain 'G' and resid 877 through 879 No H-bonds generated for 'chain 'G' and resid 877 through 879' Processing helix chain 'G' and resid 884 through 889 removed outlier: 4.028A pdb=" N LEU G 888 " --> pdb=" O MET G 884 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 889 " --> pdb=" O MET G 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 884 through 889' Processing helix chain 'G' and resid 890 through 892 No H-bonds generated for 'chain 'G' and resid 890 through 892' Processing helix chain 'G' and resid 893 through 906 removed outlier: 3.815A pdb=" N ILE G 897 " --> pdb=" O GLN G 893 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP G 903 " --> pdb=" O GLN G 899 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU G 904 " --> pdb=" O LEU G 900 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 924 removed outlier: 3.559A pdb=" N ILE G 917 " --> pdb=" O THR G 913 " (cutoff:3.500A) Processing helix chain 'H' and resid 846 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.593A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 360 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 239 Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 171 removed outlier: 7.794A pdb=" N ILE A 158 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU A 138 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY A 160 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 134 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 206 removed outlier: 5.858A pdb=" N ARG A 205 " --> pdb=" O VAL A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA6, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.036A pdb=" N ILE F 356 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.490A pdb=" N CYS B 94 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP B 302 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET B 96 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 167 through 171 removed outlier: 7.302A pdb=" N ILE B 158 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU B 138 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY B 160 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 202 removed outlier: 3.661A pdb=" N LYS B 201 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR B 192 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 205 through 206 removed outlier: 6.054A pdb=" N ARG B 205 " --> pdb=" O VAL B 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.503A pdb=" N LEU C 299 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 167 through 170 removed outlier: 7.030A pdb=" N ILE C 158 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU C 138 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY C 160 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 201 removed outlier: 4.205A pdb=" N ASP C 189 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.310A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 243 removed outlier: 3.600A pdb=" N GLU D 290 " --> pdb=" O ARG D 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.111A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 199 through 200 Processing sheet with id=AC4, first strand: chain 'E' and resid 199 through 200 Processing sheet with id=AC5, first strand: chain 'E' and resid 141 through 144 removed outlier: 3.647A pdb=" N LYS E 164 " --> pdb=" O GLU E 141 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL E 143 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N THR E 162 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC7, first strand: chain 'F' and resid 240 through 243 Processing sheet with id=AC8, first strand: chain 'F' and resid 332 through 334 912 hydrogen bonds defined for protein. 2634 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: 3.63 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6335 1.34 - 1.46: 3328 1.46 - 1.58: 9418 1.58 - 1.70: 18 1.70 - 1.82: 142 Bond restraints: 19241 Sorted by residual: bond pdb=" N ASP D 379 " pdb=" CA ASP D 379 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.41e-02 5.03e+03 6.39e+00 bond pdb=" N LEU D 395 " pdb=" CA LEU D 395 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.27e-02 6.20e+03 5.45e+00 bond pdb=" N LEU F 60 " pdb=" CA LEU F 60 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.85e+00 bond pdb=" N GLY D 394 " pdb=" CA GLY D 394 " ideal model delta sigma weight residual 1.450 1.474 -0.024 1.74e-02 3.30e+03 1.97e+00 bond pdb=" CB MET E 443 " pdb=" CG MET E 443 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.74e+00 ... (remaining 19236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 25333 2.04 - 4.08: 484 4.08 - 6.12: 103 6.12 - 8.16: 19 8.16 - 10.20: 8 Bond angle restraints: 25947 Sorted by residual: angle pdb=" CA GLU D 396 " pdb=" CB GLU D 396 " pdb=" CG GLU D 396 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" C LEU D 395 " pdb=" N GLU D 396 " pdb=" CA GLU D 396 " ideal model delta sigma weight residual 122.23 114.38 7.85 1.57e+00 4.06e-01 2.50e+01 angle pdb=" C ASP E 34 " pdb=" CA ASP E 34 " pdb=" CB ASP E 34 " ideal model delta sigma weight residual 115.79 110.03 5.76 1.19e+00 7.06e-01 2.34e+01 angle pdb=" C ASP F 34 " pdb=" CA ASP F 34 " pdb=" CB ASP F 34 " ideal model delta sigma weight residual 115.79 110.19 5.60 1.19e+00 7.06e-01 2.22e+01 angle pdb=" C ASP D 34 " pdb=" CA ASP D 34 " pdb=" CB ASP D 34 " ideal model delta sigma weight residual 115.79 110.32 5.47 1.19e+00 7.06e-01 2.11e+01 ... (remaining 25942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 10777 25.68 - 51.35: 963 51.35 - 77.03: 114 77.03 - 102.71: 23 102.71 - 128.38: 1 Dihedral angle restraints: 11878 sinusoidal: 4900 harmonic: 6978 Sorted by residual: dihedral pdb=" O2A ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PA ADP B 501 " pdb=" PB ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 68.39 -128.38 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -141.07 81.08 1 2.00e+01 2.50e-03 2.03e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 -139.58 79.58 1 2.00e+01 2.50e-03 1.97e+01 ... (remaining 11875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2598 0.061 - 0.121: 438 0.121 - 0.182: 27 0.182 - 0.242: 2 0.242 - 0.303: 1 Chirality restraints: 3066 Sorted by residual: chirality pdb=" CG LEU E 60 " pdb=" CB LEU E 60 " pdb=" CD1 LEU E 60 " pdb=" CD2 LEU E 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE D 406 " pdb=" CA ILE D 406 " pdb=" CG1 ILE D 406 " pdb=" CG2 ILE D 406 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA GLU D 396 " pdb=" N GLU D 396 " pdb=" C GLU D 396 " pdb=" CB GLU D 396 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 3063 not shown) Planarity restraints: 3289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 283 " 0.025 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP E 283 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP E 283 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 283 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 283 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 283 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 283 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 283 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 283 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 283 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 131 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" C TYR C 131 " 0.048 2.00e-02 2.50e+03 pdb=" O TYR C 131 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU C 132 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 131 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C TYR A 131 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR A 131 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 132 " 0.014 2.00e-02 2.50e+03 ... (remaining 3286 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 15 2.55 - 3.13: 14897 3.13 - 3.72: 29785 3.72 - 4.31: 40616 4.31 - 4.90: 66793 Nonbonded interactions: 152106 Sorted by model distance: nonbonded pdb=" NH2 ARG H 881 " pdb=" CE MET H 884 " model vdw 1.958 3.540 nonbonded pdb=" OH TYR F 430 " pdb=" NH2 ARG H 881 " model vdw 2.370 3.120 nonbonded pdb=" O LEU E 244 " pdb=" OD1 ASP E 248 " model vdw 2.457 3.040 nonbonded pdb=" O ARG D 392 " pdb=" OE1 GLU D 396 " model vdw 2.461 3.040 nonbonded pdb=" O ARG C 276 " pdb=" OD1 ASN C 280 " model vdw 2.490 3.040 ... (remaining 152101 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 248 or resid 272 through 449 or resid 501)) selection = (chain 'B' and (resid 7 through 448 or (resid 449 and (name N or name CA or name \ C or name CB or name CG or name OD1 or name OD2)) or resid 501)) selection = (chain 'C' and (resid 7 through 448 or (resid 449 and (name N or name CA or name \ C or name CB or name CG or name OD1 or name OD2)) or resid 501)) } ncs_group { reference = (chain 'D' and (resid 10 through 132 or resid 239 through 262 or resid 266 throu \ gh 449 or resid 501)) selection = (chain 'F' and (resid 10 through 13 or resid 19 through 252 or resid 257 through \ 501)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.880 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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 0.040 19246 Z= 0.150 Angle : 0.728 10.196 25947 Z= 0.370 Chirality : 0.044 0.303 3066 Planarity : 0.004 0.045 3289 Dihedral : 18.171 128.384 7358 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 3.11 % Allowed : 28.93 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2374 helix: 0.54 (0.16), residues: 1134 sheet: -0.79 (0.27), residues: 338 loop : -1.64 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.020 0.001 TYR G 807 PHE 0.011 0.001 PHE H 850 TRP 0.060 0.005 TRP E 283 HIS 0.004 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00317 (19241) covalent geometry : angle 0.72794 (25947) hydrogen bonds : bond 0.13513 ( 908) hydrogen bonds : angle 5.91245 ( 2634) Misc. bond : bond 0.00097 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 311 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7600 (pt0) cc_final: 0.5984 (mt-10) REVERT: A 123 ARG cc_start: 0.6436 (mtp85) cc_final: 0.6033 (mtt90) REVERT: A 278 GLU cc_start: 0.5227 (tt0) cc_final: 0.3753 (tp30) REVERT: A 317 ARG cc_start: 0.7320 (ttp-170) cc_final: 0.6912 (ttp-170) REVERT: A 357 ARG cc_start: 0.6402 (mmm160) cc_final: 0.6160 (mmp-170) REVERT: A 380 GLN cc_start: 0.7434 (mt0) cc_final: 0.6917 (mm110) REVERT: A 385 ASN cc_start: 0.8142 (m-40) cc_final: 0.7873 (m-40) REVERT: A 432 GLU cc_start: 0.7340 (tp30) cc_final: 0.6693 (mt-10) REVERT: B 64 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7261 (mtm180) REVERT: B 102 TYR cc_start: 0.7201 (m-80) cc_final: 0.6728 (m-10) REVERT: B 182 LYS cc_start: 0.5529 (OUTLIER) cc_final: 0.4557 (mmtp) REVERT: B 357 ARG cc_start: 0.5933 (mmm160) cc_final: 0.5326 (mtp85) REVERT: B 371 MET cc_start: 0.7233 (tpt) cc_final: 0.6803 (mmt) REVERT: B 376 LYS cc_start: 0.7620 (tppp) cc_final: 0.7409 (tmmt) REVERT: C 86 GLU cc_start: 0.6898 (tp30) cc_final: 0.6581 (mm-30) REVERT: C 107 LYS cc_start: 0.6849 (mtmm) cc_final: 0.5955 (mtpt) REVERT: C 110 GLU cc_start: 0.7096 (tp30) cc_final: 0.6482 (mt-10) REVERT: C 113 MET cc_start: 0.6510 (ttt) cc_final: 0.6236 (tpt) REVERT: C 114 GLU cc_start: 0.6899 (tt0) cc_final: 0.6529 (tt0) REVERT: C 123 ARG cc_start: 0.6326 (mtt90) cc_final: 0.5495 (mtm180) REVERT: C 306 MET cc_start: 0.7219 (mmt) cc_final: 0.6578 (mmm) REVERT: C 310 GLU cc_start: 0.7363 (tp30) cc_final: 0.6818 (mt-10) REVERT: C 343 ASP cc_start: 0.6371 (t0) cc_final: 0.5986 (t0) REVERT: C 356 ASP cc_start: 0.7710 (t0) cc_final: 0.6988 (m-30) REVERT: C 357 ARG cc_start: 0.6271 (mtm-85) cc_final: 0.5272 (mtp-110) REVERT: C 364 MET cc_start: 0.7288 (mtm) cc_final: 0.6803 (mpp) REVERT: C 373 GLN cc_start: 0.7679 (mt0) cc_final: 0.7279 (mt0) REVERT: D 20 GLU cc_start: 0.6393 (mt-10) cc_final: 0.6104 (mt-10) REVERT: D 29 ARG cc_start: 0.5466 (tpp80) cc_final: 0.5200 (mmt90) REVERT: D 62 MET cc_start: 0.7093 (mtt) cc_final: 0.6764 (mtt) REVERT: D 88 MET cc_start: 0.6787 (mmm) cc_final: 0.6495 (tpt) REVERT: D 378 GLU cc_start: 0.5888 (mm-30) cc_final: 0.5310 (tt0) REVERT: D 436 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6481 (tt0) REVERT: E 78 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6459 (mm110) REVERT: E 300 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7408 (mm-30) REVERT: E 306 ILE cc_start: 0.8554 (tp) cc_final: 0.8234 (tp) REVERT: E 330 ARG cc_start: 0.7750 (mmt90) cc_final: 0.7505 (mmt180) REVERT: E 378 GLU cc_start: 0.6837 (mm-30) cc_final: 0.5598 (mt-10) REVERT: E 392 ARG cc_start: 0.6562 (ttt180) cc_final: 0.6139 (ttt-90) REVERT: F 20 GLU cc_start: 0.6085 (mt-10) cc_final: 0.5731 (mm-30) REVERT: F 307 GLU cc_start: 0.6909 (tp30) cc_final: 0.6048 (mp0) REVERT: F 320 MET cc_start: 0.4908 (ptp) cc_final: 0.4525 (ptt) REVERT: F 341 GLN cc_start: 0.7929 (mt0) cc_final: 0.7350 (mp10) REVERT: F 414 ARG cc_start: 0.7363 (ttm110) cc_final: 0.6566 (mtm-85) REVERT: F 417 LYS cc_start: 0.7465 (mmmt) cc_final: 0.7170 (mmtp) REVERT: F 445 GLU cc_start: 0.5688 (tm-30) cc_final: 0.4143 (mm-30) REVERT: G 819 ARG cc_start: 0.6869 (mmp80) cc_final: 0.6562 (mtm110) REVERT: G 837 LEU cc_start: 0.6976 (tp) cc_final: 0.6677 (tt) REVERT: G 878 LYS cc_start: 0.6132 (mmmt) cc_final: 0.5098 (mtpp) REVERT: G 894 LYS cc_start: 0.5680 (mmtt) cc_final: 0.5354 (mmtt) outliers start: 64 outliers final: 31 residues processed: 365 average time/residue: 0.1628 time to fit residues: 87.5420 Evaluate side-chains 264 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 818 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain G residue 914 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 316 HIS C 42 GLN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 447 GLN G 871 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.197320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188278 restraints weight = 22029.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.160318 restraints weight = 54295.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156949 restraints weight = 55612.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.156430 restraints weight = 48142.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.156448 restraints weight = 41439.630| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19246 Z= 0.157 Angle : 0.654 10.686 25947 Z= 0.314 Chirality : 0.044 0.280 3066 Planarity : 0.004 0.050 3289 Dihedral : 8.285 121.881 2712 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 6.60 % Allowed : 24.42 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2374 helix: 0.64 (0.15), residues: 1160 sheet: -0.95 (0.27), residues: 360 loop : -1.60 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 881 TYR 0.017 0.002 TYR G 807 PHE 0.015 0.002 PHE D 257 TRP 0.038 0.003 TRP E 283 HIS 0.005 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00374 (19241) covalent geometry : angle 0.65371 (25947) hydrogen bonds : bond 0.03424 ( 908) hydrogen bonds : angle 4.72994 ( 2634) Misc. bond : bond 0.00098 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 235 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7862 (pt0) cc_final: 0.7161 (mt-10) REVERT: A 278 GLU cc_start: 0.5352 (tt0) cc_final: 0.3889 (tp30) REVERT: A 317 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6800 (ttp-170) REVERT: A 356 ASP cc_start: 0.6844 (m-30) cc_final: 0.6551 (m-30) REVERT: A 385 ASN cc_start: 0.8082 (m-40) cc_final: 0.7785 (m-40) REVERT: B 14 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7469 (mtp180) REVERT: B 64 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7603 (mtm180) REVERT: B 110 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6972 (mm-30) REVERT: B 113 MET cc_start: 0.5889 (tpt) cc_final: 0.5651 (mmm) REVERT: B 158 ILE cc_start: 0.4845 (OUTLIER) cc_final: 0.4584 (mp) REVERT: B 219 GLU cc_start: 0.1418 (OUTLIER) cc_final: -0.0537 (mt-10) REVERT: B 409 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7719 (mp) REVERT: C 60 LYS cc_start: 0.6999 (mmtp) cc_final: 0.6703 (mttp) REVERT: C 110 GLU cc_start: 0.7287 (tp30) cc_final: 0.6812 (mp0) REVERT: C 306 MET cc_start: 0.7492 (mmt) cc_final: 0.7201 (mmm) REVERT: C 353 ASP cc_start: 0.7527 (t0) cc_final: 0.7320 (t0) REVERT: C 356 ASP cc_start: 0.7883 (t0) cc_final: 0.7674 (m-30) REVERT: C 362 ARG cc_start: 0.7123 (ttt180) cc_final: 0.6820 (ttt-90) REVERT: C 402 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8561 (m) REVERT: D 250 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5615 (mt) REVERT: D 382 MET cc_start: 0.7900 (mtp) cc_final: 0.7622 (mtm) REVERT: D 426 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7563 (mp) REVERT: E 78 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6961 (mm110) REVERT: E 378 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5394 (mt-10) REVERT: E 412 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.7699 (t) REVERT: F 20 GLU cc_start: 0.5597 (mt-10) cc_final: 0.5053 (tm-30) REVERT: F 427 LYS cc_start: 0.7230 (mptt) cc_final: 0.6863 (ttmm) REVERT: F 445 GLU cc_start: 0.6221 (tm-30) cc_final: 0.5126 (mm-30) REVERT: G 868 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6048 (tp) REVERT: G 878 LYS cc_start: 0.6357 (mmmt) cc_final: 0.5440 (mtpp) REVERT: G 885 MET cc_start: 0.7195 (mmt) cc_final: 0.6967 (mmm) REVERT: G 894 LYS cc_start: 0.5972 (mmtt) cc_final: 0.5608 (mmtt) REVERT: G 924 TYR cc_start: 0.7339 (m-80) cc_final: 0.6622 (m-80) REVERT: H 884 MET cc_start: 0.4823 (ttp) cc_final: 0.4459 (mtp) outliers start: 136 outliers final: 75 residues processed: 347 average time/residue: 0.1521 time to fit residues: 79.8916 Evaluate side-chains 285 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 200 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 818 THR Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 839 MET Chi-restraints excluded: chain G residue 840 PHE Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 182 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 196 ASN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS F 404 GLN F 447 GLN G 872 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.185570 restraints weight = 22097.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.155066 restraints weight = 53650.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.153273 restraints weight = 53900.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.152844 restraints weight = 47766.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.153119 restraints weight = 41890.367| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19246 Z= 0.162 Angle : 0.633 10.361 25947 Z= 0.304 Chirality : 0.043 0.197 3066 Planarity : 0.004 0.039 3289 Dihedral : 7.938 120.426 2690 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.84 % Favored : 95.11 % Rotamer: Outliers : 6.89 % Allowed : 23.93 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.17), residues: 2374 helix: 0.69 (0.15), residues: 1159 sheet: -0.77 (0.26), residues: 369 loop : -1.68 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 123 TYR 0.014 0.002 TYR G 807 PHE 0.012 0.001 PHE G 912 TRP 0.028 0.002 TRP E 283 HIS 0.004 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00388 (19241) covalent geometry : angle 0.63297 (25947) hydrogen bonds : bond 0.03434 ( 908) hydrogen bonds : angle 4.60275 ( 2634) Misc. bond : bond 0.00078 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 220 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.5310 (tt0) cc_final: 0.3865 (tp30) REVERT: A 295 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8688 (m) REVERT: A 317 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6781 (ttp-170) REVERT: A 356 ASP cc_start: 0.7148 (m-30) cc_final: 0.6639 (m-30) REVERT: A 384 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 385 ASN cc_start: 0.7955 (m-40) cc_final: 0.7719 (m-40) REVERT: A 441 LYS cc_start: 0.8157 (tptt) cc_final: 0.7622 (tttm) REVERT: B 14 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7360 (mtp180) REVERT: B 79 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8302 (mt) REVERT: B 110 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6978 (mm-30) REVERT: B 158 ILE cc_start: 0.4899 (OUTLIER) cc_final: 0.4590 (mp) REVERT: B 182 LYS cc_start: 0.5806 (OUTLIER) cc_final: 0.4428 (mmtp) REVERT: B 219 GLU cc_start: 0.1121 (OUTLIER) cc_final: -0.0615 (mt-10) REVERT: B 392 ASN cc_start: 0.7659 (m-40) cc_final: 0.7456 (m110) REVERT: B 409 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7695 (mp) REVERT: C 60 LYS cc_start: 0.7104 (mmtp) cc_final: 0.6738 (mttp) REVERT: C 110 GLU cc_start: 0.7308 (tp30) cc_final: 0.6874 (mp0) REVERT: C 159 ILE cc_start: 0.1943 (OUTLIER) cc_final: 0.0972 (pt) REVERT: C 303 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6576 (mm-30) REVERT: C 306 MET cc_start: 0.7527 (mmt) cc_final: 0.7192 (mmm) REVERT: C 362 ARG cc_start: 0.7111 (ttt180) cc_final: 0.6863 (ttt90) REVERT: C 402 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8584 (m) REVERT: D 90 MET cc_start: 0.7466 (mtp) cc_final: 0.6910 (ttm) REVERT: D 382 MET cc_start: 0.7926 (mtp) cc_final: 0.7637 (mtm) REVERT: D 396 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: D 426 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7553 (mp) REVERT: D 447 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7533 (mm-40) REVERT: E 78 GLN cc_start: 0.7459 (mm-40) cc_final: 0.6982 (mm110) REVERT: E 378 GLU cc_start: 0.6247 (mm-30) cc_final: 0.5377 (mt-10) REVERT: E 412 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7782 (t) REVERT: F 20 GLU cc_start: 0.5332 (mt-10) cc_final: 0.4800 (tm-30) REVERT: F 242 VAL cc_start: 0.6433 (p) cc_final: 0.6140 (m) REVERT: F 288 LYS cc_start: 0.6315 (tppt) cc_final: 0.5798 (tptm) REVERT: F 400 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6754 (mmm-85) REVERT: F 427 LYS cc_start: 0.7220 (mptt) cc_final: 0.6767 (ttmm) REVERT: F 445 GLU cc_start: 0.6298 (tm-30) cc_final: 0.4777 (mm-30) REVERT: G 878 LYS cc_start: 0.6363 (mmmt) cc_final: 0.5371 (mtpp) REVERT: G 885 MET cc_start: 0.7186 (mmt) cc_final: 0.6859 (mmm) REVERT: G 894 LYS cc_start: 0.6074 (mmtt) cc_final: 0.5656 (mmtt) REVERT: G 901 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: H 853 LEU cc_start: 0.4763 (OUTLIER) cc_final: 0.4077 (tp) outliers start: 142 outliers final: 89 residues processed: 336 average time/residue: 0.1446 time to fit residues: 74.3436 Evaluate side-chains 308 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 201 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 400 ARG Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 840 PHE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 901 PHE Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain G residue 914 LEU Chi-restraints excluded: chain H residue 853 LEU Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 0.0050 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 447 GLN ** G 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.192757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183400 restraints weight = 22174.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156873 restraints weight = 56686.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.153007 restraints weight = 57044.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.152229 restraints weight = 51178.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.152423 restraints weight = 39508.161| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19246 Z= 0.195 Angle : 0.655 10.414 25947 Z= 0.316 Chirality : 0.044 0.181 3066 Planarity : 0.004 0.044 3289 Dihedral : 8.057 117.380 2683 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 7.43 % Allowed : 23.79 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2374 helix: 0.57 (0.15), residues: 1160 sheet: -0.75 (0.26), residues: 354 loop : -1.76 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 400 TYR 0.014 0.002 TYR B 366 PHE 0.013 0.002 PHE D 261 TRP 0.019 0.002 TRP E 283 HIS 0.005 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00472 (19241) covalent geometry : angle 0.65478 (25947) hydrogen bonds : bond 0.03505 ( 908) hydrogen bonds : angle 4.66089 ( 2634) Misc. bond : bond 0.00086 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 208 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 278 GLU cc_start: 0.5272 (tt0) cc_final: 0.4024 (tp30) REVERT: A 295 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8816 (m) REVERT: A 317 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6708 (ttp-170) REVERT: A 356 ASP cc_start: 0.7103 (m-30) cc_final: 0.6845 (m-30) REVERT: A 384 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 441 LYS cc_start: 0.8098 (tptt) cc_final: 0.7642 (tttm) REVERT: B 14 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7308 (mtp180) REVERT: B 158 ILE cc_start: 0.4892 (OUTLIER) cc_final: 0.4652 (mp) REVERT: B 182 LYS cc_start: 0.5894 (OUTLIER) cc_final: 0.4441 (mmtp) REVERT: B 219 GLU cc_start: 0.1405 (OUTLIER) cc_final: -0.0369 (mt-10) REVERT: B 409 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 60 LYS cc_start: 0.7086 (mmtp) cc_final: 0.6727 (mttp) REVERT: C 110 GLU cc_start: 0.7287 (tp30) cc_final: 0.6937 (mp0) REVERT: C 306 MET cc_start: 0.7474 (mmt) cc_final: 0.7175 (mmm) REVERT: C 402 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8550 (m) REVERT: D 90 MET cc_start: 0.7577 (mtp) cc_final: 0.7218 (ttm) REVERT: D 376 GLU cc_start: 0.5692 (OUTLIER) cc_final: 0.5484 (mm-30) REVERT: D 382 MET cc_start: 0.7894 (mtp) cc_final: 0.7643 (mtm) REVERT: D 396 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: D 426 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7592 (mp) REVERT: D 432 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7770 (mp) REVERT: E 78 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7030 (mm110) REVERT: E 146 GLN cc_start: -0.1020 (OUTLIER) cc_final: -0.1378 (mt0) REVERT: E 378 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5338 (mt-10) REVERT: F 88 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6696 (tmm) REVERT: F 242 VAL cc_start: 0.6435 (p) cc_final: 0.6211 (m) REVERT: F 267 GLU cc_start: 0.4552 (mm-30) cc_final: 0.4216 (tp30) REVERT: F 288 LYS cc_start: 0.6061 (tppt) cc_final: 0.5653 (tptm) REVERT: F 427 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6779 (ttmm) REVERT: G 846 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6541 (mt-10) REVERT: G 878 LYS cc_start: 0.6514 (mmmt) cc_final: 0.5671 (mtpt) REVERT: G 885 MET cc_start: 0.7128 (mmt) cc_final: 0.6814 (mmm) REVERT: G 901 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: H 853 LEU cc_start: 0.4750 (OUTLIER) cc_final: 0.3950 (tp) REVERT: H 884 MET cc_start: 0.4620 (ttp) cc_final: 0.3868 (ttp) REVERT: H 886 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.4897 (pp) outliers start: 153 outliers final: 108 residues processed: 327 average time/residue: 0.1412 time to fit residues: 71.7783 Evaluate side-chains 318 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 191 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 426 ILE Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 888 LEU Chi-restraints excluded: chain G residue 901 PHE Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain G residue 914 LEU Chi-restraints excluded: chain H residue 853 LEU Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 154 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 171 optimal weight: 50.0000 chunk 32 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.195005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.186300 restraints weight = 22015.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163771 restraints weight = 52430.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.160764 restraints weight = 64284.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.160391 restraints weight = 55358.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.160276 restraints weight = 43368.306| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19246 Z= 0.129 Angle : 0.589 10.227 25947 Z= 0.282 Chirality : 0.042 0.159 3066 Planarity : 0.004 0.041 3289 Dihedral : 7.735 117.431 2683 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 5.73 % Allowed : 25.24 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2374 helix: 0.81 (0.16), residues: 1161 sheet: -0.79 (0.26), residues: 361 loop : -1.70 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 284 TYR 0.012 0.001 TYR B 366 PHE 0.009 0.001 PHE G 912 TRP 0.014 0.001 TRP E 283 HIS 0.004 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00306 (19241) covalent geometry : angle 0.58896 (25947) hydrogen bonds : bond 0.03010 ( 908) hydrogen bonds : angle 4.44845 ( 2634) Misc. bond : bond 0.00069 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 202 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 278 GLU cc_start: 0.5064 (tt0) cc_final: 0.4072 (tp30) REVERT: A 295 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8784 (m) REVERT: A 317 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6689 (ttm170) REVERT: A 356 ASP cc_start: 0.7091 (m-30) cc_final: 0.6829 (m-30) REVERT: A 384 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8029 (mt) REVERT: A 426 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 441 LYS cc_start: 0.8034 (tptt) cc_final: 0.7681 (ttpp) REVERT: B 14 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7268 (mtp180) REVERT: B 79 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8377 (mt) REVERT: B 113 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.5419 (mtt) REVERT: B 182 LYS cc_start: 0.5791 (OUTLIER) cc_final: 0.4454 (mmtp) REVERT: B 219 GLU cc_start: 0.1814 (OUTLIER) cc_final: 0.0079 (mt-10) REVERT: B 409 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7528 (mp) REVERT: C 60 LYS cc_start: 0.7055 (mmtp) cc_final: 0.6753 (mttp) REVERT: C 110 GLU cc_start: 0.7296 (tp30) cc_final: 0.6884 (mp0) REVERT: C 159 ILE cc_start: 0.3016 (OUTLIER) cc_final: 0.2161 (pt) REVERT: C 243 LEU cc_start: 0.8132 (mm) cc_final: 0.7927 (mt) REVERT: C 303 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6506 (mm-30) REVERT: C 306 MET cc_start: 0.7422 (mmt) cc_final: 0.7127 (mmm) REVERT: C 362 ARG cc_start: 0.7048 (ttt180) cc_final: 0.6832 (ttt90) REVERT: C 402 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8519 (m) REVERT: D 90 MET cc_start: 0.7536 (mtp) cc_final: 0.7156 (ttm) REVERT: D 382 MET cc_start: 0.7866 (mtp) cc_final: 0.7603 (mtm) REVERT: D 426 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7624 (mp) REVERT: D 447 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7675 (mm-40) REVERT: E 378 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5848 (mm-30) REVERT: E 412 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7825 (t) REVERT: F 88 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.6710 (tmm) REVERT: F 242 VAL cc_start: 0.6312 (p) cc_final: 0.6076 (m) REVERT: F 267 GLU cc_start: 0.4598 (mm-30) cc_final: 0.4374 (tp30) REVERT: F 427 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6687 (ttmm) REVERT: G 878 LYS cc_start: 0.6644 (mmmt) cc_final: 0.5891 (mtpt) REVERT: G 885 MET cc_start: 0.7147 (mmt) cc_final: 0.6866 (mmm) REVERT: H 853 LEU cc_start: 0.4431 (OUTLIER) cc_final: 0.3706 (tp) REVERT: H 886 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.4789 (pp) outliers start: 118 outliers final: 79 residues processed: 295 average time/residue: 0.1394 time to fit residues: 64.2774 Evaluate side-chains 293 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 195 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain G residue 818 THR Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 839 MET Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 888 LEU Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain G residue 914 LEU Chi-restraints excluded: chain H residue 853 LEU Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 18 optimal weight: 30.0000 chunk 76 optimal weight: 0.6980 chunk 217 optimal weight: 0.9990 chunk 238 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 118 optimal weight: 0.2980 chunk 93 optimal weight: 40.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 392 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.192686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.184141 restraints weight = 21974.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.155589 restraints weight = 48811.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154064 restraints weight = 54256.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.153750 restraints weight = 46573.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154042 restraints weight = 40375.177| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19246 Z= 0.133 Angle : 0.588 10.152 25947 Z= 0.281 Chirality : 0.042 0.168 3066 Planarity : 0.004 0.041 3289 Dihedral : 7.576 115.626 2680 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 6.36 % Allowed : 24.66 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2374 helix: 0.89 (0.16), residues: 1156 sheet: -0.79 (0.27), residues: 358 loop : -1.68 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 392 TYR 0.012 0.001 TYR B 366 PHE 0.008 0.001 PHE D 261 TRP 0.012 0.001 TRP E 283 HIS 0.004 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00313 (19241) covalent geometry : angle 0.58777 (25947) hydrogen bonds : bond 0.02981 ( 908) hydrogen bonds : angle 4.38443 ( 2634) Misc. bond : bond 0.00072 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 195 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 278 GLU cc_start: 0.5167 (tt0) cc_final: 0.4078 (tp30) REVERT: A 295 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8801 (m) REVERT: A 317 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6960 (mtm-85) REVERT: A 356 ASP cc_start: 0.7144 (m-30) cc_final: 0.6862 (m-30) REVERT: A 384 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8105 (mt) REVERT: A 426 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 441 LYS cc_start: 0.8002 (tptt) cc_final: 0.7727 (ttpp) REVERT: B 14 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7258 (mtp180) REVERT: B 79 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8380 (mt) REVERT: B 113 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.5435 (mtt) REVERT: B 182 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.4446 (mmtp) REVERT: B 219 GLU cc_start: 0.1449 (OUTLIER) cc_final: -0.0231 (mt-10) REVERT: B 303 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: B 409 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7464 (mp) REVERT: C 60 LYS cc_start: 0.7027 (mmtp) cc_final: 0.6626 (mttp) REVERT: C 110 GLU cc_start: 0.7289 (tp30) cc_final: 0.6844 (mp0) REVERT: C 159 ILE cc_start: 0.2670 (OUTLIER) cc_final: 0.1871 (pt) REVERT: C 306 MET cc_start: 0.7441 (mmt) cc_final: 0.7155 (mmm) REVERT: C 362 ARG cc_start: 0.7066 (ttt180) cc_final: 0.6831 (ttt90) REVERT: C 402 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8537 (m) REVERT: D 90 MET cc_start: 0.7553 (mtp) cc_final: 0.7227 (ttm) REVERT: D 320 MET cc_start: 0.5325 (ptt) cc_final: 0.4955 (ptt) REVERT: D 376 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5474 (mm-30) REVERT: D 382 MET cc_start: 0.7907 (mtp) cc_final: 0.7639 (mtm) REVERT: D 426 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7572 (mp) REVERT: D 432 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7641 (mp) REVERT: D 447 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7588 (mm-40) REVERT: E 78 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7112 (mm110) REVERT: E 146 GLN cc_start: -0.0841 (OUTLIER) cc_final: -0.1192 (mt0) REVERT: F 88 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.6640 (tmm) REVERT: F 267 GLU cc_start: 0.4586 (mm-30) cc_final: 0.4309 (tp30) REVERT: G 878 LYS cc_start: 0.6485 (mmmt) cc_final: 0.5681 (mtpt) REVERT: H 853 LEU cc_start: 0.4686 (OUTLIER) cc_final: 0.3860 (tp) REVERT: H 882 PHE cc_start: 0.3803 (OUTLIER) cc_final: 0.3564 (t80) REVERT: H 886 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5174 (pp) outliers start: 131 outliers final: 92 residues processed: 299 average time/residue: 0.1399 time to fit residues: 65.4966 Evaluate side-chains 300 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 186 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 818 THR Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 888 LEU Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain G residue 914 LEU Chi-restraints excluded: chain H residue 853 LEU Chi-restraints excluded: chain H residue 882 PHE Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 208 optimal weight: 2.9990 chunk 99 optimal weight: 50.0000 chunk 54 optimal weight: 50.0000 chunk 90 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.196649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.187363 restraints weight = 21938.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.161780 restraints weight = 54415.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158936 restraints weight = 62451.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.158895 restraints weight = 52617.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158967 restraints weight = 39497.183| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19246 Z= 0.125 Angle : 0.581 10.111 25947 Z= 0.278 Chirality : 0.041 0.168 3066 Planarity : 0.003 0.041 3289 Dihedral : 7.481 113.970 2680 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.53 % Rotamer: Outliers : 6.02 % Allowed : 25.63 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2374 helix: 0.96 (0.16), residues: 1155 sheet: -0.79 (0.27), residues: 358 loop : -1.69 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 414 TYR 0.011 0.001 TYR B 366 PHE 0.007 0.001 PHE D 261 TRP 0.011 0.001 TRP E 283 HIS 0.003 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00294 (19241) covalent geometry : angle 0.58054 (25947) hydrogen bonds : bond 0.02908 ( 908) hydrogen bonds : angle 4.32972 ( 2634) Misc. bond : bond 0.00071 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 199 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 278 GLU cc_start: 0.5040 (tt0) cc_final: 0.4083 (tp30) REVERT: A 295 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8779 (m) REVERT: A 317 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6963 (mtm-85) REVERT: A 356 ASP cc_start: 0.7172 (m-30) cc_final: 0.6892 (m-30) REVERT: A 384 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8039 (mt) REVERT: A 426 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: A 441 LYS cc_start: 0.8015 (tptt) cc_final: 0.7728 (ttpp) REVERT: B 14 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7271 (mtp180) REVERT: B 79 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 182 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.4466 (mmtp) REVERT: B 219 GLU cc_start: 0.1515 (OUTLIER) cc_final: -0.0123 (mt-10) REVERT: B 278 GLU cc_start: 0.6142 (pp20) cc_final: 0.5449 (tm-30) REVERT: B 303 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: B 409 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7494 (mp) REVERT: C 60 LYS cc_start: 0.7006 (mmtp) cc_final: 0.6603 (mttp) REVERT: C 110 GLU cc_start: 0.7291 (tp30) cc_final: 0.6847 (mp0) REVERT: C 306 MET cc_start: 0.7468 (mmt) cc_final: 0.7194 (mmm) REVERT: C 362 ARG cc_start: 0.7053 (ttt180) cc_final: 0.6843 (ttt90) REVERT: C 402 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8524 (m) REVERT: D 90 MET cc_start: 0.7534 (mtp) cc_final: 0.6958 (ttm) REVERT: D 320 MET cc_start: 0.5279 (ptt) cc_final: 0.4944 (ptt) REVERT: D 382 MET cc_start: 0.7904 (mtp) cc_final: 0.7631 (mtm) REVERT: D 415 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.5966 (ttpt) REVERT: D 426 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7597 (mp) REVERT: D 432 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.7627 (mp) REVERT: D 447 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7670 (mm-40) REVERT: E 78 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7072 (mm110) REVERT: E 146 GLN cc_start: -0.0590 (OUTLIER) cc_final: -0.0935 (mt0) REVERT: E 412 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7809 (t) REVERT: F 88 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6857 (tmm) REVERT: F 267 GLU cc_start: 0.4539 (mm-30) cc_final: 0.3865 (pm20) REVERT: G 846 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6433 (mt-10) REVERT: G 878 LYS cc_start: 0.6526 (mmmt) cc_final: 0.5707 (mtpt) REVERT: H 853 LEU cc_start: 0.4476 (OUTLIER) cc_final: 0.3651 (tp) REVERT: H 886 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5101 (pp) outliers start: 124 outliers final: 94 residues processed: 294 average time/residue: 0.1298 time to fit residues: 59.5287 Evaluate side-chains 309 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 195 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 415 LYS Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 818 THR Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 839 MET Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 888 LEU Chi-restraints excluded: chain G residue 914 LEU Chi-restraints excluded: chain H residue 853 LEU Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 24 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 228 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 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 = 0.4208 r_free = 0.4208 target = 0.197140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.188700 restraints weight = 22092.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.159417 restraints weight = 50126.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157324 restraints weight = 51745.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.157645 restraints weight = 45162.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.157510 restraints weight = 39530.307| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19246 Z= 0.098 Angle : 0.558 10.025 25947 Z= 0.265 Chirality : 0.040 0.162 3066 Planarity : 0.003 0.040 3289 Dihedral : 7.190 112.306 2678 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 5.19 % Allowed : 26.36 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2374 helix: 1.15 (0.16), residues: 1153 sheet: -0.84 (0.26), residues: 362 loop : -1.59 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 414 TYR 0.009 0.001 TYR B 366 PHE 0.007 0.001 PHE G 912 TRP 0.009 0.001 TRP E 283 HIS 0.013 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00220 (19241) covalent geometry : angle 0.55841 (25947) hydrogen bonds : bond 0.02660 ( 908) hydrogen bonds : angle 4.21815 ( 2634) Misc. bond : bond 0.00070 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 201 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 278 GLU cc_start: 0.5162 (tt0) cc_final: 0.4004 (tp30) REVERT: A 295 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8743 (m) REVERT: A 317 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6768 (ttm170) REVERT: A 356 ASP cc_start: 0.7147 (m-30) cc_final: 0.6765 (m-30) REVERT: A 384 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7942 (mt) REVERT: A 426 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: A 441 LYS cc_start: 0.7973 (tptt) cc_final: 0.7702 (ttpp) REVERT: B 14 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7308 (mtp180) REVERT: B 182 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.4520 (mmtp) REVERT: B 219 GLU cc_start: 0.1030 (OUTLIER) cc_final: -0.0490 (mt-10) REVERT: B 278 GLU cc_start: 0.6314 (pp20) cc_final: 0.5637 (tm-30) REVERT: B 303 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7097 (mt-10) REVERT: B 307 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8615 (mt) REVERT: C 60 LYS cc_start: 0.7016 (mmtp) cc_final: 0.6592 (mttp) REVERT: C 110 GLU cc_start: 0.7281 (tp30) cc_final: 0.6804 (mp0) REVERT: C 303 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6382 (mm-30) REVERT: C 306 MET cc_start: 0.7419 (mmt) cc_final: 0.7155 (mmm) REVERT: C 402 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8510 (m) REVERT: D 83 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6873 (mtmm) REVERT: D 90 MET cc_start: 0.7426 (mtp) cc_final: 0.6916 (ttm) REVERT: D 320 MET cc_start: 0.5264 (ptt) cc_final: 0.4900 (ptt) REVERT: D 376 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.5474 (mm-30) REVERT: D 382 MET cc_start: 0.7885 (mtp) cc_final: 0.7624 (mtm) REVERT: D 415 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5909 (ttpt) REVERT: D 426 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7607 (mp) REVERT: D 445 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6810 (mt-10) REVERT: D 447 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7463 (mm-40) REVERT: E 78 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7051 (mm110) REVERT: E 146 GLN cc_start: -0.1189 (OUTLIER) cc_final: -0.1539 (mt0) REVERT: E 378 GLU cc_start: 0.5596 (mm-30) cc_final: 0.5078 (mt-10) REVERT: E 404 GLN cc_start: 0.6093 (OUTLIER) cc_final: 0.5704 (mt0) REVERT: E 412 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7847 (t) REVERT: F 41 GLN cc_start: 0.6726 (tm-30) cc_final: 0.6455 (mm-40) REVERT: F 88 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.6864 (tmm) REVERT: F 267 GLU cc_start: 0.4373 (mm-30) cc_final: 0.3675 (pm20) REVERT: G 846 GLU cc_start: 0.7598 (mm-30) cc_final: 0.6461 (mt-10) REVERT: G 878 LYS cc_start: 0.6324 (mmmt) cc_final: 0.5434 (mtpp) REVERT: H 853 LEU cc_start: 0.4501 (OUTLIER) cc_final: 0.3753 (tp) REVERT: H 882 PHE cc_start: 0.3580 (OUTLIER) cc_final: 0.3036 (t80) REVERT: H 886 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5471 (pp) outliers start: 107 outliers final: 73 residues processed: 283 average time/residue: 0.1413 time to fit residues: 62.2562 Evaluate side-chains 284 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 189 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 415 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 840 PHE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 888 LEU Chi-restraints excluded: chain G residue 914 LEU Chi-restraints excluded: chain H residue 853 LEU Chi-restraints excluded: chain H residue 882 PHE Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 156 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 18 HIS ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.188059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178419 restraints weight = 22145.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.156485 restraints weight = 57567.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152581 restraints weight = 68316.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151614 restraints weight = 58714.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.151751 restraints weight = 46311.170| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19246 Z= 0.232 Angle : 0.683 11.520 25947 Z= 0.330 Chirality : 0.045 0.185 3066 Planarity : 0.004 0.045 3289 Dihedral : 7.894 105.129 2678 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.48 % Favored : 94.48 % Rotamer: Outliers : 5.68 % Allowed : 26.17 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2374 helix: 0.69 (0.15), residues: 1152 sheet: -0.85 (0.27), residues: 357 loop : -1.80 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 414 TYR 0.015 0.002 TYR B 366 PHE 0.011 0.002 PHE D 261 TRP 0.015 0.002 TRP E 283 HIS 0.006 0.001 HIS B 393 Details of bonding type rmsd covalent geometry : bond 0.00563 (19241) covalent geometry : angle 0.68276 (25947) hydrogen bonds : bond 0.03608 ( 908) hydrogen bonds : angle 4.58796 ( 2634) Misc. bond : bond 0.00086 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 194 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 278 GLU cc_start: 0.5104 (tt0) cc_final: 0.4077 (tp30) REVERT: A 295 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8817 (m) REVERT: A 317 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6815 (ttp-170) REVERT: A 356 ASP cc_start: 0.7214 (m-30) cc_final: 0.6921 (m-30) REVERT: A 384 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8065 (mt) REVERT: A 426 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 441 LYS cc_start: 0.8075 (tptt) cc_final: 0.7806 (ttpp) REVERT: B 14 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7230 (mtp180) REVERT: B 182 LYS cc_start: 0.5775 (OUTLIER) cc_final: 0.4428 (mmtp) REVERT: B 303 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: C 60 LYS cc_start: 0.7000 (mmtp) cc_final: 0.6555 (mttp) REVERT: C 110 GLU cc_start: 0.7339 (tp30) cc_final: 0.6924 (mp0) REVERT: C 306 MET cc_start: 0.7458 (mmt) cc_final: 0.7165 (mmm) REVERT: C 402 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8601 (m) REVERT: D 83 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7241 (mtmt) REVERT: D 90 MET cc_start: 0.7610 (mtp) cc_final: 0.7320 (ttm) REVERT: D 382 MET cc_start: 0.7939 (mtp) cc_final: 0.7665 (mtm) REVERT: D 396 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: D 415 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6058 (ttpt) REVERT: D 426 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7626 (mp) REVERT: D 432 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.7733 (mp) REVERT: D 447 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7595 (mm-40) REVERT: E 123 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7949 (t80) REVERT: E 146 GLN cc_start: -0.0338 (OUTLIER) cc_final: -0.0702 (mt0) REVERT: E 404 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.5774 (mt0) REVERT: E 443 MET cc_start: 0.7462 (tmm) cc_final: 0.7191 (tmm) REVERT: F 88 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6867 (tmm) REVERT: F 267 GLU cc_start: 0.4938 (mm-30) cc_final: 0.4665 (tp30) REVERT: G 846 GLU cc_start: 0.7657 (mm-30) cc_final: 0.6429 (mt-10) REVERT: G 878 LYS cc_start: 0.6663 (mmmt) cc_final: 0.5739 (mtpp) REVERT: H 853 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.3743 (tp) REVERT: H 882 PHE cc_start: 0.3900 (OUTLIER) cc_final: 0.3609 (t80) REVERT: H 886 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5089 (pp) outliers start: 117 outliers final: 87 residues processed: 290 average time/residue: 0.1391 time to fit residues: 63.1907 Evaluate side-chains 296 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 188 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 415 LYS Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 440 THR Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 818 THR Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 839 MET Chi-restraints excluded: chain G residue 849 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 888 LEU Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain G residue 914 LEU Chi-restraints excluded: chain H residue 853 LEU Chi-restraints excluded: chain H residue 882 PHE Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 113 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 216 optimal weight: 0.0270 chunk 135 optimal weight: 1.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** 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 = 0.4178 r_free = 0.4178 target = 0.193980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.185432 restraints weight = 22091.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.162299 restraints weight = 52810.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.159236 restraints weight = 69518.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.158486 restraints weight = 58213.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158386 restraints weight = 47799.635| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19246 Z= 0.129 Angle : 0.601 11.132 25947 Z= 0.289 Chirality : 0.042 0.167 3066 Planarity : 0.003 0.041 3289 Dihedral : 7.527 106.354 2678 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 4.81 % Allowed : 27.09 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2374 helix: 0.86 (0.16), residues: 1155 sheet: -0.84 (0.27), residues: 357 loop : -1.75 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 414 TYR 0.011 0.001 TYR B 366 PHE 0.007 0.001 PHE G 912 TRP 0.011 0.001 TRP E 283 HIS 0.012 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00304 (19241) covalent geometry : angle 0.60123 (25947) hydrogen bonds : bond 0.02983 ( 908) hydrogen bonds : angle 4.42424 ( 2634) Misc. bond : bond 0.00073 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4748 Ramachandran restraints generated. 2374 Oldfield, 0 Emsley, 2374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 195 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 278 GLU cc_start: 0.5087 (tt0) cc_final: 0.4125 (tp30) REVERT: A 293 GLU cc_start: 0.6507 (tp30) cc_final: 0.6033 (mp0) REVERT: A 295 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8751 (m) REVERT: A 317 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6824 (ttp-170) REVERT: A 356 ASP cc_start: 0.7115 (m-30) cc_final: 0.6780 (m-30) REVERT: A 384 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8018 (mt) REVERT: A 426 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: A 441 LYS cc_start: 0.8055 (tptt) cc_final: 0.7723 (ttpp) REVERT: B 14 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7339 (mtp180) REVERT: B 182 LYS cc_start: 0.5714 (OUTLIER) cc_final: 0.4390 (mmtp) REVERT: B 219 GLU cc_start: 0.1657 (OUTLIER) cc_final: 0.0040 (mt-10) REVERT: B 303 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: C 60 LYS cc_start: 0.6909 (mmtp) cc_final: 0.6509 (mttp) REVERT: C 110 GLU cc_start: 0.7321 (tp30) cc_final: 0.6894 (mp0) REVERT: C 306 MET cc_start: 0.7415 (mmt) cc_final: 0.7126 (mmm) REVERT: C 402 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8492 (m) REVERT: D 83 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6820 (mtmm) REVERT: D 90 MET cc_start: 0.7530 (mtp) cc_final: 0.7173 (ttm) REVERT: D 382 MET cc_start: 0.7904 (mtp) cc_final: 0.7628 (mtm) REVERT: D 396 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: D 415 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5965 (ttpt) REVERT: D 426 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7664 (mp) REVERT: D 432 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.7645 (mp) REVERT: D 447 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7617 (mm-40) REVERT: E 404 GLN cc_start: 0.6006 (OUTLIER) cc_final: 0.5716 (mt0) REVERT: E 443 MET cc_start: 0.7342 (tmm) cc_final: 0.7139 (tmm) REVERT: F 41 GLN cc_start: 0.6739 (tm-30) cc_final: 0.6489 (mm-40) REVERT: F 88 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.6842 (tmm) REVERT: F 267 GLU cc_start: 0.5037 (mm-30) cc_final: 0.4250 (pm20) REVERT: G 846 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6386 (mt-10) REVERT: G 878 LYS cc_start: 0.6584 (mmmt) cc_final: 0.5808 (mtpt) REVERT: G 924 TYR cc_start: 0.7463 (m-80) cc_final: 0.6870 (m-80) REVERT: H 853 LEU cc_start: 0.4483 (OUTLIER) cc_final: 0.3684 (tp) REVERT: H 882 PHE cc_start: 0.3771 (OUTLIER) cc_final: 0.3222 (t80) REVERT: H 886 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5216 (pp) outliers start: 99 outliers final: 75 residues processed: 273 average time/residue: 0.1342 time to fit residues: 57.2640 Evaluate side-chains 286 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 191 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain D residue 415 LYS Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 447 GLN Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 825 CYS Chi-restraints excluded: chain G residue 839 MET Chi-restraints excluded: chain G residue 849 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 861 LEU Chi-restraints excluded: chain G residue 868 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 888 LEU Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain G residue 914 LEU Chi-restraints excluded: chain H residue 853 LEU Chi-restraints excluded: chain H residue 882 PHE Chi-restraints excluded: chain H residue 886 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 94 optimal weight: 50.0000 chunk 130 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 814 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181520 restraints weight = 22153.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.151233 restraints weight = 48828.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.149590 restraints weight = 54110.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.149889 restraints weight = 44773.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.149354 restraints weight = 40520.842| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19246 Z= 0.197 Angle : 0.655 12.661 25947 Z= 0.315 Chirality : 0.044 0.233 3066 Planarity : 0.004 0.042 3289 Dihedral : 7.771 103.736 2676 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.60 % Favored : 94.36 % Rotamer: Outliers : 5.24 % Allowed : 26.65 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2374 helix: 0.66 (0.15), residues: 1146 sheet: -0.90 (0.27), residues: 356 loop : -1.77 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 414 TYR 0.014 0.002 TYR B 366 PHE 0.008 0.001 PHE D 257 TRP 0.015 0.002 TRP E 283 HIS 0.005 0.001 HIS B 393 Details of bonding type rmsd covalent geometry : bond 0.00480 (19241) covalent geometry : angle 0.65475 (25947) hydrogen bonds : bond 0.03411 ( 908) hydrogen bonds : angle 4.56465 ( 2634) Misc. bond : bond 0.00078 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3153.50 seconds wall clock time: 55 minutes 29.40 seconds (3329.40 seconds total)