Starting phenix.real_space_refine on Fri Sep 19 07:43:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6igm_9668/09_2025/6igm_9668.cif Found real_map, /net/cci-nas-00/data/ceres_data/6igm_9668/09_2025/6igm_9668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6igm_9668/09_2025/6igm_9668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6igm_9668/09_2025/6igm_9668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6igm_9668/09_2025/6igm_9668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6igm_9668/09_2025/6igm_9668.map" } resolution = 4.0 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= 0.005 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: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 15295 2.51 5 N 4225 2.21 5 O 4622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24257 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3123 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 2 Chain: "B" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3090 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 3 Chain: "C" Number of atoms: 2852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2852 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 5 Chain: "D" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3078 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 9, 'TRANS': 386} Chain breaks: 3 Chain: "E" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2935 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 15, 'TRANS': 364} Chain breaks: 3 Chain: "F" Number of atoms: 2852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2852 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 8, 'TRANS': 357} Chain breaks: 4 Chain: "G" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2987 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain breaks: 1 Chain: "H" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3030 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 26, 'TRANS': 346} Chain breaks: 4 Chain: "X" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 310 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'UNK:plan-1': 62} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 4.96, per 1000 atoms: 0.20 Number of scatterers: 24257 At special positions: 0 Unit cell: (162, 167.4, 139.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 4622 8.00 N 4225 7.00 C 15295 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: 1.62 Conformation dependent library (CDL) restraints added in 899.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5818 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 28 sheets defined 42.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.620A pdb=" N ILE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.584A pdb=" N LEU A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.602A pdb=" N ILE A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 4.094A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.556A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.551A pdb=" N GLU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.996A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.507A pdb=" N ASP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 388 through 401 removed outlier: 3.663A pdb=" N THR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 421 removed outlier: 3.979A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.807A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'B' and resid 49 through 66 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.735A pdb=" N ILE B 86 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.560A pdb=" N ILE B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.797A pdb=" N ILE B 179 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 180 " --> pdb=" O LYS B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 180' Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.689A pdb=" N VAL B 249 " --> pdb=" O HIS B 245 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 removed outlier: 3.648A pdb=" N LEU B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 305 through 316 removed outlier: 3.755A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.851A pdb=" N GLY B 345 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 346 " --> pdb=" O PRO B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 346' Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 363 through 378 removed outlier: 3.520A pdb=" N GLN B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 398 through 417 removed outlier: 3.537A pdb=" N ALA B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 433 removed outlier: 3.830A pdb=" N ILE B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 removed outlier: 4.003A pdb=" N LYS B 444 " --> pdb=" O GLN B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.261A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 110 through 120 removed outlier: 4.238A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.524A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.501A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.748A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 446 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.890A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.928A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.929A pdb=" N ASP D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.898A pdb=" N GLN D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.558A pdb=" N MET D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.766A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 354 removed outlier: 3.598A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.502A pdb=" N GLU D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 397 removed outlier: 3.809A pdb=" N GLU D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 417 Processing helix chain 'D' and resid 422 through 433 removed outlier: 3.528A pdb=" N PHE D 433 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 442 Processing helix chain 'E' and resid 42 through 59 removed outlier: 4.106A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E 53 " --> pdb=" O CYS E 49 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 86 removed outlier: 3.605A pdb=" N LEU E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.840A pdb=" N VAL E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.789A pdb=" N VAL E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 removed outlier: 3.539A pdb=" N PHE E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 271 through 288 removed outlier: 3.676A pdb=" N LEU E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP E 288 " --> pdb=" O ASN E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 319 Processing helix chain 'E' and resid 346 through 350 removed outlier: 3.632A pdb=" N GLY E 349 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 removed outlier: 3.517A pdb=" N LEU E 355 " --> pdb=" O PRO E 351 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 356' Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 370 through 383 removed outlier: 4.065A pdb=" N ILE E 377 " --> pdb=" O GLN E 373 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 402 through 409 removed outlier: 3.863A pdb=" N SER E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 409 " --> pdb=" O TYR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 421 removed outlier: 3.536A pdb=" N ASN E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.527A pdb=" N ILE F 86 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.680A pdb=" N ASN F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER F 252 " --> pdb=" O ASP F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 286 removed outlier: 4.237A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.697A pdb=" N PHE F 309 " --> pdb=" O ASP F 305 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 removed outlier: 3.627A pdb=" N GLY F 345 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.985A pdb=" N LEU F 354 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 375 Processing helix chain 'F' and resid 385 through 397 removed outlier: 4.137A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 417 removed outlier: 3.633A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.631A pdb=" N ILE F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 440 Processing helix chain 'G' and resid 68 through 80 removed outlier: 3.918A pdb=" N GLY G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 116 removed outlier: 3.546A pdb=" N GLN G 106 " --> pdb=" O PHE G 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 107 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU G 116 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 135 removed outlier: 3.888A pdb=" N LEU G 130 " --> pdb=" O ASN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 191 Processing helix chain 'G' and resid 200 through 209 Processing helix chain 'G' and resid 216 through 223 Processing helix chain 'G' and resid 271 through 275 removed outlier: 4.243A pdb=" N ARG G 274 " --> pdb=" O ALA G 271 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE G 275 " --> pdb=" O ASN G 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 271 through 275' Processing helix chain 'G' and resid 277 through 283 removed outlier: 4.287A pdb=" N LEU G 281 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE G 282 " --> pdb=" O PRO G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 287 Processing helix chain 'G' and resid 296 through 302 Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 309 through 315 removed outlier: 3.707A pdb=" N LYS G 315 " --> pdb=" O PRO G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 326 removed outlier: 4.132A pdb=" N PHE G 326 " --> pdb=" O ASN G 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 323 through 326' Processing helix chain 'G' and resid 328 through 339 removed outlier: 3.958A pdb=" N ARG G 332 " --> pdb=" O GLY G 328 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS G 339 " --> pdb=" O SER G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 367 Processing helix chain 'G' and resid 378 through 382 Processing helix chain 'H' and resid 862 through 873 removed outlier: 3.853A pdb=" N MET H 873 " --> pdb=" O TYR H 869 " (cutoff:3.500A) Processing helix chain 'H' and resid 894 through 901 removed outlier: 3.877A pdb=" N ARG H 898 " --> pdb=" O LEU H 894 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS H 899 " --> pdb=" O MET H 895 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL H 900 " --> pdb=" O GLN H 896 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS H 901 " --> pdb=" O LEU H 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 894 through 901' Processing helix chain 'H' and resid 954 through 974 Proline residue: H 965 - end of helix Processing helix chain 'H' and resid 1901 through 1928 Proline residue: H1916 - end of helix Processing helix chain 'H' and resid 2004 through 2015 removed outlier: 4.447A pdb=" N LEU H2010 " --> pdb=" O PHE H2006 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA H2011 " --> pdb=" O GLN H2007 " (cutoff:3.500A) Processing helix chain 'H' and resid 2016 through 2018 No H-bonds generated for 'chain 'H' and resid 2016 through 2018' Processing helix chain 'H' and resid 2036 through 2042 removed outlier: 3.684A pdb=" N TYR H2040 " --> pdb=" O ARG H2036 " (cutoff:3.500A) Processing helix chain 'H' and resid 2042 through 2056 Processing helix chain 'H' and resid 2068 through 2080 removed outlier: 3.964A pdb=" N THR H2080 " --> pdb=" O GLU H2076 " (cutoff:3.500A) Processing helix chain 'H' and resid 2094 through 2103 Processing helix chain 'H' and resid 2144 through 2153 removed outlier: 3.693A pdb=" N ALA H2148 " --> pdb=" O MET H2144 " (cutoff:3.500A) Processing helix chain 'H' and resid 2172 through 2190 Processing helix chain 'X' and resid 53 through 62 removed outlier: 4.333A pdb=" N UNK X 59 " --> pdb=" O UNK X 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 97 removed outlier: 3.914A pdb=" N CYS A 94 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 300 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.889A pdb=" N GLY A 121 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 removed outlier: 3.988A pdb=" N CYS A 336 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 346 " --> pdb=" O CYS A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.025A pdb=" N LEU B 296 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA B 327 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 298 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 326 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 77 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 355 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.684A pdb=" N ARG B 130 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 290 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 134 through 137 removed outlier: 3.915A pdb=" N LYS B 234 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 141 through 142 removed outlier: 4.251A pdb=" N GLU B 141 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 164 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 381 through 382 removed outlier: 7.608A pdb=" N GLU B 381 " --> pdb=" O VAL B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 96 removed outlier: 6.441A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 232 through 239 Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 162 removed outlier: 3.942A pdb=" N ILE C 159 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 170 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.426A pdb=" N VAL D 73 " --> pdb=" O MET D 326 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 236 through 243 removed outlier: 3.681A pdb=" N LYS D 236 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 135 " --> pdb=" O LYS D 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.553A pdb=" N LEU D 161 " --> pdb=" O TYR D 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 332 through 334 removed outlier: 3.613A pdb=" N THR D 333 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 342 " --> pdb=" O THR D 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 95 removed outlier: 4.085A pdb=" N CYS E 94 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE E 300 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 230 through 239 Processing sheet with id=AC3, first strand: chain 'E' and resid 134 through 137 removed outlier: 3.571A pdb=" N THR E 136 " --> pdb=" O GLY E 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 103 removed outlier: 6.966A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 192 through 197 removed outlier: 7.609A pdb=" N GLU F 136 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 192 through 197 removed outlier: 7.609A pdb=" N GLU F 136 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 13 through 16 removed outlier: 5.976A pdb=" N LEU G 4 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE G 93 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 171 through 173 removed outlier: 3.745A pdb=" N VAL G 350 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU G 319 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 854 through 859 removed outlier: 4.366A pdb=" N ARG H2165 " --> pdb=" O HIS H 855 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE H 857 " --> pdb=" O ARG H2165 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE H2167 " --> pdb=" O ILE H 857 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 2062 through 2066 906 hydrogen bonds defined for protein. 2616 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: 3.12 Time building geometry restraints manager: 2.26 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: 7984 1.34 - 1.46: 2926 1.46 - 1.57: 13490 1.57 - 1.69: 0 1.69 - 1.81: 191 Bond restraints: 24591 Sorted by residual: bond pdb=" N PRO A 174 " pdb=" CD PRO A 174 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.61e+01 bond pdb=" N PRO G 306 " pdb=" CD PRO G 306 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.60e+01 bond pdb=" N PRO G 51 " pdb=" CD PRO G 51 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.24e+01 bond pdb=" C ASP A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.51e-02 4.39e+03 2.15e+01 bond pdb=" C SER H1934 " pdb=" N PRO H1935 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.11e-02 8.12e+03 1.71e+01 ... (remaining 24586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 32794 3.32 - 6.65: 320 6.65 - 9.97: 40 9.97 - 13.29: 14 13.29 - 16.61: 3 Bond angle restraints: 33171 Sorted by residual: angle pdb=" C ILE G 294 " pdb=" N PRO G 295 " pdb=" CA PRO G 295 " ideal model delta sigma weight residual 119.47 131.15 -11.68 1.16e+00 7.43e-01 1.01e+02 angle pdb=" C PHE H1961 " pdb=" N PRO H1962 " pdb=" CA PRO H1962 " ideal model delta sigma weight residual 119.84 130.51 -10.67 1.25e+00 6.40e-01 7.28e+01 angle pdb=" C ILE H 949 " pdb=" CA ILE H 949 " pdb=" CB ILE H 949 " ideal model delta sigma weight residual 111.74 104.53 7.21 9.40e-01 1.13e+00 5.88e+01 angle pdb=" N GLU G 308 " pdb=" CA GLU G 308 " pdb=" C GLU G 308 " ideal model delta sigma weight residual 113.28 104.68 8.60 1.22e+00 6.72e-01 4.97e+01 angle pdb=" N GLU G 291 " pdb=" CA GLU G 291 " pdb=" C GLU G 291 " ideal model delta sigma weight residual 109.79 120.75 -10.96 1.56e+00 4.11e-01 4.93e+01 ... (remaining 33166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 14565 17.62 - 35.23: 449 35.23 - 52.85: 99 52.85 - 70.47: 27 70.47 - 88.08: 10 Dihedral angle restraints: 15150 sinusoidal: 6170 harmonic: 8980 Sorted by residual: dihedral pdb=" CA ASN G 354 " pdb=" C ASN G 354 " pdb=" N PRO G 355 " pdb=" CA PRO G 355 " ideal model delta harmonic sigma weight residual 180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LYS F 164 " pdb=" C LYS F 164 " pdb=" N THR F 165 " pdb=" CA THR F 165 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA PRO H1935 " pdb=" C PRO H1935 " pdb=" N ILE H1936 " pdb=" CA ILE H1936 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 15147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3331 0.071 - 0.142: 492 0.142 - 0.213: 49 0.213 - 0.284: 11 0.284 - 0.355: 2 Chirality restraints: 3885 Sorted by residual: chirality pdb=" CB ILE C 193 " pdb=" CA ILE C 193 " pdb=" CG1 ILE C 193 " pdb=" CG2 ILE C 193 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA GLU G 291 " pdb=" N GLU G 291 " pdb=" C GLU G 291 " pdb=" CB GLU G 291 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ILE G 57 " pdb=" N ILE G 57 " pdb=" C ILE G 57 " pdb=" CB ILE G 57 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3882 not shown) Planarity restraints: 4263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 948 " -0.022 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C LEU H 948 " 0.076 2.00e-02 2.50e+03 pdb=" O LEU H 948 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE H 949 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS H 936 " 0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO H 937 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO H 937 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 937 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H1930 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO H1931 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO H1931 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO H1931 " -0.039 5.00e-02 4.00e+02 ... (remaining 4260 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 51 1.86 - 2.62: 418 2.62 - 3.38: 29591 3.38 - 4.14: 52201 4.14 - 4.90: 91652 Nonbonded interactions: 173913 Sorted by model distance: nonbonded pdb=" C ALA G 42 " pdb=" CG ASP G 46 " model vdw 1.101 3.500 nonbonded pdb=" O ALA G 42 " pdb=" OD2 ASP G 46 " model vdw 1.153 3.040 nonbonded pdb=" OE2 GLU F 144 " pdb=" O LYS F 160 " model vdw 1.177 3.040 nonbonded pdb=" C ALA G 42 " pdb=" OD2 ASP G 46 " model vdw 1.222 3.270 nonbonded pdb=" CD GLU F 144 " pdb=" O LYS F 160 " model vdw 1.230 3.270 ... (remaining 173908 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 13 through 136 or resid 157 through 178 or resid 189 throu \ gh 194 or resid 224 through 443)) selection = (chain 'C' and (resid 13 through 194 or resid 224 through 250 or resid 269 throu \ gh 443)) selection = (chain 'E' and (resid 13 through 136 or resid 157 through 178 or resid 189 throu \ gh 194 or resid 224 through 250 or resid 269 through 443)) } ncs_group { reference = (chain 'B' and (resid 18 through 94 or resid 98 through 146 or resid 159 through \ 172 or resid 175 or resid 191 through 197 or resid 232 through 261 or resid 265 \ through 447)) selection = (chain 'D' and (resid 18 through 94 or resid 98 through 172 or resid 175 or resi \ d 191 through 197 or resid 232 through 447)) selection = (chain 'F' and (resid 18 through 172 or resid 190 through 261 or resid 265 throu \ gh 447)) } 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=0.01 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: 2.440 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.420 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 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 : 0.006 0.407 24596 Z= 0.500 Angle : 0.881 16.613 33171 Z= 0.505 Chirality : 0.052 0.355 3885 Planarity : 0.006 0.087 4263 Dihedral : 10.126 88.083 9332 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 1.10 % Allowed : 7.26 % Favored : 91.63 % Rotamer: Outliers : 2.70 % Allowed : 1.98 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.12), residues: 2988 helix: -2.90 (0.10), residues: 1179 sheet: -1.18 (0.23), residues: 448 loop : -3.38 (0.13), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 124 TYR 0.024 0.001 TYR B 387 PHE 0.025 0.002 PHE H 963 TRP 0.004 0.001 TRP H1998 HIS 0.006 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00354 (24591) covalent geometry : angle 0.88139 (33171) hydrogen bonds : bond 0.15509 ( 901) hydrogen bonds : angle 6.47696 ( 2616) Misc. bond : bond 0.31947 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1004 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8765 (ttp) cc_final: 0.8322 (ttm) REVERT: A 100 GLU cc_start: 0.6906 (tt0) cc_final: 0.6289 (tp30) REVERT: A 170 LEU cc_start: 0.7239 (tp) cc_final: 0.5926 (tp) REVERT: A 333 ARG cc_start: 0.5970 (ptp90) cc_final: 0.5341 (tpm170) REVERT: B 178 MET cc_start: 0.6736 (mmm) cc_final: 0.6230 (tpp) REVERT: B 299 ASP cc_start: 0.8027 (m-30) cc_final: 0.7615 (t0) REVERT: B 420 GLU cc_start: 0.6113 (tt0) cc_final: 0.5870 (pm20) REVERT: C 91 VAL cc_start: 0.9087 (t) cc_final: 0.8827 (t) REVERT: C 129 GLU cc_start: 0.6136 (pm20) cc_final: 0.4511 (tm-30) REVERT: C 173 ASP cc_start: 0.7428 (m-30) cc_final: 0.7181 (m-30) REVERT: C 299 LEU cc_start: 0.8706 (tp) cc_final: 0.8376 (tp) REVERT: C 314 TYR cc_start: 0.6924 (t80) cc_final: 0.6058 (t80) REVERT: C 322 SER cc_start: 0.8464 (p) cc_final: 0.8077 (m) REVERT: C 356 ASP cc_start: 0.7855 (t0) cc_final: 0.7530 (t70) REVERT: D 172 TYR cc_start: 0.7167 (m-80) cc_final: 0.6922 (t80) REVERT: D 269 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7425 (pttp) REVERT: D 435 ASP cc_start: 0.6110 (m-30) cc_final: 0.5075 (m-30) REVERT: E 49 CYS cc_start: 0.7856 (p) cc_final: 0.7429 (t) REVERT: E 89 SER cc_start: 0.8277 (m) cc_final: 0.8011 (p) REVERT: E 278 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7459 (tt0) REVERT: F 121 GLN cc_start: 0.7725 (mt0) cc_final: 0.7215 (tp40) REVERT: F 132 LYS cc_start: 0.7377 (ttpp) cc_final: 0.6980 (tmmt) REVERT: F 144 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.3463 (mp0) REVERT: F 326 MET cc_start: 0.8320 (mmt) cc_final: 0.8005 (mmm) REVERT: G 43 ASN cc_start: 0.5425 (t0) cc_final: 0.4374 (p0) REVERT: G 72 ARG cc_start: 0.7537 (ptp-170) cc_final: 0.6581 (ptm-80) REVERT: G 96 THR cc_start: 0.5432 (p) cc_final: 0.5139 (p) REVERT: G 111 GLU cc_start: 0.8754 (tt0) cc_final: 0.8458 (tp30) REVERT: G 205 VAL cc_start: 0.6930 (t) cc_final: 0.6378 (p) REVERT: G 269 ARG cc_start: 0.7511 (tpp-160) cc_final: 0.7266 (tpp80) REVERT: G 291 GLU cc_start: 0.0751 (OUTLIER) cc_final: -0.0127 (tp30) REVERT: H 902 ASN cc_start: 0.5869 (m-40) cc_final: 0.5274 (m-40) REVERT: H 913 THR cc_start: 0.6991 (m) cc_final: 0.6618 (m) REVERT: H 934 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: H 940 ARG cc_start: 0.4255 (OUTLIER) cc_final: 0.2006 (ptt-90) REVERT: H 951 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4798 (mt) REVERT: H 952 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.3834 (mm-30) REVERT: H 954 ARG cc_start: 0.5734 (mtt180) cc_final: 0.5500 (mtp85) REVERT: H 2024 ILE cc_start: 0.8609 (mm) cc_final: 0.8402 (mp) REVERT: H 2038 ILE cc_start: 0.6794 (mt) cc_final: 0.6562 (mt) REVERT: H 2102 MET cc_start: 0.5245 (mmm) cc_final: 0.4949 (tpp) outliers start: 71 outliers final: 23 residues processed: 1062 average time/residue: 0.2093 time to fit residues: 324.9615 Evaluate side-chains 526 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 496 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 236 TYR Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 934 ASP Chi-restraints excluded: chain H residue 935 VAL Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 943 MET Chi-restraints excluded: chain H residue 951 LEU Chi-restraints excluded: chain H residue 952 GLU Chi-restraints excluded: chain H residue 2027 ASN Chi-restraints excluded: chain H residue 2028 MET Chi-restraints excluded: chain H residue 2037 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0030 chunk 298 optimal weight: 5.9990 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 429 HIS B 41 GLN B 146 GLN B 240 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 236 GLN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN C 393 HIS C 414 ASN C 429 HIS D 240 HIS D 245 HIS E 18 HIS E 42 GLN E 284 ASN E 332 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 245 HIS F 447 GLN G 21 ASN G 73 GLN G 183 HIS H 967 HIS H2022 HIS H2060 HIS H2153 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.165916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.146092 restraints weight = 63712.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.148848 restraints weight = 38525.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.150765 restraints weight = 26015.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.152091 restraints weight = 19060.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.153038 restraints weight = 14953.263| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24596 Z= 0.143 Angle : 0.735 10.339 33171 Z= 0.373 Chirality : 0.046 0.202 3885 Planarity : 0.009 0.441 4263 Dihedral : 7.215 143.802 3427 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.41 % Rotamer: Outliers : 3.69 % Allowed : 13.62 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -2.81 (0.14), residues: 2988 helix: -1.17 (0.13), residues: 1187 sheet: -0.80 (0.23), residues: 450 loop : -2.91 (0.15), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG H 945 TYR 0.027 0.002 TYR G 77 PHE 0.027 0.002 PHE H 872 TRP 0.013 0.002 TRP H2015 HIS 0.009 0.001 HIS D 240 Details of bonding type rmsd covalent geometry : bond 0.00312 (24591) covalent geometry : angle 0.73517 (33171) hydrogen bonds : bond 0.03581 ( 901) hydrogen bonds : angle 4.68764 ( 2616) Misc. bond : bond 0.00775 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 545 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.6967 (tt0) cc_final: 0.6403 (tp30) REVERT: A 124 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7757 (pp) REVERT: A 333 ARG cc_start: 0.6109 (ptp90) cc_final: 0.5552 (tpm170) REVERT: B 107 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7723 (mp0) REVERT: B 196 ASP cc_start: 0.7798 (p0) cc_final: 0.7487 (p0) REVERT: B 299 ASP cc_start: 0.8100 (m-30) cc_final: 0.7782 (t70) REVERT: B 303 MET cc_start: 0.5446 (ppp) cc_final: 0.5234 (ppp) REVERT: C 115 ASN cc_start: 0.7654 (m-40) cc_final: 0.6688 (m-40) REVERT: C 173 ASP cc_start: 0.7450 (m-30) cc_final: 0.7209 (m-30) REVERT: C 299 LEU cc_start: 0.8740 (tp) cc_final: 0.8516 (tt) REVERT: C 322 SER cc_start: 0.8251 (p) cc_final: 0.7944 (m) REVERT: C 356 ASP cc_start: 0.7675 (t0) cc_final: 0.7131 (t0) REVERT: C 359 MET cc_start: 0.6542 (tpt) cc_final: 0.6295 (tpt) REVERT: D 46 MET cc_start: 0.7424 (mmm) cc_final: 0.7022 (tpt) REVERT: D 237 GLU cc_start: 0.6276 (mm-30) cc_final: 0.5046 (tp30) REVERT: D 441 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: E 49 CYS cc_start: 0.7920 (p) cc_final: 0.7363 (t) REVERT: E 113 MET cc_start: 0.8833 (mmm) cc_final: 0.8581 (mmm) REVERT: E 278 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7320 (tt0) REVERT: F 46 MET cc_start: 0.4464 (mtt) cc_final: 0.4227 (ttm) REVERT: F 125 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7538 (mmt-90) REVERT: F 285 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7827 (mm-30) REVERT: F 326 MET cc_start: 0.8355 (mmt) cc_final: 0.8147 (mmm) REVERT: F 334 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6981 (mmp80) REVERT: G 1 MET cc_start: 0.1953 (ppp) cc_final: 0.1746 (ppp) REVERT: G 45 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.6205 (pt) REVERT: G 204 GLN cc_start: 0.7800 (mt0) cc_final: 0.7530 (tm-30) REVERT: G 215 ASP cc_start: 0.7844 (t70) cc_final: 0.6735 (m-30) REVERT: G 270 LEU cc_start: 0.5252 (OUTLIER) cc_final: 0.4982 (tt) REVERT: H 940 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.4691 (mtm-85) REVERT: H 1903 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.7211 (mmm-85) REVERT: H 1960 LEU cc_start: 0.1187 (OUTLIER) cc_final: 0.0452 (tp) REVERT: H 1965 ARG cc_start: 0.6724 (ptm160) cc_final: 0.6457 (ptt180) REVERT: H 2008 GLU cc_start: 0.5727 (mt-10) cc_final: 0.5525 (mt-10) REVERT: H 2027 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.7015 (p0) REVERT: H 2102 MET cc_start: 0.5341 (mmm) cc_final: 0.4762 (tmm) REVERT: H 2105 PHE cc_start: 0.3913 (p90) cc_final: 0.3573 (p90) outliers start: 97 outliers final: 45 residues processed: 612 average time/residue: 0.1793 time to fit residues: 170.2304 Evaluate side-chains 467 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 415 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 897 LEU Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 1960 LEU Chi-restraints excluded: chain H residue 2021 LEU Chi-restraints excluded: chain H residue 2025 VAL Chi-restraints excluded: chain H residue 2027 ASN Chi-restraints excluded: chain H residue 2028 MET Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 11 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 295 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 277 optimal weight: 0.1980 chunk 271 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN D 25 HIS D 240 HIS E 18 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN ** H1968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2082 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.157175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.136428 restraints weight = 62101.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.139189 restraints weight = 37473.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.141076 restraints weight = 25366.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.142387 restraints weight = 18776.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.143319 restraints weight = 14876.276| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 24596 Z= 0.142 Angle : 0.690 11.652 33171 Z= 0.349 Chirality : 0.047 0.784 3885 Planarity : 0.007 0.324 4263 Dihedral : 5.847 136.544 3373 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.54 % Rotamer: Outliers : 3.77 % Allowed : 15.98 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -2.08 (0.14), residues: 2988 helix: -0.34 (0.14), residues: 1210 sheet: -0.64 (0.23), residues: 442 loop : -2.67 (0.15), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 284 TYR 0.025 0.001 TYR C 405 PHE 0.019 0.001 PHE H1978 TRP 0.027 0.002 TRP H2015 HIS 0.007 0.001 HIS F 245 Details of bonding type rmsd covalent geometry : bond 0.00313 (24591) covalent geometry : angle 0.68982 (33171) hydrogen bonds : bond 0.03272 ( 901) hydrogen bonds : angle 4.43430 ( 2616) Misc. bond : bond 0.00697 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 448 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7223 (tt0) cc_final: 0.6595 (tp30) REVERT: A 124 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7834 (pp) REVERT: A 308 ASP cc_start: 0.6982 (t0) cc_final: 0.6583 (t0) REVERT: A 333 ARG cc_start: 0.6328 (ptp90) cc_final: 0.5657 (tpm170) REVERT: A 406 SER cc_start: 0.8807 (p) cc_final: 0.8582 (t) REVERT: B 107 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7570 (mp0) REVERT: B 196 ASP cc_start: 0.7939 (p0) cc_final: 0.7545 (p0) REVERT: B 239 VAL cc_start: 0.8549 (t) cc_final: 0.8259 (p) REVERT: B 299 ASP cc_start: 0.8384 (m-30) cc_final: 0.8111 (t0) REVERT: B 443 MET cc_start: 0.7596 (mmp) cc_final: 0.6472 (mtt) REVERT: C 113 MET cc_start: 0.8308 (tpt) cc_final: 0.8015 (tpt) REVERT: C 115 ASN cc_start: 0.7675 (m-40) cc_final: 0.7340 (m-40) REVERT: C 322 SER cc_start: 0.8448 (p) cc_final: 0.8125 (m) REVERT: C 356 ASP cc_start: 0.8011 (t0) cc_final: 0.7711 (t70) REVERT: D 46 MET cc_start: 0.7488 (mmm) cc_final: 0.7226 (tpt) REVERT: D 237 GLU cc_start: 0.6468 (mm-30) cc_final: 0.5163 (tp30) REVERT: D 303 MET cc_start: 0.7906 (ppp) cc_final: 0.7616 (ppp) REVERT: D 428 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8132 (ttp80) REVERT: E 49 CYS cc_start: 0.8078 (p) cc_final: 0.7551 (t) REVERT: E 278 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7442 (tt0) REVERT: F 125 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.7583 (mmt180) REVERT: F 145 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5754 (pp) REVERT: F 285 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7935 (mm-30) REVERT: F 326 MET cc_start: 0.8445 (mmt) cc_final: 0.8220 (mmm) REVERT: F 334 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7144 (mmp80) REVERT: F 403 ILE cc_start: 0.9131 (mt) cc_final: 0.8926 (mt) REVERT: G 1 MET cc_start: 0.2446 (ppp) cc_final: 0.1794 (ppp) REVERT: G 43 ASN cc_start: 0.5440 (t0) cc_final: 0.3842 (p0) REVERT: G 45 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6433 (pt) REVERT: G 73 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7765 (pt0) REVERT: G 204 GLN cc_start: 0.7879 (mt0) cc_final: 0.7547 (tm-30) REVERT: G 220 MET cc_start: 0.7366 (mmt) cc_final: 0.7074 (mmt) REVERT: G 221 ASP cc_start: 0.8729 (t70) cc_final: 0.8413 (t0) REVERT: G 286 ASP cc_start: 0.6429 (p0) cc_final: 0.6192 (p0) REVERT: H 1930 GLN cc_start: 0.7764 (pp30) cc_final: 0.7449 (pp30) outliers start: 99 outliers final: 61 residues processed: 517 average time/residue: 0.1610 time to fit residues: 130.9194 Evaluate side-chains 464 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 399 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1964 GLN Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2026 CYS Chi-restraints excluded: chain H residue 2028 MET Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 123 optimal weight: 0.6980 chunk 278 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 281 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 222 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 247 ASN C 414 ASN D 240 HIS D 302 HIS E 18 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN H 936 HIS H1968 GLN ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.151658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.130729 restraints weight = 61514.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.133382 restraints weight = 37637.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.135204 restraints weight = 25697.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.136460 restraints weight = 19189.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.137413 restraints weight = 15306.705| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24596 Z= 0.143 Angle : 0.661 9.146 33171 Z= 0.334 Chirality : 0.045 0.367 3885 Planarity : 0.005 0.085 4263 Dihedral : 5.912 171.545 3371 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.37 % Rotamer: Outliers : 4.34 % Allowed : 17.15 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.63 (0.15), residues: 2988 helix: 0.16 (0.15), residues: 1219 sheet: -0.38 (0.23), residues: 468 loop : -2.62 (0.15), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG D 284 TYR 0.016 0.001 TYR C 405 PHE 0.025 0.002 PHE E 177 TRP 0.014 0.002 TRP H2015 HIS 0.007 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00316 (24591) covalent geometry : angle 0.66051 (33171) hydrogen bonds : bond 0.03126 ( 901) hydrogen bonds : angle 4.25599 ( 2616) Misc. bond : bond 0.00492 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 453 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7442 (tt0) cc_final: 0.6799 (tp30) REVERT: A 124 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.7905 (pp) REVERT: A 218 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6307 (mm-30) REVERT: A 219 GLU cc_start: 0.3824 (pm20) cc_final: 0.2741 (pm20) REVERT: A 235 ILE cc_start: 0.7017 (mt) cc_final: 0.6564 (pt) REVERT: A 333 ARG cc_start: 0.7069 (ptp90) cc_final: 0.6208 (tpm170) REVERT: B 106 SER cc_start: 0.9139 (p) cc_final: 0.8776 (m) REVERT: B 107 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7645 (mp0) REVERT: B 196 ASP cc_start: 0.7901 (p0) cc_final: 0.7452 (p0) REVERT: B 239 VAL cc_start: 0.8641 (t) cc_final: 0.8391 (p) REVERT: B 320 MET cc_start: 0.7893 (mmp) cc_final: 0.7689 (mmt) REVERT: B 334 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7894 (ptm-80) REVERT: B 443 MET cc_start: 0.7836 (mmp) cc_final: 0.6918 (mtt) REVERT: C 97 VAL cc_start: 0.8520 (m) cc_final: 0.7721 (m) REVERT: C 242 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6249 (m-30) REVERT: C 322 SER cc_start: 0.8460 (p) cc_final: 0.8083 (m) REVERT: C 329 PHE cc_start: 0.7865 (m-10) cc_final: 0.7621 (m-10) REVERT: C 356 ASP cc_start: 0.8224 (t0) cc_final: 0.8006 (t0) REVERT: D 46 MET cc_start: 0.7592 (mmm) cc_final: 0.7390 (tpt) REVERT: D 75 ILE cc_start: 0.8971 (mt) cc_final: 0.8768 (mt) REVERT: D 179 ILE cc_start: 0.7108 (tp) cc_final: 0.6879 (tt) REVERT: D 237 GLU cc_start: 0.6646 (mm-30) cc_final: 0.5484 (tp30) REVERT: E 49 CYS cc_start: 0.8200 (p) cc_final: 0.7688 (t) REVERT: E 113 MET cc_start: 0.8820 (mmm) cc_final: 0.8305 (mmm) REVERT: E 115 ASN cc_start: 0.7424 (m110) cc_final: 0.7163 (m110) REVERT: E 278 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7431 (tt0) REVERT: E 388 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6846 (mm-30) REVERT: F 117 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6380 (mt-10) REVERT: F 285 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8054 (mm-30) REVERT: F 334 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7235 (mmp80) REVERT: G 1 MET cc_start: 0.2380 (ppp) cc_final: 0.1998 (ppp) REVERT: G 43 ASN cc_start: 0.5358 (t0) cc_final: 0.3871 (p0) REVERT: G 45 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6331 (pt) REVERT: G 215 ASP cc_start: 0.7935 (t70) cc_final: 0.7269 (m-30) REVERT: G 286 ASP cc_start: 0.6830 (p0) cc_final: 0.6539 (p0) REVERT: G 306 PRO cc_start: 0.5970 (Cg_exo) cc_final: 0.5678 (Cg_endo) REVERT: G 309 MET cc_start: 0.6249 (mtp) cc_final: 0.5560 (mtm) REVERT: H 1930 GLN cc_start: 0.8332 (pp30) cc_final: 0.7972 (pp30) REVERT: H 1963 GLN cc_start: 0.7439 (mt0) cc_final: 0.6993 (pt0) REVERT: H 2036 ARG cc_start: 0.7343 (ttt-90) cc_final: 0.7128 (ttt-90) outliers start: 114 outliers final: 71 residues processed: 525 average time/residue: 0.1640 time to fit residues: 137.5192 Evaluate side-chains 476 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 401 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 1907 LEU Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1968 GLN Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2026 CYS Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 251 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 8 optimal weight: 0.0170 chunk 1 optimal weight: 5.9990 chunk 43 optimal weight: 0.0040 chunk 23 optimal weight: 0.6980 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 115 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS ** H 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1968 GLN ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2027 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.150897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129935 restraints weight = 61739.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.132575 restraints weight = 37719.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.134380 restraints weight = 25827.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135649 restraints weight = 19316.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.136568 restraints weight = 15462.751| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 24596 Z= 0.118 Angle : 0.639 9.301 33171 Z= 0.322 Chirality : 0.044 0.312 3885 Planarity : 0.005 0.140 4263 Dihedral : 5.713 166.097 3368 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.54 % Rotamer: Outliers : 3.99 % Allowed : 18.60 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.37 (0.15), residues: 2988 helix: 0.40 (0.15), residues: 1206 sheet: -0.38 (0.24), residues: 463 loop : -2.43 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG D 284 TYR 0.021 0.001 TYR C 314 PHE 0.025 0.001 PHE G 314 TRP 0.011 0.001 TRP B 283 HIS 0.007 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00269 (24591) covalent geometry : angle 0.63905 (33171) hydrogen bonds : bond 0.03049 ( 901) hydrogen bonds : angle 4.17809 ( 2616) Misc. bond : bond 0.00494 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 431 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7270 (tt0) cc_final: 0.6792 (tp30) REVERT: A 124 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8008 (pp) REVERT: A 218 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6206 (mm-30) REVERT: A 235 ILE cc_start: 0.7099 (mt) cc_final: 0.6580 (pt) REVERT: A 333 ARG cc_start: 0.7004 (ptp90) cc_final: 0.6494 (tpm170) REVERT: B 106 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8751 (m) REVERT: B 107 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 196 ASP cc_start: 0.7928 (p0) cc_final: 0.7492 (p0) REVERT: B 239 VAL cc_start: 0.8796 (t) cc_final: 0.8589 (p) REVERT: B 334 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7917 (ptm-80) REVERT: B 353 ARG cc_start: 0.7745 (mmm160) cc_final: 0.7408 (tpp80) REVERT: B 443 MET cc_start: 0.7835 (mmp) cc_final: 0.7004 (mtt) REVERT: C 85 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7999 (mt0) REVERT: C 96 MET cc_start: 0.6442 (ttm) cc_final: 0.5791 (ttm) REVERT: C 97 VAL cc_start: 0.8338 (m) cc_final: 0.8016 (m) REVERT: C 242 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6171 (m-30) REVERT: C 314 TYR cc_start: 0.8697 (t80) cc_final: 0.8093 (t80) REVERT: C 322 SER cc_start: 0.8485 (p) cc_final: 0.8069 (m) REVERT: C 356 ASP cc_start: 0.8282 (t0) cc_final: 0.8031 (t0) REVERT: C 360 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7966 (tp) REVERT: D 112 GLU cc_start: 0.7938 (pt0) cc_final: 0.7635 (mp0) REVERT: D 119 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8835 (mm) REVERT: D 183 THR cc_start: 0.7246 (p) cc_final: 0.6828 (p) REVERT: D 303 MET cc_start: 0.7856 (ppp) cc_final: 0.7597 (ppp) REVERT: E 49 CYS cc_start: 0.8243 (p) cc_final: 0.7708 (t) REVERT: E 113 MET cc_start: 0.8840 (mmm) cc_final: 0.8343 (mmm) REVERT: E 278 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7414 (tt0) REVERT: F 285 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8071 (mm-30) REVERT: G 1 MET cc_start: 0.2377 (ppp) cc_final: 0.2134 (ppp) REVERT: G 43 ASN cc_start: 0.5601 (t0) cc_final: 0.3973 (p0) REVERT: G 83 MET cc_start: 0.6879 (ppp) cc_final: 0.6447 (ppp) REVERT: G 118 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: G 215 ASP cc_start: 0.8075 (t70) cc_final: 0.7278 (m-30) REVERT: G 309 MET cc_start: 0.5993 (mtp) cc_final: 0.5380 (mtm) REVERT: H 949 ILE cc_start: 0.4708 (mm) cc_final: 0.4274 (mm) REVERT: H 1930 GLN cc_start: 0.8359 (pp30) cc_final: 0.8011 (pp30) REVERT: H 1963 GLN cc_start: 0.7561 (mt0) cc_final: 0.7177 (pt0) REVERT: H 1999 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6806 (pp) REVERT: H 2027 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6738 (p0) outliers start: 105 outliers final: 70 residues processed: 505 average time/residue: 0.1626 time to fit residues: 132.0633 Evaluate side-chains 456 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 377 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 380 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 1907 LEU Chi-restraints excluded: chain H residue 1968 GLN Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2027 ASN Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2152 CYS Chi-restraints excluded: chain H residue 2172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 214 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 275 optimal weight: 0.2980 chunk 211 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 257 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 236 GLN E 18 HIS E 115 ASN E 284 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** H 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2031 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.146041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.124996 restraints weight = 62317.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127506 restraints weight = 38343.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.129272 restraints weight = 26501.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.130502 restraints weight = 19949.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.131299 restraints weight = 16045.802| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24596 Z= 0.142 Angle : 0.668 11.203 33171 Z= 0.336 Chirality : 0.045 0.302 3885 Planarity : 0.007 0.315 4263 Dihedral : 5.439 139.022 3364 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.73 % Favored : 93.17 % Rotamer: Outliers : 4.22 % Allowed : 18.87 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.20 (0.15), residues: 2988 helix: 0.59 (0.15), residues: 1208 sheet: -0.33 (0.24), residues: 471 loop : -2.36 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 945 TYR 0.014 0.001 TYR B 172 PHE 0.017 0.002 PHE G 314 TRP 0.009 0.001 TRP G 360 HIS 0.010 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00328 (24591) covalent geometry : angle 0.66849 (33171) hydrogen bonds : bond 0.03161 ( 901) hydrogen bonds : angle 4.24428 ( 2616) Misc. bond : bond 0.00456 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 408 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7672 (ttt) cc_final: 0.7129 (ttt) REVERT: A 66 VAL cc_start: 0.9029 (t) cc_final: 0.8679 (m) REVERT: A 100 GLU cc_start: 0.7284 (tt0) cc_final: 0.6933 (tp30) REVERT: A 124 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8104 (pp) REVERT: A 218 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6174 (mm-30) REVERT: A 219 GLU cc_start: 0.4535 (pm20) cc_final: 0.4142 (pm20) REVERT: A 235 ILE cc_start: 0.7320 (mt) cc_final: 0.6850 (pt) REVERT: A 314 TYR cc_start: 0.9037 (t80) cc_final: 0.8746 (t80) REVERT: B 106 SER cc_start: 0.9167 (p) cc_final: 0.8773 (m) REVERT: B 107 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7633 (mp0) REVERT: B 196 ASP cc_start: 0.7707 (p0) cc_final: 0.7323 (p0) REVERT: B 239 VAL cc_start: 0.9049 (t) cc_final: 0.8828 (p) REVERT: B 320 MET cc_start: 0.7627 (mmt) cc_final: 0.7339 (mmt) REVERT: B 334 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7955 (ptm-80) REVERT: B 353 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7619 (tpp80) REVERT: B 443 MET cc_start: 0.7921 (mmp) cc_final: 0.7156 (mtt) REVERT: C 85 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8114 (mt0) REVERT: C 242 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: C 299 LEU cc_start: 0.8905 (tp) cc_final: 0.8564 (tp) REVERT: C 356 ASP cc_start: 0.8486 (t0) cc_final: 0.8265 (t0) REVERT: C 360 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7754 (tp) REVERT: C 423 ASP cc_start: 0.7717 (t0) cc_final: 0.7477 (t0) REVERT: C 432 GLU cc_start: 0.8916 (tp30) cc_final: 0.8522 (tp30) REVERT: D 112 GLU cc_start: 0.8078 (pt0) cc_final: 0.7651 (mp0) REVERT: D 119 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8826 (mm) REVERT: E 49 CYS cc_start: 0.8127 (p) cc_final: 0.7610 (t) REVERT: E 113 MET cc_start: 0.8868 (mmm) cc_final: 0.8572 (mmm) REVERT: E 278 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7573 (tt0) REVERT: G 1 MET cc_start: 0.2735 (ppp) cc_final: 0.2445 (ppp) REVERT: G 43 ASN cc_start: 0.5709 (t0) cc_final: 0.4052 (p0) REVERT: G 215 ASP cc_start: 0.7933 (t70) cc_final: 0.7194 (m-30) REVERT: G 309 MET cc_start: 0.5795 (mtp) cc_final: 0.5385 (mtm) REVERT: H 949 ILE cc_start: 0.4488 (mm) cc_final: 0.4180 (mm) REVERT: H 1930 GLN cc_start: 0.8283 (pp30) cc_final: 0.7922 (pp30) REVERT: H 1999 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6887 (pp) REVERT: H 2007 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7367 (mt0) outliers start: 111 outliers final: 78 residues processed: 477 average time/residue: 0.1568 time to fit residues: 122.2151 Evaluate side-chains 458 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 374 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 947 ASP Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2024 ILE Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2069 THR Chi-restraints excluded: chain H residue 2172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 205 optimal weight: 0.8980 chunk 302 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 220 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 332 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 115 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 HIS H1968 GLN ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.143453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122168 restraints weight = 61969.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.124741 restraints weight = 37586.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126553 restraints weight = 25732.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.127871 restraints weight = 19123.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.128688 restraints weight = 15281.471| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24596 Z= 0.139 Angle : 0.677 10.704 33171 Z= 0.337 Chirality : 0.045 0.285 3885 Planarity : 0.006 0.251 4263 Dihedral : 5.535 148.399 3364 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.83 % Favored : 93.07 % Rotamer: Outliers : 4.07 % Allowed : 20.24 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.15 (0.15), residues: 2988 helix: 0.60 (0.15), residues: 1211 sheet: -0.32 (0.24), residues: 469 loop : -2.31 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 379 TYR 0.017 0.001 TYR C 314 PHE 0.033 0.002 PHE H1978 TRP 0.014 0.001 TRP B 283 HIS 0.008 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00327 (24591) covalent geometry : angle 0.67653 (33171) hydrogen bonds : bond 0.03099 ( 901) hydrogen bonds : angle 4.22417 ( 2616) Misc. bond : bond 0.00374 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 414 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7614 (ttt) cc_final: 0.7210 (ttt) REVERT: A 66 VAL cc_start: 0.9059 (t) cc_final: 0.8728 (m) REVERT: A 124 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8192 (pp) REVERT: A 218 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6023 (mm-30) REVERT: A 235 ILE cc_start: 0.7482 (mt) cc_final: 0.6998 (pt) REVERT: B 106 SER cc_start: 0.9121 (p) cc_final: 0.8815 (m) REVERT: B 107 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7579 (mp0) REVERT: B 239 VAL cc_start: 0.9095 (t) cc_final: 0.8882 (p) REVERT: B 334 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7976 (ptm-80) REVERT: B 443 MET cc_start: 0.7967 (mmp) cc_final: 0.7310 (mtt) REVERT: C 29 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7784 (t) REVERT: C 85 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8135 (mt0) REVERT: C 97 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.7662 (p) REVERT: C 242 ASP cc_start: 0.7123 (t0) cc_final: 0.6605 (m-30) REVERT: C 299 LEU cc_start: 0.8990 (tp) cc_final: 0.8694 (tp) REVERT: C 332 ASN cc_start: 0.7739 (t0) cc_final: 0.7488 (t0) REVERT: C 355 LEU cc_start: 0.9170 (tp) cc_final: 0.8928 (tp) REVERT: C 356 ASP cc_start: 0.8427 (t0) cc_final: 0.8139 (t70) REVERT: C 423 ASP cc_start: 0.7868 (t0) cc_final: 0.7595 (t0) REVERT: C 432 GLU cc_start: 0.8908 (tp30) cc_final: 0.8491 (tp30) REVERT: D 88 MET cc_start: 0.8184 (mmm) cc_final: 0.7944 (mmm) REVERT: D 112 GLU cc_start: 0.7955 (pt0) cc_final: 0.7563 (mp0) REVERT: D 119 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8881 (mm) REVERT: D 237 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6045 (tp30) REVERT: E 49 CYS cc_start: 0.8150 (p) cc_final: 0.7608 (t) REVERT: E 113 MET cc_start: 0.8893 (mmm) cc_final: 0.8515 (mmm) REVERT: E 278 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7606 (tt0) REVERT: E 389 GLU cc_start: 0.7268 (pm20) cc_final: 0.7042 (pm20) REVERT: F 113 MET cc_start: 0.7134 (ttm) cc_final: 0.6603 (ttp) REVERT: F 317 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: G 1 MET cc_start: 0.2844 (ppp) cc_final: 0.2475 (ppp) REVERT: G 43 ASN cc_start: 0.5675 (t0) cc_final: 0.4101 (p0) REVERT: G 79 PHE cc_start: 0.5262 (m-10) cc_final: 0.4977 (m-10) REVERT: G 215 ASP cc_start: 0.7994 (t70) cc_final: 0.7148 (m-30) REVERT: G 309 MET cc_start: 0.5855 (mtp) cc_final: 0.5592 (mtm) REVERT: H 873 MET cc_start: -0.0163 (OUTLIER) cc_final: -0.2618 (ppp) REVERT: H 949 ILE cc_start: 0.4674 (mm) cc_final: 0.4437 (mm) REVERT: H 1930 GLN cc_start: 0.8214 (pp30) cc_final: 0.7967 (pp30) REVERT: H 1964 GLN cc_start: 0.5299 (OUTLIER) cc_final: 0.5039 (pp30) REVERT: H 1965 ARG cc_start: 0.5553 (ptt180) cc_final: 0.5148 (ttt180) REVERT: H 1972 ILE cc_start: 0.3068 (OUTLIER) cc_final: 0.2791 (tp) REVERT: H 1999 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7086 (pp) REVERT: H 2054 GLN cc_start: 0.8014 (tm-30) cc_final: 0.6734 (mt0) outliers start: 107 outliers final: 76 residues processed: 479 average time/residue: 0.1676 time to fit residues: 129.3712 Evaluate side-chains 451 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 365 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 873 MET Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1964 GLN Chi-restraints excluded: chain H residue 1968 GLN Chi-restraints excluded: chain H residue 1972 ILE Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 265 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 270 optimal weight: 0.6980 chunk 299 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 171 optimal weight: 6.9990 chunk 175 optimal weight: 0.0270 chunk 100 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 115 ASN F 49 GLN ** H 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 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 = 0.4044 r_free = 0.4044 target = 0.142544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.121709 restraints weight = 62089.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124235 restraints weight = 37888.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125992 restraints weight = 26030.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127193 restraints weight = 19463.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127984 restraints weight = 15662.003| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.7849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24596 Z= 0.131 Angle : 0.681 12.305 33171 Z= 0.339 Chirality : 0.045 0.314 3885 Planarity : 0.005 0.207 4263 Dihedral : 5.566 154.604 3364 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.37 % Rotamer: Outliers : 3.65 % Allowed : 21.26 % Favored : 75.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.10 (0.15), residues: 2988 helix: 0.62 (0.15), residues: 1220 sheet: -0.25 (0.24), residues: 451 loop : -2.26 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 284 TYR 0.019 0.001 TYR A 314 PHE 0.035 0.002 PHE H1978 TRP 0.012 0.001 TRP B 283 HIS 0.008 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00303 (24591) covalent geometry : angle 0.68099 (33171) hydrogen bonds : bond 0.03052 ( 901) hydrogen bonds : angle 4.23445 ( 2616) Misc. bond : bond 0.00464 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 404 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7642 (ttt) cc_final: 0.7153 (ttt) REVERT: A 66 VAL cc_start: 0.9073 (t) cc_final: 0.8791 (m) REVERT: A 124 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8240 (pp) REVERT: A 218 GLU cc_start: 0.6482 (mm-30) cc_final: 0.6097 (mm-30) REVERT: A 235 ILE cc_start: 0.7321 (mt) cc_final: 0.6845 (pt) REVERT: B 106 SER cc_start: 0.9098 (p) cc_final: 0.8801 (m) REVERT: B 107 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7852 (mp0) REVERT: B 239 VAL cc_start: 0.9081 (t) cc_final: 0.8829 (p) REVERT: B 334 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7975 (ptm-80) REVERT: C 29 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7522 (t) REVERT: C 85 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8067 (mt0) REVERT: C 242 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: C 299 LEU cc_start: 0.8956 (tp) cc_final: 0.8615 (tp) REVERT: C 356 ASP cc_start: 0.8543 (t0) cc_final: 0.8163 (t70) REVERT: C 359 MET cc_start: 0.6643 (tpt) cc_final: 0.6363 (tpt) REVERT: C 423 ASP cc_start: 0.7914 (t0) cc_final: 0.7708 (t0) REVERT: C 432 GLU cc_start: 0.8913 (tp30) cc_final: 0.8486 (tp30) REVERT: D 112 GLU cc_start: 0.7910 (pt0) cc_final: 0.7497 (mp0) REVERT: D 119 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8847 (mm) REVERT: D 237 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6017 (tp30) REVERT: D 317 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7068 (mm-30) REVERT: E 49 CYS cc_start: 0.8228 (p) cc_final: 0.7645 (t) REVERT: E 113 MET cc_start: 0.8877 (mmm) cc_final: 0.8496 (mmm) REVERT: E 278 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7627 (tt0) REVERT: E 359 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7669 (ttt) REVERT: E 389 GLU cc_start: 0.7340 (pm20) cc_final: 0.7100 (pm20) REVERT: F 90 MET cc_start: 0.8763 (tpp) cc_final: 0.8509 (tpp) REVERT: F 113 MET cc_start: 0.7236 (ttm) cc_final: 0.6700 (ttp) REVERT: F 317 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: F 403 ILE cc_start: 0.9286 (mt) cc_final: 0.9006 (mt) REVERT: G 1 MET cc_start: 0.2809 (ppp) cc_final: 0.2261 (ppp) REVERT: G 43 ASN cc_start: 0.5488 (t0) cc_final: 0.3884 (p0) REVERT: G 109 MET cc_start: 0.6811 (ttp) cc_final: 0.6559 (ptm) REVERT: G 118 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: G 137 ARG cc_start: 0.4669 (mmm160) cc_final: 0.4374 (mmm160) REVERT: G 309 MET cc_start: 0.6063 (mtp) cc_final: 0.5723 (mtm) REVERT: H 873 MET cc_start: -0.0201 (OUTLIER) cc_final: -0.2681 (ppp) REVERT: H 1921 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6663 (tm-30) REVERT: H 1960 LEU cc_start: 0.1742 (mt) cc_final: 0.1490 (tp) REVERT: H 2013 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7187 (tm-30) outliers start: 96 outliers final: 73 residues processed: 471 average time/residue: 0.1564 time to fit residues: 120.2144 Evaluate side-chains 452 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 370 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 873 MET Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 288 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 119 optimal weight: 0.4980 chunk 156 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 303 optimal weight: 2.9990 chunk 244 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN D 275 GLN E 115 ASN ** H 855 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 = 0.4048 r_free = 0.4048 target = 0.142738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122107 restraints weight = 61502.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.124638 restraints weight = 37350.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.126294 restraints weight = 25592.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.127568 restraints weight = 19236.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128336 restraints weight = 15333.790| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24596 Z= 0.125 Angle : 0.704 16.270 33171 Z= 0.346 Chirality : 0.046 0.572 3885 Planarity : 0.005 0.187 4263 Dihedral : 5.584 157.314 3364 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.34 % Rotamer: Outliers : 3.20 % Allowed : 22.18 % Favored : 74.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.99 (0.15), residues: 2988 helix: 0.69 (0.15), residues: 1221 sheet: -0.24 (0.24), residues: 450 loop : -2.17 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 284 TYR 0.025 0.001 TYR A 220 PHE 0.036 0.002 PHE H1978 TRP 0.014 0.001 TRP D 283 HIS 0.007 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00290 (24591) covalent geometry : angle 0.70374 (33171) hydrogen bonds : bond 0.03050 ( 901) hydrogen bonds : angle 4.17105 ( 2616) Misc. bond : bond 0.00311 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 391 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7590 (ttt) cc_final: 0.7128 (ttt) REVERT: A 66 VAL cc_start: 0.9069 (t) cc_final: 0.8767 (m) REVERT: A 124 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8252 (pp) REVERT: A 235 ILE cc_start: 0.7345 (mt) cc_final: 0.6876 (pt) REVERT: A 308 ASP cc_start: 0.7140 (t0) cc_final: 0.6469 (t0) REVERT: B 106 SER cc_start: 0.9045 (p) cc_final: 0.8760 (m) REVERT: B 107 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7841 (mp0) REVERT: B 181 SER cc_start: 0.7045 (p) cc_final: 0.6788 (t) REVERT: B 239 VAL cc_start: 0.9026 (t) cc_final: 0.8805 (p) REVERT: B 334 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8027 (ptm-80) REVERT: B 387 TYR cc_start: 0.7774 (m-80) cc_final: 0.7573 (m-80) REVERT: B 419 THR cc_start: 0.6852 (m) cc_final: 0.6548 (t) REVERT: B 443 MET cc_start: 0.7879 (mmp) cc_final: 0.7475 (ttt) REVERT: C 29 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7586 (t) REVERT: C 85 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8008 (mt0) REVERT: C 242 ASP cc_start: 0.7010 (t0) cc_final: 0.6537 (m-30) REVERT: C 299 LEU cc_start: 0.8977 (tp) cc_final: 0.8641 (tp) REVERT: C 356 ASP cc_start: 0.8553 (t0) cc_final: 0.8192 (t70) REVERT: C 423 ASP cc_start: 0.7928 (t0) cc_final: 0.7718 (t0) REVERT: C 432 GLU cc_start: 0.8848 (tp30) cc_final: 0.8421 (tp30) REVERT: D 88 MET cc_start: 0.8162 (mmm) cc_final: 0.7904 (mmt) REVERT: D 119 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8871 (mm) REVERT: D 237 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6137 (tp30) REVERT: E 49 CYS cc_start: 0.8200 (p) cc_final: 0.7665 (t) REVERT: E 113 MET cc_start: 0.8876 (mmm) cc_final: 0.8507 (mmm) REVERT: E 278 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7598 (tt0) REVERT: E 359 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7733 (ttt) REVERT: E 389 GLU cc_start: 0.7279 (pm20) cc_final: 0.7051 (pm20) REVERT: F 90 MET cc_start: 0.8737 (tpp) cc_final: 0.8497 (tpp) REVERT: F 168 MET cc_start: 0.5775 (mpp) cc_final: 0.5328 (tpt) REVERT: F 403 ILE cc_start: 0.9185 (mt) cc_final: 0.8909 (mt) REVERT: G 1 MET cc_start: 0.3082 (ppp) cc_final: 0.2511 (ppp) REVERT: G 43 ASN cc_start: 0.5757 (t0) cc_final: 0.4019 (p0) REVERT: G 79 PHE cc_start: 0.5064 (m-10) cc_final: 0.4847 (m-10) REVERT: G 109 MET cc_start: 0.6735 (ttp) cc_final: 0.6505 (ptm) REVERT: G 118 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: G 215 ASP cc_start: 0.7902 (t70) cc_final: 0.7292 (m-30) REVERT: G 309 MET cc_start: 0.6045 (mtp) cc_final: 0.5712 (mtm) REVERT: H 2054 GLN cc_start: 0.8017 (tm-30) cc_final: 0.6798 (mt0) outliers start: 84 outliers final: 69 residues processed: 451 average time/residue: 0.1566 time to fit residues: 114.9999 Evaluate side-chains 442 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 367 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 1914 LEU Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 207 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.0070 chunk 160 optimal weight: 1.9990 chunk 164 optimal weight: 0.0040 chunk 112 optimal weight: 1.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN E 115 ASN ** H 855 HIS ** 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 = 0.4035 r_free = 0.4035 target = 0.141886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.121252 restraints weight = 61616.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.123774 restraints weight = 37336.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125525 restraints weight = 25529.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126673 restraints weight = 19031.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.127572 restraints weight = 15333.092| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.8262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24596 Z= 0.129 Angle : 0.737 16.544 33171 Z= 0.361 Chirality : 0.046 0.358 3885 Planarity : 0.005 0.166 4263 Dihedral : 5.760 175.123 3362 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.73 % Favored : 93.21 % Rotamer: Outliers : 3.31 % Allowed : 22.63 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.91 (0.16), residues: 2988 helix: 0.68 (0.15), residues: 1221 sheet: -0.15 (0.24), residues: 464 loop : -2.08 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 137 TYR 0.022 0.001 TYR A 192 PHE 0.032 0.002 PHE H1978 TRP 0.020 0.002 TRP D 283 HIS 0.007 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00301 (24591) covalent geometry : angle 0.73666 (33171) hydrogen bonds : bond 0.03066 ( 901) hydrogen bonds : angle 4.22326 ( 2616) Misc. bond : bond 0.00489 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 390 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7607 (ttt) cc_final: 0.7116 (ttt) REVERT: A 66 VAL cc_start: 0.9066 (t) cc_final: 0.8755 (m) REVERT: A 96 MET cc_start: 0.8542 (ttm) cc_final: 0.8273 (ttm) REVERT: A 124 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8255 (pp) REVERT: A 235 ILE cc_start: 0.7353 (mt) cc_final: 0.6870 (pt) REVERT: B 106 SER cc_start: 0.8948 (p) cc_final: 0.8626 (m) REVERT: B 107 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7748 (mp0) REVERT: B 181 SER cc_start: 0.7347 (p) cc_final: 0.7075 (t) REVERT: B 239 VAL cc_start: 0.9147 (t) cc_final: 0.8924 (p) REVERT: B 303 MET cc_start: 0.7242 (ppp) cc_final: 0.6820 (ppp) REVERT: B 334 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8041 (ptm-80) REVERT: B 353 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7464 (tpp80) REVERT: B 387 TYR cc_start: 0.7864 (m-80) cc_final: 0.7622 (m-80) REVERT: B 419 THR cc_start: 0.7104 (m) cc_final: 0.6796 (t) REVERT: B 443 MET cc_start: 0.7953 (mmp) cc_final: 0.7408 (mtt) REVERT: C 29 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7613 (t) REVERT: C 85 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8089 (mt0) REVERT: C 242 ASP cc_start: 0.7031 (t0) cc_final: 0.6573 (m-30) REVERT: C 299 LEU cc_start: 0.8995 (tp) cc_final: 0.8649 (tp) REVERT: C 355 LEU cc_start: 0.9300 (tp) cc_final: 0.8789 (tp) REVERT: C 423 ASP cc_start: 0.7865 (t0) cc_final: 0.7647 (t0) REVERT: C 432 GLU cc_start: 0.8884 (tp30) cc_final: 0.8439 (tp30) REVERT: D 88 MET cc_start: 0.8154 (mmm) cc_final: 0.7895 (mmt) REVERT: D 119 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8773 (mm) REVERT: D 237 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6199 (tp30) REVERT: E 49 CYS cc_start: 0.8229 (p) cc_final: 0.7576 (t) REVERT: E 110 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7465 (mm-30) REVERT: E 113 MET cc_start: 0.8889 (mmm) cc_final: 0.8482 (mmm) REVERT: E 278 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7634 (tt0) REVERT: E 359 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7741 (ttt) REVERT: F 90 MET cc_start: 0.8769 (tpp) cc_final: 0.8517 (tpp) REVERT: F 168 MET cc_start: 0.5522 (mpp) cc_final: 0.5125 (mmt) REVERT: F 405 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8442 (tp) REVERT: G 1 MET cc_start: 0.3265 (ppp) cc_final: 0.2699 (ppp) REVERT: G 43 ASN cc_start: 0.5130 (t0) cc_final: 0.3467 (p0) REVERT: G 79 PHE cc_start: 0.5318 (m-10) cc_final: 0.5088 (m-10) REVERT: G 109 MET cc_start: 0.6842 (ttp) cc_final: 0.6642 (ptm) REVERT: G 118 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6700 (tm-30) REVERT: G 204 GLN cc_start: 0.8547 (tp40) cc_final: 0.7946 (tm-30) REVERT: G 215 ASP cc_start: 0.7948 (t70) cc_final: 0.7305 (m-30) REVERT: G 309 MET cc_start: 0.5890 (mtp) cc_final: 0.5593 (mtm) REVERT: H 946 PHE cc_start: 0.6440 (t80) cc_final: 0.5550 (p90) REVERT: H 1921 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6673 (tm-30) REVERT: H 1965 ARG cc_start: 0.5872 (ttt180) cc_final: 0.5439 (ptt180) REVERT: H 2007 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7412 (mt0) REVERT: H 2013 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7403 (tm-30) REVERT: H 2054 GLN cc_start: 0.7974 (tm-30) cc_final: 0.6785 (mt0) outliers start: 87 outliers final: 67 residues processed: 451 average time/residue: 0.1528 time to fit residues: 112.5602 Evaluate side-chains 436 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 362 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 210 CYS Chi-restraints excluded: chain H residue 936 HIS Chi-restraints excluded: chain H residue 938 LEU Chi-restraints excluded: chain H residue 940 ARG Chi-restraints excluded: chain H residue 1914 LEU Chi-restraints excluded: chain H residue 1922 VAL Chi-restraints excluded: chain H residue 1999 LEU Chi-restraints excluded: chain H residue 2038 ILE Chi-restraints excluded: chain H residue 2152 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN C 115 ASN E 115 ASN G 387 HIS ** H 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.135664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115179 restraints weight = 62022.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.117584 restraints weight = 37757.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119157 restraints weight = 25902.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.120360 restraints weight = 19601.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.121223 restraints weight = 15810.139| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.8965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24596 Z= 0.186 Angle : 0.804 16.725 33171 Z= 0.402 Chirality : 0.048 0.400 3885 Planarity : 0.005 0.141 4263 Dihedral : 6.090 177.575 3362 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.46 % Favored : 92.47 % Rotamer: Outliers : 3.35 % Allowed : 22.78 % Favored : 73.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.08 (0.15), residues: 2988 helix: 0.52 (0.15), residues: 1215 sheet: -0.25 (0.23), residues: 458 loop : -2.12 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 945 TYR 0.042 0.002 TYR A 220 PHE 0.031 0.002 PHE H1978 TRP 0.019 0.002 TRP G 360 HIS 0.009 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00431 (24591) covalent geometry : angle 0.80418 (33171) hydrogen bonds : bond 0.03665 ( 901) hydrogen bonds : angle 4.55788 ( 2616) Misc. bond : bond 0.00379 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4602.22 seconds wall clock time: 80 minutes 19.06 seconds (4819.06 seconds total)