Starting phenix.real_space_refine on Sun Feb 8 05:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge5_51290/02_2026/9ge5_51290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge5_51290/02_2026/9ge5_51290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ge5_51290/02_2026/9ge5_51290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge5_51290/02_2026/9ge5_51290.map" model { file = "/net/cci-nas-00/data/ceres_data/9ge5_51290/02_2026/9ge5_51290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge5_51290/02_2026/9ge5_51290.cif" } resolution = 3.35 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= 0.005 sd= 0.053 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 243 5.49 5 S 168 5.16 5 C 24450 2.51 5 N 7130 2.21 5 O 8025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 322 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40017 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3345 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3454 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "C" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 425} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3318 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain breaks: 2 Chain: "E" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3404 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 427} Chain: "F" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3377 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5609 Classifications: {'peptide': 682} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 653} Chain breaks: 3 Chain: "H" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 851 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "J" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3278 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 382} Chain breaks: 2 Chain: "K" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2334 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "L" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2299 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "M" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "Q" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 767 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "R" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "T" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.99, per 1000 atoms: 0.22 Number of scatterers: 40017 At special positions: 0 Unit cell: (135.222, 188.293, 187.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 168 16.00 P 243 15.00 O 8025 8.00 N 7130 7.00 C 24450 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=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.6 seconds 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8308 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 34 sheets defined 48.9% alpha, 10.6% beta 98 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.598A pdb=" N ALA A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.828A pdb=" N ALA A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.726A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 272 through 289 removed outlier: 4.073A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.068A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.960A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.580A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'A' and resid 450 through 454 removed outlier: 4.229A pdb=" N TYR A 454 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 4.318A pdb=" N ALA B 48 " --> pdb=" O ASN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.564A pdb=" N GLY B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.660A pdb=" N TYR B 102 " --> pdb=" O SER B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.510A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.505A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.560A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'B' and resid 272 through 289 removed outlier: 3.620A pdb=" N ARG B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.671A pdb=" N MET B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 4.219A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 320 " --> pdb=" O HIS B 316 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.632A pdb=" N GLY B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.904A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.571A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.759A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 Processing helix chain 'B' and resid 451 through 454 removed outlier: 3.818A pdb=" N TYR B 454 " --> pdb=" O GLN B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 454' Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.574A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.908A pdb=" N TYR C 102 " --> pdb=" O SER C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 174 through 180 removed outlier: 4.330A pdb=" N GLU C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.768A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 319 removed outlier: 4.574A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.639A pdb=" N THR C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.519A pdb=" N HIS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.692A pdb=" N ILE C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 454 removed outlier: 4.360A pdb=" N TYR C 454 " --> pdb=" O GLN C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 454' Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.667A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.574A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 244 through 253 removed outlier: 4.302A pdb=" N ARG D 253 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.596A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.626A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 4.038A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 379 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 399 through 416 removed outlier: 4.383A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 444 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 175 through 185 removed outlier: 3.688A pdb=" N GLU E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 214 Processing helix chain 'E' and resid 244 through 253 removed outlier: 4.112A pdb=" N ARG E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.692A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 4.077A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.726A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 443 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.694A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 244 through 251 Processing helix chain 'F' and resid 257 through 263 removed outlier: 4.115A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 286 removed outlier: 3.652A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.749A pdb=" N MET F 303 " --> pdb=" O GLU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.635A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.503A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 379 removed outlier: 3.891A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.763A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 445 removed outlier: 3.956A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 450 Processing helix chain 'G' and resid 519 through 536 Processing helix chain 'G' and resid 550 through 559 removed outlier: 3.610A pdb=" N ALA G 555 " --> pdb=" O VAL G 551 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU G 556 " --> pdb=" O GLN G 552 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA G 558 " --> pdb=" O ILE G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 568 removed outlier: 3.838A pdb=" N TRP G 567 " --> pdb=" O ARG G 563 " (cutoff:3.500A) Processing helix chain 'G' and resid 575 through 579 Processing helix chain 'G' and resid 580 through 585 Processing helix chain 'G' and resid 586 through 588 No H-bonds generated for 'chain 'G' and resid 586 through 588' Processing helix chain 'G' and resid 601 through 606 Processing helix chain 'G' and resid 608 through 613 removed outlier: 3.533A pdb=" N SER G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 642 removed outlier: 4.239A pdb=" N GLN G 636 " --> pdb=" O GLN G 632 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS G 639 " --> pdb=" O VAL G 635 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR G 640 " --> pdb=" O GLN G 636 " (cutoff:3.500A) Processing helix chain 'G' and resid 654 through 658 Processing helix chain 'G' and resid 662 through 669 Processing helix chain 'G' and resid 687 through 690 Processing helix chain 'G' and resid 691 through 699 removed outlier: 3.761A pdb=" N LEU G 695 " --> pdb=" O LEU G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 710 removed outlier: 4.178A pdb=" N PHE G 709 " --> pdb=" O SER G 705 " (cutoff:3.500A) Processing helix chain 'G' and resid 730 through 740 Processing helix chain 'G' and resid 748 through 753 Processing helix chain 'G' and resid 770 through 780 removed outlier: 3.851A pdb=" N LEU G 774 " --> pdb=" O ARG G 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 809 through 818 removed outlier: 4.031A pdb=" N VAL G 815 " --> pdb=" O GLN G 811 " (cutoff:3.500A) Processing helix chain 'G' and resid 819 through 822 Processing helix chain 'G' and resid 841 through 848 Processing helix chain 'G' and resid 849 through 854 removed outlier: 3.550A pdb=" N ASN G 854 " --> pdb=" O ILE G 850 " (cutoff:3.500A) Processing helix chain 'G' and resid 854 through 864 removed outlier: 4.300A pdb=" N TRP G 860 " --> pdb=" O SER G 856 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 861 " --> pdb=" O ARG G 857 " (cutoff:3.500A) Processing helix chain 'G' and resid 868 through 877 Processing helix chain 'G' and resid 888 through 893 Processing helix chain 'G' and resid 897 through 907 Processing helix chain 'G' and resid 908 through 932 removed outlier: 3.560A pdb=" N LYS G 921 " --> pdb=" O PHE G 917 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR G 924 " --> pdb=" O LEU G 920 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG G 925 " --> pdb=" O LYS G 921 " (cutoff:3.500A) Processing helix chain 'G' and resid 958 through 965 Processing helix chain 'G' and resid 967 through 972 removed outlier: 3.877A pdb=" N LEU G 971 " --> pdb=" O LEU G 967 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1041 removed outlier: 3.912A pdb=" N TYR G1033 " --> pdb=" O ARG G1029 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU G1034 " --> pdb=" O SER G1030 " (cutoff:3.500A) Processing helix chain 'G' and resid 1043 through 1053 Processing helix chain 'G' and resid 1054 through 1062 Processing helix chain 'G' and resid 1063 through 1067 Processing helix chain 'G' and resid 1075 through 1079 Processing helix chain 'G' and resid 1094 through 1100 removed outlier: 3.857A pdb=" N SER G1100 " --> pdb=" O LEU G1096 " (cutoff:3.500A) Processing helix chain 'G' and resid 1100 through 1117 Processing helix chain 'G' and resid 1126 through 1140 Processing helix chain 'G' and resid 1154 through 1164 removed outlier: 4.001A pdb=" N ASP G1158 " --> pdb=" O SER G1154 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET G1159 " --> pdb=" O GLU G1155 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G1160 " --> pdb=" O ARG G1156 " (cutoff:3.500A) Processing helix chain 'G' and resid 1201 through 1208 Processing helix chain 'G' and resid 1231 through 1248 removed outlier: 3.575A pdb=" N LEU G1235 " --> pdb=" O GLU G1231 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU G1243 " --> pdb=" O LYS G1239 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE G1244 " --> pdb=" O GLU G1240 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 235 removed outlier: 4.168A pdb=" N LEU H 213 " --> pdb=" O THR H 209 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG H 216 " --> pdb=" O MET H 212 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG H 219 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU H 233 " --> pdb=" O ARG H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 340 Processing helix chain 'I' and resid 143 through 151 Processing helix chain 'I' and resid 152 through 154 No H-bonds generated for 'chain 'I' and resid 152 through 154' Processing helix chain 'I' and resid 162 through 166 removed outlier: 3.890A pdb=" N ILE I 166 " --> pdb=" O TYR I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 207 removed outlier: 3.583A pdb=" N ARG I 207 " --> pdb=" O PHE I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 220 removed outlier: 3.824A pdb=" N GLY I 216 " --> pdb=" O ASP I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 121 Processing helix chain 'J' and resid 141 through 155 Processing helix chain 'J' and resid 165 through 175 Processing helix chain 'J' and resid 214 through 230 Processing helix chain 'J' and resid 238 through 249 removed outlier: 4.715A pdb=" N GLU J 244 " --> pdb=" O SER J 240 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE J 245 " --> pdb=" O ARG J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 263 Processing helix chain 'J' and resid 265 through 273 removed outlier: 3.978A pdb=" N ASN J 271 " --> pdb=" O ASP J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 454 removed outlier: 3.526A pdb=" N ALA J 451 " --> pdb=" O GLU J 447 " (cutoff:3.500A) Proline residue: J 452 - end of helix Processing helix chain 'J' and resid 455 through 456 No H-bonds generated for 'chain 'J' and resid 455 through 456' Processing helix chain 'J' and resid 457 through 461 Processing helix chain 'J' and resid 466 through 477 removed outlier: 4.081A pdb=" N GLU J 470 " --> pdb=" O ALA J 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 489 removed outlier: 3.671A pdb=" N GLN J 489 " --> pdb=" O GLU J 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 500 Processing helix chain 'J' and resid 502 through 513 removed outlier: 3.686A pdb=" N LYS J 509 " --> pdb=" O ALA J 505 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 544 Processing helix chain 'J' and resid 554 through 558 Processing helix chain 'M' and resid 46 through 57 removed outlier: 3.816A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 79 Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 132 removed outlier: 3.673A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG M 131 " --> pdb=" O ALA M 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 77 removed outlier: 4.640A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA N 76 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.551A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 52 removed outlier: 4.234A pdb=" N ILE Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.194A pdb=" N ARG Q 72 " --> pdb=" O GLN Q 68 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE Q 74 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.703A pdb=" N ALA Q 91 " --> pdb=" O SER Q 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN Q 93 " --> pdb=" O VAL Q 89 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU Q 94 " --> pdb=" O MET Q 90 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU Q 109 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 4.157A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG Q 129 " --> pdb=" O GLN Q 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 removed outlier: 3.599A pdb=" N GLY R 28 " --> pdb=" O ASN R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.592A pdb=" N HIS R 75 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 76 " --> pdb=" O TYR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 removed outlier: 4.114A pdb=" N ARG S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 37 removed outlier: 3.726A pdb=" N ARG S 35 " --> pdb=" O HIS S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 73 removed outlier: 3.619A pdb=" N LEU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 89 Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'T' and resid 37 through 46 removed outlier: 4.123A pdb=" N LYS T 46 " --> pdb=" O TYR T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 84 removed outlier: 3.600A pdb=" N ASN T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 102 removed outlier: 3.550A pdb=" N ILE T 94 " --> pdb=" O THR T 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG T 99 " --> pdb=" O GLN T 95 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.423A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 141 removed outlier: 5.637A pdb=" N VAL A 135 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS A 162 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 137 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS A 156 " --> pdb=" O CYS A 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 172 current: chain 'A' and resid 200 through 206 removed outlier: 6.072A pdb=" N VAL A 221 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG A 205 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.501A pdb=" N ILE B 3 " --> pdb=" O LEU G 762 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR G 764 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU B 5 " --> pdb=" O TYR G 764 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU G1121 " --> pdb=" O ILE G1192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 97 removed outlier: 7.027A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 143 removed outlier: 5.668A pdb=" N VAL B 135 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 162 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR B 143 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE B 154 " --> pdb=" O THR B 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 172 current: chain 'B' and resid 200 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 437 through 438 removed outlier: 6.802A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 73 " --> pdb=" O MET E 326 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR E 328 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE E 75 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.187A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 299 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA C 330 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 301 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 120 through 142 removed outlier: 5.742A pdb=" N VAL C 135 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS C 162 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C 137 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 156 " --> pdb=" O CYS C 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 172 current: chain 'C' and resid 200 through 205 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 200 through 205 current: chain 'E' and resid 158 through 164 removed outlier: 4.356A pdb=" N GLY E 159 " --> pdb=" O LEU E 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 174 current: chain 'E' and resid 204 through 207 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 204 through 207 current: chain 'G' and resid 996 through 1005 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 996 through 1005 current: chain 'H' and resid 281 through 286 Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.680A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 147 removed outlier: 6.812A pdb=" N THR D 162 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 174 current: chain 'D' and resid 202 through 208 removed outlier: 6.209A pdb=" N VAL D 225 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG D 207 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AB7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'E' and resid 333 through 334 Processing sheet with id=AB9, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC1, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.459A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 127 through 148 removed outlier: 5.362A pdb=" N VAL F 142 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS F 164 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU F 144 " --> pdb=" O THR F 162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 172 current: chain 'F' and resid 201 through 208 removed outlier: 6.209A pdb=" N VAL F 225 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG F 207 " --> pdb=" O VAL F 225 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 224 through 225 current: chain 'H' and resid 328 through 329 Processing sheet with id=AC3, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AC4, first strand: chain 'G' and resid 539 through 540 removed outlier: 6.647A pdb=" N GLY G 539 " --> pdb=" O LEU G 678 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET G 649 " --> pdb=" O LEU G 677 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU G 679 " --> pdb=" O MET G 649 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU G 571 " --> pdb=" O VAL G 650 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP G 652 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE G 573 " --> pdb=" O ASP G 652 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 831 through 833 removed outlier: 6.377A pdb=" N PHE G 831 " --> pdb=" O THR G1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AC7, first strand: chain 'J' and resid 58 through 62 removed outlier: 4.125A pdb=" N GLN J 60 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL J 42 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY J 164 " --> pdb=" O LEU J 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AC9, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AD1, first strand: chain 'J' and resid 183 through 188 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 202 through 203 current: chain 'J' and resid 523 through 525 Processing sheet with id=AD2, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.960A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AD4, first strand: chain 'N' and resid 96 through 97 removed outlier: 6.937A pdb=" N THR N 96 " --> pdb=" O THR S 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.708A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'S' and resid 42 through 43 removed outlier: 6.863A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'S' and resid 77 through 78 1446 hydrogen bonds defined for protein. 4119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 250 hydrogen bonds 500 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 9.89 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.57: 40406 1.57 - 1.94: 745 1.94 - 2.30: 4 2.30 - 2.67: 0 2.67 - 3.03: 1 Bond restraints: 41156 Sorted by residual: bond pdb=" CA LYS I 136 " pdb=" CB LYS I 136 " ideal model delta sigma weight residual 1.530 3.033 -1.503 1.68e-02 3.54e+03 8.00e+03 bond pdb=" O4' DG K 3 " pdb=" C1' DG K 3 " ideal model delta sigma weight residual 1.414 1.939 -0.525 2.00e-02 2.50e+03 6.88e+02 bond pdb=" C2' DG K 3 " pdb=" C1' DG K 3 " ideal model delta sigma weight residual 1.525 2.024 -0.499 2.00e-02 2.50e+03 6.22e+02 bond pdb=" C4' DG K 3 " pdb=" C3' DG K 3 " ideal model delta sigma weight residual 1.523 2.018 -0.495 2.00e-02 2.50e+03 6.13e+02 bond pdb=" C3' DG K 3 " pdb=" C2' DG K 3 " ideal model delta sigma weight residual 1.525 1.998 -0.473 2.00e-02 2.50e+03 5.60e+02 ... (remaining 41151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 54690 4.08 - 8.16: 1799 8.16 - 12.23: 34 12.23 - 16.31: 16 16.31 - 20.39: 5 Bond angle restraints: 56544 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.11 19.76 1.00e+00 1.00e+00 3.91e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 118.83 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" N LYS I 136 " pdb=" CA LYS I 136 " pdb=" C LYS I 136 " ideal model delta sigma weight residual 112.89 95.39 17.50 1.24e+00 6.50e-01 1.99e+02 angle pdb=" N LYS I 136 " pdb=" CA LYS I 136 " pdb=" CB LYS I 136 " ideal model delta sigma weight residual 110.40 127.20 -16.80 1.63e+00 3.76e-01 1.06e+02 angle pdb=" CA LYS I 136 " pdb=" CB LYS I 136 " pdb=" CG LYS I 136 " ideal model delta sigma weight residual 114.10 134.49 -20.39 2.00e+00 2.50e-01 1.04e+02 ... (remaining 56539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 23284 35.30 - 70.60: 1187 70.60 - 105.90: 84 105.90 - 141.20: 7 141.20 - 176.50: 7 Dihedral angle restraints: 24569 sinusoidal: 11688 harmonic: 12881 Sorted by residual: dihedral pdb=" N LYS I 136 " pdb=" C LYS I 136 " pdb=" CA LYS I 136 " pdb=" CB LYS I 136 " ideal model delta harmonic sigma weight residual 122.80 142.94 -20.14 0 2.50e+00 1.60e-01 6.49e+01 dihedral pdb=" C LYS I 136 " pdb=" N LYS I 136 " pdb=" CA LYS I 136 " pdb=" CB LYS I 136 " ideal model delta harmonic sigma weight residual -122.60 -141.24 18.64 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" C5' ADP J 701 " pdb=" O5' ADP J 701 " pdb=" PA ADP J 701 " pdb=" O2A ADP J 701 " ideal model delta sinusoidal sigma weight residual 300.00 151.61 148.39 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 24566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 6368 0.279 - 0.557: 47 0.557 - 0.836: 1 0.836 - 1.115: 0 1.115 - 1.393: 3 Chirality restraints: 6419 Sorted by residual: chirality pdb=" C3' DG K 3 " pdb=" C4' DG K 3 " pdb=" O3' DG K 3 " pdb=" C2' DG K 3 " both_signs ideal model delta sigma weight residual False -2.66 -4.05 1.39 2.00e-01 2.50e+01 4.85e+01 chirality pdb=" CA LYS I 136 " pdb=" N LYS I 136 " pdb=" C LYS I 136 " pdb=" CB LYS I 136 " both_signs ideal model delta sigma weight residual False 2.51 3.88 -1.37 2.00e-01 2.50e+01 4.68e+01 chirality pdb=" C4' DG K 3 " pdb=" C5' DG K 3 " pdb=" O4' DG K 3 " pdb=" C3' DG K 3 " both_signs ideal model delta sigma weight residual False -2.53 -3.69 1.16 2.00e-01 2.50e+01 3.38e+01 ... (remaining 6416 not shown) Planarity restraints: 6443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG K -29 " 0.055 2.00e-02 2.50e+03 1.33e-01 5.28e+02 pdb=" N9 DG K -29 " 0.069 2.00e-02 2.50e+03 pdb=" C8 DG K -29 " -0.178 2.00e-02 2.50e+03 pdb=" N7 DG K -29 " -0.195 2.00e-02 2.50e+03 pdb=" C5 DG K -29 " 0.041 2.00e-02 2.50e+03 pdb=" C6 DG K -29 " 0.101 2.00e-02 2.50e+03 pdb=" O6 DG K -29 " 0.071 2.00e-02 2.50e+03 pdb=" N1 DG K -29 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DG K -29 " 0.023 2.00e-02 2.50e+03 pdb=" N2 DG K -29 " -0.279 2.00e-02 2.50e+03 pdb=" N3 DG K -29 " 0.152 2.00e-02 2.50e+03 pdb=" C4 DG K -29 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K 32 " -0.323 2.00e-02 2.50e+03 1.32e-01 5.24e+02 pdb=" N9 DG K 32 " 0.042 2.00e-02 2.50e+03 pdb=" C8 DG K 32 " 0.149 2.00e-02 2.50e+03 pdb=" N7 DG K 32 " 0.118 2.00e-02 2.50e+03 pdb=" C5 DG K 32 " 0.054 2.00e-02 2.50e+03 pdb=" C6 DG K 32 " -0.055 2.00e-02 2.50e+03 pdb=" O6 DG K 32 " -0.202 2.00e-02 2.50e+03 pdb=" N1 DG K 32 " -0.047 2.00e-02 2.50e+03 pdb=" C2 DG K 32 " 0.039 2.00e-02 2.50e+03 pdb=" N2 DG K 32 " 0.080 2.00e-02 2.50e+03 pdb=" N3 DG K 32 " 0.066 2.00e-02 2.50e+03 pdb=" C4 DG K 32 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG L -56 " 0.300 2.00e-02 2.50e+03 1.28e-01 4.94e+02 pdb=" N9 DG L -56 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG L -56 " -0.137 2.00e-02 2.50e+03 pdb=" N7 DG L -56 " -0.122 2.00e-02 2.50e+03 pdb=" C5 DG L -56 " -0.058 2.00e-02 2.50e+03 pdb=" C6 DG L -56 " 0.045 2.00e-02 2.50e+03 pdb=" O6 DG L -56 " 0.233 2.00e-02 2.50e+03 pdb=" N1 DG L -56 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DG L -56 " -0.056 2.00e-02 2.50e+03 pdb=" N2 DG L -56 " -0.042 2.00e-02 2.50e+03 pdb=" N3 DG L -56 " -0.057 2.00e-02 2.50e+03 pdb=" C4 DG L -56 " -0.072 2.00e-02 2.50e+03 ... (remaining 6440 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 742 2.71 - 3.26: 39271 3.26 - 3.81: 63023 3.81 - 4.35: 86414 4.35 - 4.90: 134871 Nonbonded interactions: 324321 Sorted by model distance: nonbonded pdb=" CA LYS I 136 " pdb=" O4' DG K 3 " model vdw 2.167 3.470 nonbonded pdb=" CB LYS I 136 " pdb=" O4' DG K 3 " model vdw 2.192 3.440 nonbonded pdb=" CA LYS I 136 " pdb=" C1' DG K 3 " model vdw 2.259 3.900 nonbonded pdb=" CB LYS I 136 " pdb=" C1' DG K 3 " model vdw 2.268 3.870 nonbonded pdb=" CA LYS I 136 " pdb=" C2' DG K 3 " model vdw 2.273 3.870 ... (remaining 324316 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 12 through 141 or resid 152 through 454)) selection = (chain 'B' and (resid 12 through 141 or resid 152 through 454)) selection = (chain 'C' and (resid 12 through 141 or resid 152 through 454)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) selection = (chain 'F' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) } ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 43 through 133) } ncs_group { reference = (chain 'N' and resid 25 through 102) selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 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: 0.790 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 40.650 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.016 1.503 41156 Z= 0.913 Angle : 1.880 20.388 56544 Z= 1.234 Chirality : 0.098 1.393 6419 Planarity : 0.019 0.240 6443 Dihedral : 18.962 176.501 16261 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.87 % Favored : 95.56 % Rotamer: Outliers : 1.15 % Allowed : 4.90 % Favored : 93.94 % Cbeta Deviations : 0.34 % 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 are not related in a simple way. whole: -1.79 (0.11), residues: 4415 helix: -1.75 (0.09), residues: 1942 sheet: 0.14 (0.19), residues: 629 loop : -0.80 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG J 43 TYR 0.191 0.023 TYR S 57 PHE 0.058 0.011 PHE G1193 TRP 0.172 0.023 TRP J 540 HIS 0.016 0.004 HIS J 119 Details of bonding type rmsd covalent geometry : bond 0.01566 (41156) covalent geometry : angle 1.88041 (56544) hydrogen bonds : bond 0.16366 ( 1696) hydrogen bonds : angle 7.54402 ( 4619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 999 time to evaluate : 2.191 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: symmetry clash revert: symmetry clash revert: 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 40 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.9112 (p) REVERT: A 61 MET cc_start: 0.7919 (mmm) cc_final: 0.7666 (mmm) REVERT: A 90 LYS cc_start: 0.8521 (mppt) cc_final: 0.8024 (tptt) REVERT: A 183 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7753 (tp30) REVERT: A 259 MET cc_start: 0.7313 (ptm) cc_final: 0.7097 (tpp) REVERT: A 449 ASP cc_start: 0.9513 (m-30) cc_final: 0.9271 (m-30) REVERT: B 5 GLU cc_start: 0.6634 (mt-10) cc_final: 0.5920 (mt-10) REVERT: B 100 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7699 (tp30) REVERT: B 134 GLU cc_start: 0.7928 (tt0) cc_final: 0.7661 (tm-30) REVERT: B 168 LYS cc_start: 0.8347 (mttp) cc_final: 0.8071 (mtpt) REVERT: B 335 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8422 (t0) REVERT: B 371 MET cc_start: 0.8730 (mmt) cc_final: 0.8500 (mtt) REVERT: C 40 VAL cc_start: 0.8719 (p) cc_final: 0.8500 (m) REVERT: C 106 ILE cc_start: 0.8735 (tt) cc_final: 0.8457 (pt) REVERT: C 165 LYS cc_start: 0.8861 (tttp) cc_final: 0.8562 (mptt) REVERT: C 190 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7504 (t) REVERT: C 192 TYR cc_start: 0.8930 (p90) cc_final: 0.8497 (p90) REVERT: C 268 LYS cc_start: 0.8192 (mttt) cc_final: 0.7941 (mttm) REVERT: C 363 THR cc_start: 0.9293 (m) cc_final: 0.8917 (p) REVERT: D 134 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8970 (mm-30) REVERT: D 146 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7589 (pt0) REVERT: D 149 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7127 (ppt170) REVERT: D 235 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.8234 (ttp80) REVERT: D 447 GLN cc_start: 0.8496 (tt0) cc_final: 0.8099 (tp-100) REVERT: E 47 VAL cc_start: 0.8677 (m) cc_final: 0.8206 (p) REVERT: E 88 MET cc_start: 0.8720 (mmp) cc_final: 0.8478 (mmm) REVERT: E 124 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8013 (mtp85) REVERT: E 215 TYR cc_start: 0.6930 (t80) cc_final: 0.6571 (t80) REVERT: E 353 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8296 (ttm170) REVERT: E 446 TYR cc_start: 0.8127 (m-10) cc_final: 0.7869 (m-10) REVERT: F 34 ASP cc_start: 0.8160 (m-30) cc_final: 0.7741 (p0) REVERT: F 88 MET cc_start: 0.8214 (mmp) cc_final: 0.7997 (mmm) REVERT: F 112 GLU cc_start: 0.8672 (pt0) cc_final: 0.8396 (pp20) REVERT: F 116 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7499 (p) REVERT: F 172 TYR cc_start: 0.8688 (m-80) cc_final: 0.8471 (m-80) REVERT: F 248 ASP cc_start: 0.8139 (m-30) cc_final: 0.7732 (m-30) REVERT: F 274 GLU cc_start: 0.8697 (pt0) cc_final: 0.8475 (tm-30) REVERT: G 573 ILE cc_start: 0.8349 (mp) cc_final: 0.7987 (mt) REVERT: G 593 PHE cc_start: 0.6980 (m-80) cc_final: 0.6571 (m-80) REVERT: G 599 TRP cc_start: 0.8879 (p-90) cc_final: 0.7927 (p90) REVERT: G 646 TRP cc_start: 0.8014 (m100) cc_final: 0.7276 (m-90) REVERT: G 649 MET cc_start: 0.5524 (mmm) cc_final: 0.5204 (mmm) REVERT: G 688 MET cc_start: 0.7278 (mmm) cc_final: 0.7036 (mmm) REVERT: G 765 CYS cc_start: 0.7445 (m) cc_final: 0.7155 (p) REVERT: G 770 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8438 (ttt180) REVERT: G 810 MET cc_start: 0.8549 (mmm) cc_final: 0.8131 (mmt) REVERT: G 821 LEU cc_start: 0.9029 (mt) cc_final: 0.8790 (mt) REVERT: G 856 SER cc_start: 0.9189 (p) cc_final: 0.8978 (t) REVERT: G 880 LYS cc_start: 0.8848 (mttt) cc_final: 0.8599 (mmtt) REVERT: G 1123 TYR cc_start: 0.6693 (m-80) cc_final: 0.6403 (m-80) REVERT: G 1129 MET cc_start: 0.8956 (tpp) cc_final: 0.8718 (tpt) REVERT: G 1144 TYR cc_start: 0.8277 (p90) cc_final: 0.8025 (p90) REVERT: G 1145 MET cc_start: 0.8186 (mtt) cc_final: 0.7953 (mtm) REVERT: G 1216 THR cc_start: 0.8375 (p) cc_final: 0.8103 (t) REVERT: I 120 LYS cc_start: 0.8586 (mttt) cc_final: 0.8383 (tptt) REVERT: I 146 GLN cc_start: 0.8934 (mp10) cc_final: 0.8653 (mp10) REVERT: I 159 ASN cc_start: 0.6013 (m-40) cc_final: 0.5630 (p0) REVERT: I 192 GLN cc_start: 0.8521 (mt0) cc_final: 0.8268 (mt0) REVERT: I 208 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8004 (ptt180) REVERT: I 220 LEU cc_start: 0.9255 (tp) cc_final: 0.9028 (tt) REVERT: J 12 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7999 (tmt170) REVERT: J 36 ASP cc_start: 0.9039 (m-30) cc_final: 0.8698 (t0) REVERT: J 93 MET cc_start: 0.3359 (tpt) cc_final: 0.2635 (tpt) REVERT: J 132 ILE cc_start: 0.8967 (pt) cc_final: 0.8632 (tt) REVERT: J 133 VAL cc_start: 0.8905 (p) cc_final: 0.8598 (m) REVERT: J 163 TYR cc_start: 0.7589 (m-80) cc_final: 0.7166 (m-10) REVERT: J 242 MET cc_start: 0.7946 (mmp) cc_final: 0.7687 (mmp) REVERT: J 475 ILE cc_start: 0.9156 (pt) cc_final: 0.8839 (mt) REVERT: J 540 TRP cc_start: 0.8800 (t60) cc_final: 0.8442 (t60) REVERT: J 555 LYS cc_start: 0.9099 (pttt) cc_final: 0.8856 (mmmm) REVERT: M 50 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7294 (mp0) REVERT: M 61 LEU cc_start: 0.7380 (mt) cc_final: 0.7154 (mt) REVERT: M 67 PHE cc_start: 0.8575 (t80) cc_final: 0.7985 (t80) REVERT: M 99 TYR cc_start: 0.7852 (t80) cc_final: 0.7353 (t80) REVERT: N 88 TYR cc_start: 0.7159 (m-10) cc_final: 0.6774 (m-80) REVERT: Q 67 PHE cc_start: 0.7277 (t80) cc_final: 0.7018 (t80) REVERT: Q 104 PHE cc_start: 0.7464 (m-80) cc_final: 0.7253 (m-10) REVERT: Q 122 LYS cc_start: 0.8039 (ptmm) cc_final: 0.7792 (ptmt) REVERT: Q 134 ARG cc_start: 0.6958 (ttm170) cc_final: 0.6644 (ttm-80) REVERT: R 32 PRO cc_start: 0.5508 (Cg_endo) cc_final: 0.4968 (Cg_exo) REVERT: R 49 LEU cc_start: 0.7404 (mp) cc_final: 0.6746 (mt) REVERT: R 58 LEU cc_start: 0.8565 (tp) cc_final: 0.8264 (tp) REVERT: R 75 HIS cc_start: 0.7025 (t70) cc_final: 0.6688 (t-170) REVERT: S 91 GLU cc_start: 0.8713 (pm20) cc_final: 0.8478 (pp20) REVERT: T 44 VAL cc_start: 0.8357 (t) cc_final: 0.8109 (p) REVERT: T 92 ARG cc_start: 0.7473 (ptm160) cc_final: 0.7140 (ptt-90) REVERT: T 113 GLU cc_start: 0.8089 (tp30) cc_final: 0.7337 (tp30) outliers start: 44 outliers final: 11 residues processed: 1035 average time/residue: 0.2821 time to fit residues: 451.9248 Evaluate side-chains 601 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 586 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain T residue 33 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN A 181 GLN A 247 ASN B 247 ASN B 262 GLN B 335 ASN C 18 HIS C 20 HIS C 393 HIS E 146 GLN E 221 GLN E 233 GLN E 240 HIS F 240 HIS G 580 ASN G 832 HIS G 873 GLN G1184 ASN H 226 GLN J 37 ASN J 227 GLN R 25 ASN R 64 ASN ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 ASN T 67 ASN T 109 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.125654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.085464 restraints weight = 95632.375| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.74 r_work: 0.3215 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.306 41156 Z= 0.188 Angle : 0.775 14.711 56544 Z= 0.415 Chirality : 0.048 0.298 6419 Planarity : 0.005 0.076 6443 Dihedral : 21.128 174.921 7488 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 2.94 % Allowed : 11.85 % Favored : 85.21 % Cbeta Deviations : 0.02 % 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 are not related in a simple way. whole: -0.65 (0.12), residues: 4415 helix: -0.34 (0.11), residues: 1964 sheet: -0.12 (0.18), residues: 665 loop : -0.42 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 67 TYR 0.023 0.002 TYR E 215 PHE 0.033 0.002 PHE G 641 TRP 0.017 0.002 TRP G 665 HIS 0.006 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00429 (41156) covalent geometry : angle 0.77514 (56544) hydrogen bonds : bond 0.05370 ( 1696) hydrogen bonds : angle 5.00089 ( 4619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 646 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8846 (mtpt) REVERT: B 405 TYR cc_start: 0.8763 (t80) cc_final: 0.8551 (t80) REVERT: C 105 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8421 (mt-10) REVERT: C 181 GLN cc_start: 0.8671 (pt0) cc_final: 0.8044 (tm-30) REVERT: C 260 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.8025 (tpt) REVERT: C 363 THR cc_start: 0.9416 (m) cc_final: 0.9178 (p) REVERT: D 236 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8342 (mmtm) REVERT: D 267 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8212 (mm-30) REVERT: E 46 MET cc_start: 0.7514 (mtp) cc_final: 0.7144 (mtp) REVERT: E 88 MET cc_start: 0.8738 (mmp) cc_final: 0.8263 (mmm) REVERT: E 103 ILE cc_start: 0.8786 (mm) cc_final: 0.8542 (mt) REVERT: E 124 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8332 (mtp85) REVERT: E 168 MET cc_start: 0.7888 (mmm) cc_final: 0.7429 (mpp) REVERT: F 34 ASP cc_start: 0.8134 (m-30) cc_final: 0.7857 (p0) REVERT: G 582 TRP cc_start: 0.8459 (m100) cc_final: 0.8177 (m100) REVERT: G 593 PHE cc_start: 0.7488 (m-80) cc_final: 0.6990 (m-80) REVERT: G 641 PHE cc_start: 0.7484 (m-80) cc_final: 0.6913 (m-80) REVERT: G 646 TRP cc_start: 0.7078 (m100) cc_final: 0.6865 (m100) REVERT: G 688 MET cc_start: 0.7279 (mmm) cc_final: 0.7070 (tpp) REVERT: G 691 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8061 (mm) REVERT: G 880 LYS cc_start: 0.8422 (mttt) cc_final: 0.8175 (mmtt) REVERT: G 1123 TYR cc_start: 0.8128 (m-80) cc_final: 0.7675 (m-80) REVERT: H 272 MET cc_start: 0.8655 (mmt) cc_final: 0.7956 (mmm) REVERT: H 273 VAL cc_start: 0.8076 (t) cc_final: 0.7873 (p) REVERT: I 120 LYS cc_start: 0.8173 (mttt) cc_final: 0.7936 (tptm) REVERT: I 139 ARG cc_start: 0.4198 (mtt180) cc_final: 0.2843 (tpm170) REVERT: I 140 THR cc_start: 0.7290 (t) cc_final: 0.6925 (t) REVERT: I 146 GLN cc_start: 0.8178 (mp10) cc_final: 0.7882 (mp10) REVERT: I 206 ILE cc_start: 0.8829 (mt) cc_final: 0.8617 (mt) REVERT: I 208 ARG cc_start: 0.8570 (mtm110) cc_final: 0.7929 (ptt180) REVERT: J 93 MET cc_start: 0.3707 (tpt) cc_final: 0.3490 (tpt) REVERT: J 148 MET cc_start: 0.8771 (tpp) cc_final: 0.8478 (tpp) REVERT: J 152 LEU cc_start: 0.9218 (mt) cc_final: 0.8905 (mt) REVERT: J 192 CYS cc_start: 0.8392 (p) cc_final: 0.8121 (p) REVERT: J 254 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8073 (mp0) REVERT: J 276 MET cc_start: 0.1481 (mmp) cc_final: 0.0689 (mmp) REVERT: J 475 ILE cc_start: 0.9389 (pt) cc_final: 0.9140 (mt) REVERT: J 497 ASN cc_start: 0.8668 (m110) cc_final: 0.8342 (m-40) REVERT: J 540 TRP cc_start: 0.9016 (t60) cc_final: 0.8808 (t60) REVERT: M 50 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8065 (mp0) REVERT: M 67 PHE cc_start: 0.8664 (t80) cc_final: 0.8298 (t80) REVERT: M 117 VAL cc_start: 0.6586 (m) cc_final: 0.5849 (p) REVERT: M 123 ASP cc_start: 0.7254 (m-30) cc_final: 0.6640 (t0) REVERT: Q 134 ARG cc_start: 0.6357 (ttm170) cc_final: 0.5803 (ttm110) REVERT: R 49 LEU cc_start: 0.7406 (mp) cc_final: 0.7176 (mt) REVERT: R 59 LYS cc_start: 0.8703 (tptp) cc_final: 0.8480 (tptp) REVERT: R 72 TYR cc_start: 0.7359 (m-80) cc_final: 0.6873 (m-80) REVERT: R 75 HIS cc_start: 0.7669 (t70) cc_final: 0.7000 (t70) REVERT: R 88 TYR cc_start: 0.7840 (m-80) cc_final: 0.7571 (m-80) REVERT: S 57 TYR cc_start: 0.5554 (t80) cc_final: 0.5191 (t80) REVERT: S 87 ILE cc_start: 0.9023 (mt) cc_final: 0.8747 (mt) REVERT: S 92 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5587 (tp30) REVERT: S 94 ASN cc_start: 0.8505 (t0) cc_final: 0.8297 (m-40) REVERT: S 95 LYS cc_start: 0.7959 (mttt) cc_final: 0.7725 (tmmt) REVERT: S 101 THR cc_start: 0.7776 (m) cc_final: 0.7397 (p) REVERT: T 76 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8211 (pt0) REVERT: T 92 ARG cc_start: 0.7439 (ptm160) cc_final: 0.6838 (mtp180) REVERT: T 93 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6447 (mt-10) REVERT: T 113 GLU cc_start: 0.8078 (tp30) cc_final: 0.7499 (tp30) outliers start: 112 outliers final: 59 residues processed: 718 average time/residue: 0.2612 time to fit residues: 300.9589 Evaluate side-chains 577 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 515 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 675 ASN Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 809 VAL Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1109 LEU Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 11 optimal weight: 7.9990 chunk 320 optimal weight: 30.0000 chunk 317 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 429 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 89 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 279 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 388 optimal weight: 20.0000 overall best weight: 4.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS B 289 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN J 247 HIS R 25 ASN R 64 ASN ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.121493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080684 restraints weight = 95632.346| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.71 r_work: 0.3152 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 41156 Z= 0.267 Angle : 0.778 11.366 56544 Z= 0.407 Chirality : 0.048 0.256 6419 Planarity : 0.005 0.073 6443 Dihedral : 21.209 178.972 7475 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.62 % Favored : 96.24 % Rotamer: Outliers : 3.83 % Allowed : 13.42 % Favored : 82.75 % 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 are not related in a simple way. whole: -0.69 (0.12), residues: 4415 helix: -0.17 (0.11), residues: 2006 sheet: -0.44 (0.18), residues: 681 loop : -0.59 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG Q 72 TYR 0.024 0.002 TYR I 178 PHE 0.031 0.002 PHE Q 84 TRP 0.021 0.002 TRP G 599 HIS 0.018 0.002 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00620 (41156) covalent geometry : angle 0.77792 (56544) hydrogen bonds : bond 0.05196 ( 1696) hydrogen bonds : angle 4.86522 ( 4619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 533 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8587 (mppt) cc_final: 0.8192 (mptt) REVERT: A 244 ASP cc_start: 0.8618 (m-30) cc_final: 0.8062 (m-30) REVERT: A 432 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8427 (tp30) REVERT: C 105 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: C 137 GLU cc_start: 0.8413 (pm20) cc_final: 0.8089 (pm20) REVERT: C 181 GLN cc_start: 0.8600 (pt0) cc_final: 0.8092 (tm-30) REVERT: C 317 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7560 (tmm-80) REVERT: C 363 THR cc_start: 0.9407 (m) cc_final: 0.9194 (p) REVERT: D 163 LEU cc_start: 0.8627 (mt) cc_final: 0.8377 (mp) REVERT: D 300 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8414 (mm-30) REVERT: D 303 MET cc_start: 0.8932 (mmm) cc_final: 0.8263 (mmm) REVERT: E 46 MET cc_start: 0.7539 (mtp) cc_final: 0.7255 (mtp) REVERT: E 88 MET cc_start: 0.8860 (mmp) cc_final: 0.8378 (mmm) REVERT: E 303 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8657 (mmm) REVERT: E 441 GLN cc_start: 0.8479 (tp40) cc_final: 0.8273 (tp40) REVERT: F 139 GLU cc_start: 0.8177 (tt0) cc_final: 0.7794 (tp30) REVERT: F 227 CYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8675 (m) REVERT: G 582 TRP cc_start: 0.8418 (m100) cc_final: 0.8063 (m100) REVERT: G 593 PHE cc_start: 0.7478 (m-80) cc_final: 0.6979 (m-80) REVERT: G 641 PHE cc_start: 0.7902 (m-80) cc_final: 0.7244 (m-80) REVERT: G 675 ASN cc_start: 0.6219 (t0) cc_final: 0.5831 (t0) REVERT: G 691 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8192 (mm) REVERT: G 880 LYS cc_start: 0.8458 (mttt) cc_final: 0.8213 (mmtt) REVERT: G 967 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8028 (tt) REVERT: G 1123 TYR cc_start: 0.8508 (m-80) cc_final: 0.8138 (m-80) REVERT: H 272 MET cc_start: 0.8836 (mmt) cc_final: 0.8115 (mmm) REVERT: I 120 LYS cc_start: 0.8093 (mttt) cc_final: 0.7788 (tttm) REVERT: I 151 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8182 (mt-10) REVERT: I 206 ILE cc_start: 0.8802 (mt) cc_final: 0.8409 (mp) REVERT: J 93 MET cc_start: 0.4329 (tpt) cc_final: 0.4114 (tpp) REVERT: J 147 MET cc_start: 0.8153 (mmt) cc_final: 0.7856 (mmt) REVERT: J 190 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7262 (t80) REVERT: J 276 MET cc_start: 0.1707 (mmp) cc_final: 0.0861 (mmp) REVERT: J 497 ASN cc_start: 0.8757 (m110) cc_final: 0.8474 (m-40) REVERT: J 540 TRP cc_start: 0.8996 (t60) cc_final: 0.8768 (t60) REVERT: M 50 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7916 (mp0) REVERT: M 67 PHE cc_start: 0.8697 (t80) cc_final: 0.8261 (t80) REVERT: M 107 THR cc_start: 0.8506 (m) cc_final: 0.8072 (t) REVERT: M 123 ASP cc_start: 0.7331 (m-30) cc_final: 0.6842 (t0) REVERT: N 44 LYS cc_start: 0.8146 (tptp) cc_final: 0.7911 (tptp) REVERT: Q 105 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8447 (mt-10) REVERT: Q 115 LYS cc_start: 0.7766 (tppt) cc_final: 0.6878 (tttt) REVERT: Q 134 ARG cc_start: 0.6495 (ttm170) cc_final: 0.6030 (ttm-80) REVERT: R 52 GLU cc_start: 0.8030 (pm20) cc_final: 0.7679 (pm20) REVERT: R 63 GLU cc_start: 0.8355 (pt0) cc_final: 0.8046 (pt0) REVERT: R 75 HIS cc_start: 0.7642 (t70) cc_final: 0.7140 (t70) REVERT: R 88 TYR cc_start: 0.7951 (m-80) cc_final: 0.7702 (m-80) REVERT: S 87 ILE cc_start: 0.8964 (mt) cc_final: 0.8731 (mt) REVERT: S 92 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5884 (tp30) REVERT: T 76 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7916 (pt0) REVERT: T 92 ARG cc_start: 0.7181 (ptm160) cc_final: 0.6731 (mtp180) REVERT: T 93 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6382 (mt-10) REVERT: T 113 GLU cc_start: 0.7926 (tp30) cc_final: 0.7498 (tp30) outliers start: 146 outliers final: 97 residues processed: 634 average time/residue: 0.2536 time to fit residues: 262.6531 Evaluate side-chains 571 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 466 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 677 LEU Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 809 VAL Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 958 SER Chi-restraints excluded: chain G residue 967 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1109 LEU Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1196 SER Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 190 TYR Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 485 GLU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 20.0000 chunk 425 optimal weight: 5.9990 chunk 400 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 347 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 446 optimal weight: 6.9990 chunk 339 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 247 ASN B 348 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 ASN I 157 GLN J 207 ASN Q 93 GLN R 25 ASN R 64 ASN S 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.123060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082831 restraints weight = 94888.909| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.99 r_work: 0.3175 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41156 Z= 0.165 Angle : 0.673 12.582 56544 Z= 0.353 Chirality : 0.044 0.195 6419 Planarity : 0.004 0.057 6443 Dihedral : 21.100 178.592 7475 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.04 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 15.34 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4415 helix: 0.17 (0.12), residues: 1977 sheet: -0.39 (0.19), residues: 681 loop : -0.56 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 208 TYR 0.031 0.001 TYR R 72 PHE 0.034 0.002 PHE I 164 TRP 0.044 0.002 TRP G 599 HIS 0.011 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00377 (41156) covalent geometry : angle 0.67321 (56544) hydrogen bonds : bond 0.04332 ( 1696) hydrogen bonds : angle 4.51177 ( 4619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 501 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8620 (mppt) cc_final: 0.8208 (mptt) REVERT: A 244 ASP cc_start: 0.8564 (m-30) cc_final: 0.8106 (m-30) REVERT: C 105 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8455 (mt-10) REVERT: C 137 GLU cc_start: 0.8370 (pm20) cc_final: 0.8056 (pm20) REVERT: C 181 GLN cc_start: 0.8532 (pt0) cc_final: 0.8002 (tm-30) REVERT: C 260 MET cc_start: 0.8539 (ttm) cc_final: 0.8170 (tpt) REVERT: C 317 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7686 (tmm-80) REVERT: C 363 THR cc_start: 0.9411 (m) cc_final: 0.9198 (p) REVERT: C 364 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8127 (mmm) REVERT: D 147 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8321 (pt) REVERT: E 46 MET cc_start: 0.7485 (mtp) cc_final: 0.7241 (mtp) REVERT: E 88 MET cc_start: 0.8784 (mmp) cc_final: 0.8313 (mmm) REVERT: E 303 MET cc_start: 0.9043 (mmp) cc_final: 0.8720 (mmm) REVERT: F 88 MET cc_start: 0.8237 (mmp) cc_final: 0.7901 (mmm) REVERT: F 227 CYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8675 (m) REVERT: G 523 LEU cc_start: 0.7950 (mm) cc_final: 0.7368 (tp) REVERT: G 582 TRP cc_start: 0.8087 (m100) cc_final: 0.7885 (m100) REVERT: G 593 PHE cc_start: 0.7408 (m-80) cc_final: 0.6899 (m-80) REVERT: G 641 PHE cc_start: 0.8158 (m-80) cc_final: 0.7488 (m-80) REVERT: G 658 LYS cc_start: 0.7405 (pttm) cc_final: 0.7023 (pttm) REVERT: G 675 ASN cc_start: 0.6080 (t0) cc_final: 0.5620 (t0) REVERT: G 691 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8237 (mm) REVERT: G 880 LYS cc_start: 0.8499 (mttt) cc_final: 0.8225 (mmtt) REVERT: G 967 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8102 (tt) REVERT: G 991 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6831 (mmp80) REVERT: G 1123 TYR cc_start: 0.8494 (m-80) cc_final: 0.8111 (m-80) REVERT: H 272 MET cc_start: 0.8832 (mmt) cc_final: 0.8097 (mmm) REVERT: I 151 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7592 (mp0) REVERT: I 206 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8686 (mp) REVERT: J 101 ASN cc_start: 0.7822 (p0) cc_final: 0.7479 (p0) REVERT: J 263 TRP cc_start: 0.8818 (m100) cc_final: 0.8555 (m100) REVERT: J 276 MET cc_start: 0.1934 (mmp) cc_final: 0.1389 (mmp) REVERT: J 481 LYS cc_start: 0.8674 (pptt) cc_final: 0.8188 (tptp) REVERT: J 497 ASN cc_start: 0.8770 (m110) cc_final: 0.8430 (m-40) REVERT: J 540 TRP cc_start: 0.9002 (t60) cc_final: 0.8769 (t60) REVERT: M 50 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7880 (mp0) REVERT: M 67 PHE cc_start: 0.8759 (t80) cc_final: 0.8322 (t80) REVERT: M 78 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5075 (t80) REVERT: M 79 LYS cc_start: 0.7154 (mtpt) cc_final: 0.6917 (mtpt) REVERT: M 107 THR cc_start: 0.8560 (m) cc_final: 0.8127 (p) REVERT: M 123 ASP cc_start: 0.7230 (m-30) cc_final: 0.6528 (t70) REVERT: N 88 TYR cc_start: 0.7332 (m-10) cc_final: 0.7019 (m-80) REVERT: Q 115 LYS cc_start: 0.7768 (tppt) cc_final: 0.6914 (tttt) REVERT: Q 134 ARG cc_start: 0.6504 (ttm170) cc_final: 0.5831 (ttm110) REVERT: R 52 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: R 72 TYR cc_start: 0.8012 (m-80) cc_final: 0.7755 (m-80) REVERT: R 75 HIS cc_start: 0.7682 (t70) cc_final: 0.7104 (t70) REVERT: R 88 TYR cc_start: 0.7952 (m-80) cc_final: 0.7629 (m-80) REVERT: S 101 THR cc_start: 0.7736 (m) cc_final: 0.7389 (p) REVERT: T 76 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7836 (pt0) REVERT: T 92 ARG cc_start: 0.7141 (ptm160) cc_final: 0.6695 (mtp180) REVERT: T 93 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6345 (mt-10) REVERT: T 113 GLU cc_start: 0.8098 (tp30) cc_final: 0.7621 (tp30) outliers start: 132 outliers final: 85 residues processed: 599 average time/residue: 0.2549 time to fit residues: 249.5937 Evaluate side-chains 554 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 459 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 809 VAL Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 967 LEU Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 991 ARG Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain G residue 1236 GLN Chi-restraints excluded: chain G residue 1249 ILE Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 87 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 391 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN G 583 HIS ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 878 HIS R 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.120968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080136 restraints weight = 95108.092| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.71 r_work: 0.3139 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 41156 Z= 0.250 Angle : 0.723 12.454 56544 Z= 0.374 Chirality : 0.045 0.197 6419 Planarity : 0.005 0.056 6443 Dihedral : 21.144 178.407 7475 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.71 % Favored : 96.15 % Rotamer: Outliers : 4.38 % Allowed : 15.63 % Favored : 79.99 % 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 are not related in a simple way. whole: -0.52 (0.12), residues: 4415 helix: 0.16 (0.12), residues: 1997 sheet: -0.54 (0.19), residues: 679 loop : -0.69 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 734 TYR 0.024 0.002 TYR R 72 PHE 0.027 0.002 PHE N 61 TRP 0.022 0.002 TRP G 646 HIS 0.018 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00577 (41156) covalent geometry : angle 0.72283 (56544) hydrogen bonds : bond 0.04695 ( 1696) hydrogen bonds : angle 4.63948 ( 4619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 483 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8673 (mppt) cc_final: 0.8265 (mptt) REVERT: A 244 ASP cc_start: 0.8584 (m-30) cc_final: 0.8175 (m-30) REVERT: B 54 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: C 105 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8352 (mt-10) REVERT: C 137 GLU cc_start: 0.8483 (pm20) cc_final: 0.8165 (pm20) REVERT: C 181 GLN cc_start: 0.8494 (pt0) cc_final: 0.8046 (tm-30) REVERT: C 260 MET cc_start: 0.8629 (ttm) cc_final: 0.8246 (tpt) REVERT: C 317 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7532 (tmm-80) REVERT: C 359 MET cc_start: 0.8605 (mtp) cc_final: 0.8405 (mtm) REVERT: C 364 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8207 (mmm) REVERT: D 147 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8356 (pt) REVERT: D 207 ARG cc_start: 0.6823 (mmm160) cc_final: 0.6399 (mmm160) REVERT: E 46 MET cc_start: 0.7501 (mtp) cc_final: 0.7278 (mtp) REVERT: E 88 MET cc_start: 0.8851 (mmp) cc_final: 0.8386 (mmm) REVERT: E 161 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8906 (tp) REVERT: E 303 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8719 (mmm) REVERT: F 227 CYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8655 (m) REVERT: G 523 LEU cc_start: 0.7942 (mm) cc_final: 0.7341 (tp) REVERT: G 593 PHE cc_start: 0.7384 (m-80) cc_final: 0.6815 (m-80) REVERT: G 641 PHE cc_start: 0.8214 (m-80) cc_final: 0.7598 (m-80) REVERT: G 658 LYS cc_start: 0.7446 (pttm) cc_final: 0.6931 (pttm) REVERT: G 675 ASN cc_start: 0.6404 (t0) cc_final: 0.5994 (t0) REVERT: G 684 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7268 (tp) REVERT: G 880 LYS cc_start: 0.8539 (mttt) cc_final: 0.8239 (mmtt) REVERT: G 967 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8150 (tt) REVERT: G 1123 TYR cc_start: 0.8529 (m-80) cc_final: 0.8118 (m-80) REVERT: H 272 MET cc_start: 0.8881 (mmt) cc_final: 0.8204 (mmm) REVERT: I 206 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8680 (mp) REVERT: J 93 MET cc_start: 0.4221 (tpt) cc_final: 0.3938 (tpp) REVERT: J 497 ASN cc_start: 0.8759 (m110) cc_final: 0.8437 (m-40) REVERT: J 540 TRP cc_start: 0.9009 (t60) cc_final: 0.8761 (t60) REVERT: M 50 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7909 (mp0) REVERT: M 67 PHE cc_start: 0.8605 (t80) cc_final: 0.8040 (t80) REVERT: N 62 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7958 (pp) REVERT: Q 115 LYS cc_start: 0.7827 (tppt) cc_final: 0.6883 (tttt) REVERT: Q 134 ARG cc_start: 0.6561 (ttm170) cc_final: 0.6080 (ttm-80) REVERT: R 36 ARG cc_start: 0.9000 (mtt180) cc_final: 0.8784 (mtt180) REVERT: R 39 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7108 (mmt90) REVERT: R 52 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: R 75 HIS cc_start: 0.7717 (t70) cc_final: 0.7128 (t70) REVERT: R 88 TYR cc_start: 0.7972 (m-80) cc_final: 0.7657 (m-80) REVERT: S 101 THR cc_start: 0.7599 (m) cc_final: 0.7385 (p) REVERT: T 76 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7668 (pt0) REVERT: T 92 ARG cc_start: 0.7139 (ptm160) cc_final: 0.6693 (mtp180) REVERT: T 93 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6382 (mt-10) REVERT: T 113 GLU cc_start: 0.7997 (tp30) cc_final: 0.7565 (tp30) outliers start: 167 outliers final: 112 residues processed: 606 average time/residue: 0.2471 time to fit residues: 246.3728 Evaluate side-chains 577 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 451 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 646 TRP Chi-restraints excluded: chain G residue 677 LEU Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 967 LEU Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1196 SER Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain H residue 283 THR Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 414 optimal weight: 7.9990 chunk 447 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 370 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 349 optimal weight: 0.7980 chunk 413 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.122724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.082516 restraints weight = 95424.974| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.68 r_work: 0.3155 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41156 Z= 0.158 Angle : 0.659 11.494 56544 Z= 0.343 Chirality : 0.043 0.242 6419 Planarity : 0.004 0.047 6443 Dihedral : 21.111 178.899 7475 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.63 % Rotamer: Outliers : 3.88 % Allowed : 16.83 % Favored : 79.29 % 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 are not related in a simple way. whole: -0.36 (0.13), residues: 4415 helix: 0.33 (0.12), residues: 2000 sheet: -0.48 (0.19), residues: 674 loop : -0.65 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 208 TYR 0.031 0.001 TYR N 72 PHE 0.026 0.001 PHE T 65 TRP 0.024 0.002 TRP G 646 HIS 0.010 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00360 (41156) covalent geometry : angle 0.65910 (56544) hydrogen bonds : bond 0.04119 ( 1696) hydrogen bonds : angle 4.42558 ( 4619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 496 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8665 (mppt) cc_final: 0.8234 (mptt) REVERT: B 54 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: C 105 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8387 (mt-10) REVERT: C 137 GLU cc_start: 0.8394 (pm20) cc_final: 0.8070 (pm20) REVERT: C 181 GLN cc_start: 0.8474 (pt0) cc_final: 0.8088 (tm-30) REVERT: C 260 MET cc_start: 0.8502 (ttm) cc_final: 0.8172 (tpt) REVERT: C 317 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7628 (tmm-80) REVERT: D 147 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8751 (mm) REVERT: E 46 MET cc_start: 0.7518 (mtp) cc_final: 0.7214 (mtp) REVERT: E 88 MET cc_start: 0.8782 (mmp) cc_final: 0.8290 (mmm) REVERT: E 124 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8029 (mtp85) REVERT: E 161 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8868 (tp) REVERT: E 191 ASP cc_start: 0.7451 (m-30) cc_final: 0.6719 (m-30) REVERT: E 303 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8736 (mmm) REVERT: E 401 TYR cc_start: 0.8046 (t80) cc_final: 0.7805 (t80) REVERT: F 88 MET cc_start: 0.8212 (mmp) cc_final: 0.7889 (mmm) REVERT: F 227 CYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8681 (m) REVERT: G 523 LEU cc_start: 0.7897 (mm) cc_final: 0.7318 (tp) REVERT: G 593 PHE cc_start: 0.7425 (m-80) cc_final: 0.6856 (m-80) REVERT: G 641 PHE cc_start: 0.8283 (m-80) cc_final: 0.7697 (m-80) REVERT: G 658 LYS cc_start: 0.7374 (pttm) cc_final: 0.6835 (pttm) REVERT: G 684 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7229 (tp) REVERT: G 880 LYS cc_start: 0.8553 (mttt) cc_final: 0.8216 (mmtt) REVERT: G 967 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8145 (tt) REVERT: G 1123 TYR cc_start: 0.8455 (m-80) cc_final: 0.8002 (m-80) REVERT: G 1236 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8300 (pp30) REVERT: H 272 MET cc_start: 0.8859 (mmt) cc_final: 0.8140 (mmm) REVERT: I 139 ARG cc_start: 0.4010 (mtt180) cc_final: 0.3282 (tpm170) REVERT: I 206 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8646 (mp) REVERT: J 93 MET cc_start: 0.4358 (tpt) cc_final: 0.4087 (tpp) REVERT: J 243 GLU cc_start: 0.8424 (tp30) cc_final: 0.8216 (pp20) REVERT: J 263 TRP cc_start: 0.8822 (m100) cc_final: 0.8612 (m100) REVERT: J 276 MET cc_start: 0.1745 (mmp) cc_final: 0.1268 (mmp) REVERT: J 481 LYS cc_start: 0.8650 (pptt) cc_final: 0.8152 (tptp) REVERT: J 540 TRP cc_start: 0.8990 (t60) cc_final: 0.8568 (t60) REVERT: M 50 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7956 (mp0) REVERT: M 67 PHE cc_start: 0.8498 (t80) cc_final: 0.8230 (t80) REVERT: M 116 ARG cc_start: 0.5694 (OUTLIER) cc_final: 0.3535 (ttp-110) REVERT: N 58 LEU cc_start: 0.8439 (tt) cc_final: 0.8068 (mp) REVERT: N 88 TYR cc_start: 0.7043 (m-10) cc_final: 0.6609 (m-80) REVERT: Q 62 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6394 (mt) REVERT: Q 105 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8237 (tp30) REVERT: Q 134 ARG cc_start: 0.6504 (ttm170) cc_final: 0.6041 (ttm-80) REVERT: R 36 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8573 (mtt180) REVERT: R 39 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7089 (mmt90) REVERT: R 52 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: R 75 HIS cc_start: 0.7709 (t70) cc_final: 0.7175 (t70) REVERT: R 88 TYR cc_start: 0.7947 (m-80) cc_final: 0.7674 (m-80) REVERT: S 101 THR cc_start: 0.7744 (m) cc_final: 0.7522 (p) REVERT: T 76 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7517 (pt0) REVERT: T 92 ARG cc_start: 0.7105 (ptm160) cc_final: 0.6587 (mmm160) REVERT: T 93 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6433 (mt-10) REVERT: T 113 GLU cc_start: 0.7976 (tp30) cc_final: 0.7557 (tp30) outliers start: 148 outliers final: 97 residues processed: 602 average time/residue: 0.2566 time to fit residues: 252.3840 Evaluate side-chains 577 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 465 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 677 LEU Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 967 LEU Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1181 LEU Chi-restraints excluded: chain G residue 1196 SER Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain G residue 1236 GLN Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 527 SER Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 393 optimal weight: 30.0000 chunk 200 optimal weight: 0.4980 chunk 419 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 304 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 343 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 334 optimal weight: 0.0370 overall best weight: 1.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083137 restraints weight = 94536.631| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.72 r_work: 0.3173 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41156 Z= 0.145 Angle : 0.654 18.047 56544 Z= 0.336 Chirality : 0.042 0.243 6419 Planarity : 0.004 0.048 6443 Dihedral : 21.073 179.115 7475 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.22 % Favored : 96.65 % Rotamer: Outliers : 3.43 % Allowed : 17.75 % Favored : 78.81 % 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 are not related in a simple way. whole: -0.17 (0.13), residues: 4415 helix: 0.53 (0.12), residues: 1975 sheet: -0.42 (0.19), residues: 671 loop : -0.58 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG M 116 TYR 0.030 0.001 TYR N 72 PHE 0.026 0.001 PHE T 65 TRP 0.017 0.001 TRP G 612 HIS 0.013 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00331 (41156) covalent geometry : angle 0.65394 (56544) hydrogen bonds : bond 0.03938 ( 1696) hydrogen bonds : angle 4.30804 ( 4619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 514 time to evaluate : 1.513 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 90 LYS cc_start: 0.8693 (mppt) cc_final: 0.8244 (mptt) REVERT: A 343 ASP cc_start: 0.8032 (p0) cc_final: 0.7806 (p0) REVERT: A 353 ASP cc_start: 0.7681 (m-30) cc_final: 0.7384 (p0) REVERT: B 54 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: C 105 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: C 137 GLU cc_start: 0.8387 (pm20) cc_final: 0.8035 (pm20) REVERT: C 165 LYS cc_start: 0.9085 (tttp) cc_final: 0.8730 (mptt) REVERT: C 181 GLN cc_start: 0.8409 (pt0) cc_final: 0.8129 (tm-30) REVERT: C 260 MET cc_start: 0.8491 (ttm) cc_final: 0.8145 (tpt) REVERT: C 317 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7630 (tmm-80) REVERT: E 46 MET cc_start: 0.7476 (mtp) cc_final: 0.7119 (mtp) REVERT: E 88 MET cc_start: 0.8784 (mmp) cc_final: 0.8246 (mmm) REVERT: E 124 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8018 (mtp85) REVERT: E 191 ASP cc_start: 0.7493 (m-30) cc_final: 0.6762 (m-30) REVERT: E 303 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8743 (mmm) REVERT: E 326 MET cc_start: 0.8600 (mmt) cc_final: 0.8337 (mmt) REVERT: F 88 MET cc_start: 0.8246 (mmp) cc_final: 0.7879 (mmm) REVERT: F 133 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: F 227 CYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8687 (m) REVERT: G 523 LEU cc_start: 0.7796 (mm) cc_final: 0.7226 (tp) REVERT: G 593 PHE cc_start: 0.7445 (m-80) cc_final: 0.6898 (m-80) REVERT: G 641 PHE cc_start: 0.8250 (m-80) cc_final: 0.7659 (m-80) REVERT: G 658 LYS cc_start: 0.7361 (pttm) cc_final: 0.6804 (pttm) REVERT: G 684 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7221 (tp) REVERT: G 880 LYS cc_start: 0.8558 (mttt) cc_final: 0.8208 (mmtt) REVERT: G 901 MET cc_start: 0.8823 (tpp) cc_final: 0.8404 (tpp) REVERT: G 967 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8138 (tt) REVERT: G 1123 TYR cc_start: 0.8433 (m-80) cc_final: 0.7945 (m-80) REVERT: H 272 MET cc_start: 0.8875 (mmt) cc_final: 0.8191 (mmm) REVERT: I 139 ARG cc_start: 0.3924 (mtt180) cc_final: 0.3321 (tpm170) REVERT: I 206 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8750 (mp) REVERT: J 65 CYS cc_start: 0.4678 (OUTLIER) cc_final: 0.4075 (m) REVERT: J 93 MET cc_start: 0.4436 (tpt) cc_final: 0.4180 (tpp) REVERT: J 276 MET cc_start: 0.1679 (mmp) cc_final: 0.1277 (mmp) REVERT: J 464 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8370 (pp20) REVERT: J 481 LYS cc_start: 0.8655 (pptt) cc_final: 0.8147 (tptm) REVERT: J 540 TRP cc_start: 0.8991 (t60) cc_final: 0.8572 (t60) REVERT: M 50 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7956 (mp0) REVERT: N 39 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.8282 (tpp-160) REVERT: N 55 ARG cc_start: 0.6002 (mtt180) cc_final: 0.5756 (mtt-85) REVERT: N 58 LEU cc_start: 0.8455 (tt) cc_final: 0.8055 (mp) REVERT: N 88 TYR cc_start: 0.7225 (m-10) cc_final: 0.6785 (m-80) REVERT: Q 62 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6425 (mt) REVERT: Q 105 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8239 (tp30) REVERT: Q 134 ARG cc_start: 0.6482 (ttm170) cc_final: 0.6016 (ttm-80) REVERT: R 52 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: R 75 HIS cc_start: 0.7785 (t70) cc_final: 0.7180 (t70) REVERT: S 101 THR cc_start: 0.7719 (m) cc_final: 0.7519 (p) REVERT: T 76 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7503 (pt0) REVERT: T 92 ARG cc_start: 0.7071 (ptm160) cc_final: 0.6595 (mmm160) REVERT: T 93 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6470 (mt-10) REVERT: T 113 GLU cc_start: 0.7934 (tp30) cc_final: 0.7393 (tp30) outliers start: 131 outliers final: 95 residues processed: 610 average time/residue: 0.2428 time to fit residues: 241.8202 Evaluate side-chains 587 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 479 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 677 LEU Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 967 LEU Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1181 LEU Chi-restraints excluded: chain G residue 1196 SER Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain H residue 283 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 454 ILE Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 514 MET Chi-restraints excluded: chain J residue 527 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 349 optimal weight: 4.9990 chunk 439 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 411 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 360 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN B 181 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS R 25 ASN T 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.122356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081876 restraints weight = 95180.964| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.72 r_work: 0.3169 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41156 Z= 0.189 Angle : 0.669 15.112 56544 Z= 0.344 Chirality : 0.043 0.226 6419 Planarity : 0.004 0.062 6443 Dihedral : 21.133 179.720 7475 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 3.64 % Allowed : 18.12 % Favored : 78.24 % 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 are not related in a simple way. whole: -0.23 (0.13), residues: 4415 helix: 0.48 (0.12), residues: 1987 sheet: -0.47 (0.19), residues: 672 loop : -0.60 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 208 TYR 0.040 0.002 TYR N 72 PHE 0.027 0.001 PHE T 65 TRP 0.021 0.001 TRP G 582 HIS 0.011 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00436 (41156) covalent geometry : angle 0.66885 (56544) hydrogen bonds : bond 0.04140 ( 1696) hydrogen bonds : angle 4.37056 ( 4619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 474 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8711 (mppt) cc_final: 0.8297 (mptt) REVERT: A 353 ASP cc_start: 0.7755 (m-30) cc_final: 0.7518 (p0) REVERT: B 54 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: C 105 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: C 137 GLU cc_start: 0.8415 (pm20) cc_final: 0.8105 (pm20) REVERT: C 181 GLN cc_start: 0.8418 (pt0) cc_final: 0.8173 (tm-30) REVERT: C 260 MET cc_start: 0.8459 (ttm) cc_final: 0.8247 (tpt) REVERT: C 317 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7584 (tmm-80) REVERT: E 46 MET cc_start: 0.7467 (mtp) cc_final: 0.7163 (mtp) REVERT: E 88 MET cc_start: 0.8779 (mmp) cc_final: 0.8295 (mmm) REVERT: E 124 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8062 (mtp85) REVERT: E 191 ASP cc_start: 0.7513 (m-30) cc_final: 0.6776 (m-30) REVERT: E 303 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8760 (mmm) REVERT: E 401 TYR cc_start: 0.8104 (t80) cc_final: 0.7896 (t80) REVERT: F 227 CYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8650 (m) REVERT: G 523 LEU cc_start: 0.7803 (mm) cc_final: 0.7249 (tp) REVERT: G 582 TRP cc_start: 0.7972 (m100) cc_final: 0.7685 (m100) REVERT: G 593 PHE cc_start: 0.7460 (m-80) cc_final: 0.6855 (m-80) REVERT: G 641 PHE cc_start: 0.8242 (m-80) cc_final: 0.7707 (m-80) REVERT: G 658 LYS cc_start: 0.7403 (pttm) cc_final: 0.6851 (pttm) REVERT: G 684 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7260 (tp) REVERT: G 880 LYS cc_start: 0.8542 (mttt) cc_final: 0.8241 (mmtt) REVERT: G 976 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.8127 (t-90) REVERT: G 1123 TYR cc_start: 0.8479 (m-80) cc_final: 0.7959 (m-80) REVERT: I 139 ARG cc_start: 0.3921 (mtt180) cc_final: 0.3427 (tpm170) REVERT: I 206 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8713 (mp) REVERT: J 65 CYS cc_start: 0.4702 (OUTLIER) cc_final: 0.4092 (m) REVERT: J 93 MET cc_start: 0.4377 (tpt) cc_final: 0.4129 (tpp) REVERT: J 263 TRP cc_start: 0.8815 (m100) cc_final: 0.8098 (m100) REVERT: J 276 MET cc_start: 0.1774 (mmp) cc_final: 0.1346 (mmp) REVERT: J 481 LYS cc_start: 0.8662 (pptt) cc_final: 0.8165 (tptm) REVERT: J 540 TRP cc_start: 0.9020 (t60) cc_final: 0.8601 (t60) REVERT: M 50 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7906 (mp0) REVERT: M 120 MET cc_start: 0.7325 (mpp) cc_final: 0.6904 (pmm) REVERT: N 39 ARG cc_start: 0.8469 (tpp-160) cc_final: 0.8236 (tpp-160) REVERT: N 55 ARG cc_start: 0.6010 (mtt180) cc_final: 0.5753 (mtt-85) REVERT: N 58 LEU cc_start: 0.8462 (tt) cc_final: 0.8018 (mp) REVERT: N 88 TYR cc_start: 0.7388 (m-10) cc_final: 0.6965 (m-80) REVERT: Q 62 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6465 (mt) REVERT: Q 134 ARG cc_start: 0.6445 (ttm170) cc_final: 0.5973 (ttm-80) REVERT: R 52 GLU cc_start: 0.7887 (pm20) cc_final: 0.7605 (pm20) REVERT: R 75 HIS cc_start: 0.7732 (t70) cc_final: 0.7122 (t70) REVERT: T 76 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7493 (pt0) REVERT: T 92 ARG cc_start: 0.7076 (ptm160) cc_final: 0.6594 (mmm160) REVERT: T 93 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6496 (mt-10) REVERT: T 113 GLU cc_start: 0.7989 (tp30) cc_final: 0.7515 (tp30) outliers start: 139 outliers final: 106 residues processed: 576 average time/residue: 0.2483 time to fit residues: 235.0262 Evaluate side-chains 576 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 460 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 206 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 454 ILE Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 514 MET Chi-restraints excluded: chain J residue 527 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 421 optimal weight: 30.0000 chunk 427 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 372 optimal weight: 9.9990 chunk 395 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 chunk 435 optimal weight: 6.9990 chunk 448 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN T 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079578 restraints weight = 95314.591| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.68 r_work: 0.3131 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 41156 Z= 0.259 Angle : 0.733 14.769 56544 Z= 0.374 Chirality : 0.045 0.215 6419 Planarity : 0.004 0.057 6443 Dihedral : 21.271 179.943 7475 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.65 % Rotamer: Outliers : 3.75 % Allowed : 18.41 % Favored : 77.84 % 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 are not related in a simple way. whole: -0.50 (0.12), residues: 4415 helix: 0.29 (0.12), residues: 1993 sheet: -0.65 (0.19), residues: 678 loop : -0.78 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 208 TYR 0.036 0.002 TYR N 72 PHE 0.027 0.002 PHE T 65 TRP 0.018 0.002 TRP G 582 HIS 0.009 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00600 (41156) covalent geometry : angle 0.73256 (56544) hydrogen bonds : bond 0.04569 ( 1696) hydrogen bonds : angle 4.57862 ( 4619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 476 time to evaluate : 1.421 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 90 LYS cc_start: 0.8735 (mppt) cc_final: 0.8350 (mptt) REVERT: A 244 ASP cc_start: 0.8585 (m-30) cc_final: 0.8045 (m-30) REVERT: B 54 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: B 105 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: B 113 MET cc_start: 0.8844 (mmm) cc_final: 0.8460 (tpt) REVERT: B 212 GLU cc_start: 0.8169 (pt0) cc_final: 0.7929 (pt0) REVERT: C 105 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8321 (mt-10) REVERT: C 137 GLU cc_start: 0.8468 (pm20) cc_final: 0.8137 (pm20) REVERT: C 181 GLN cc_start: 0.8446 (pt0) cc_final: 0.8196 (tm-30) REVERT: C 260 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8284 (tpt) REVERT: C 317 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7556 (tmm-80) REVERT: D 355 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8703 (mm) REVERT: E 46 MET cc_start: 0.7464 (mtp) cc_final: 0.7215 (mtp) REVERT: E 88 MET cc_start: 0.8846 (mmp) cc_final: 0.8393 (mmm) REVERT: E 191 ASP cc_start: 0.7545 (m-30) cc_final: 0.6753 (m-30) REVERT: E 303 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8757 (mmm) REVERT: F 88 MET cc_start: 0.8259 (mmp) cc_final: 0.7890 (mmm) REVERT: F 162 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7912 (p) REVERT: F 227 CYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8638 (m) REVERT: G 523 LEU cc_start: 0.7857 (mm) cc_final: 0.7318 (tp) REVERT: G 563 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7106 (mtp180) REVERT: G 593 PHE cc_start: 0.7432 (m-80) cc_final: 0.6837 (m-80) REVERT: G 641 PHE cc_start: 0.8272 (m-80) cc_final: 0.8017 (m-80) REVERT: G 658 LYS cc_start: 0.7418 (pttm) cc_final: 0.6880 (pttm) REVERT: G 684 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7235 (tp) REVERT: G 699 MET cc_start: 0.3874 (ttm) cc_final: 0.3672 (ttm) REVERT: G 745 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5199 (ttt180) REVERT: G 880 LYS cc_start: 0.8595 (mttt) cc_final: 0.8276 (mmtt) REVERT: G 976 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8244 (t-90) REVERT: G 1123 TYR cc_start: 0.8454 (m-80) cc_final: 0.7905 (m-80) REVERT: H 272 MET cc_start: 0.8877 (mmm) cc_final: 0.8449 (mmm) REVERT: I 139 ARG cc_start: 0.4008 (mtt180) cc_final: 0.3583 (tpm170) REVERT: I 151 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7506 (mt-10) REVERT: J 65 CYS cc_start: 0.4904 (OUTLIER) cc_final: 0.4334 (m) REVERT: J 93 MET cc_start: 0.4423 (tpt) cc_final: 0.4166 (tpp) REVERT: J 263 TRP cc_start: 0.8869 (m100) cc_final: 0.8167 (m100) REVERT: J 276 MET cc_start: 0.1869 (mmp) cc_final: 0.1214 (mmp) REVERT: J 464 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8330 (pp20) REVERT: J 540 TRP cc_start: 0.9044 (t60) cc_final: 0.8666 (t60) REVERT: M 50 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7866 (mp0) REVERT: M 67 PHE cc_start: 0.8266 (t80) cc_final: 0.8061 (t80) REVERT: M 99 TYR cc_start: 0.8068 (t80) cc_final: 0.7850 (t80) REVERT: M 103 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8343 (mm) REVERT: M 120 MET cc_start: 0.7478 (mpp) cc_final: 0.7256 (pmm) REVERT: N 39 ARG cc_start: 0.8446 (tpp-160) cc_final: 0.8196 (tpp-160) REVERT: N 58 LEU cc_start: 0.8459 (tt) cc_final: 0.8042 (mp) REVERT: Q 115 LYS cc_start: 0.8036 (tppt) cc_final: 0.7105 (tttt) REVERT: Q 134 ARG cc_start: 0.6475 (ttm170) cc_final: 0.6012 (ttm-80) REVERT: R 52 GLU cc_start: 0.7836 (pm20) cc_final: 0.7589 (pm20) REVERT: R 63 GLU cc_start: 0.7882 (pt0) cc_final: 0.7642 (pm20) REVERT: R 75 HIS cc_start: 0.7716 (t70) cc_final: 0.7226 (t70) REVERT: S 25 PHE cc_start: 0.7429 (m-80) cc_final: 0.7123 (m-80) REVERT: T 113 GLU cc_start: 0.7967 (tp30) cc_final: 0.7455 (tp30) outliers start: 143 outliers final: 105 residues processed: 580 average time/residue: 0.2380 time to fit residues: 228.4167 Evaluate side-chains 578 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 458 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 206 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 745 ARG Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain J residue 514 MET Chi-restraints excluded: chain J residue 527 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 315 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 234 optimal weight: 0.0470 chunk 450 optimal weight: 9.9990 chunk 331 optimal weight: 1.9990 chunk 382 optimal weight: 0.0970 chunk 344 optimal weight: 0.7980 chunk 268 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 314 optimal weight: 6.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN E 302 HIS ** F 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 HIS ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN T 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.124183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.083816 restraints weight = 95114.484| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.71 r_work: 0.3185 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41156 Z= 0.133 Angle : 0.678 15.457 56544 Z= 0.344 Chirality : 0.042 0.204 6419 Planarity : 0.004 0.061 6443 Dihedral : 21.193 179.080 7471 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.33 % Favored : 96.53 % Rotamer: Outliers : 2.33 % Allowed : 20.08 % Favored : 77.58 % 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 are not related in a simple way. whole: -0.22 (0.13), residues: 4415 helix: 0.55 (0.12), residues: 1987 sheet: -0.47 (0.19), residues: 661 loop : -0.68 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 208 TYR 0.034 0.001 TYR N 72 PHE 0.027 0.001 PHE T 65 TRP 0.015 0.002 TRP G 612 HIS 0.017 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00298 (41156) covalent geometry : angle 0.67805 (56544) hydrogen bonds : bond 0.03820 ( 1696) hydrogen bonds : angle 4.29745 ( 4619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 511 time to evaluate : 1.633 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 90 LYS cc_start: 0.8770 (mppt) cc_final: 0.8305 (mptt) REVERT: B 54 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: B 212 GLU cc_start: 0.8086 (pt0) cc_final: 0.7844 (pt0) REVERT: B 408 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8545 (mt0) REVERT: C 105 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: C 137 GLU cc_start: 0.8392 (pm20) cc_final: 0.8056 (pm20) REVERT: C 165 LYS cc_start: 0.9091 (tttp) cc_final: 0.8749 (mptt) REVERT: C 260 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8186 (tpt) REVERT: C 317 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7677 (tmm-80) REVERT: D 303 MET cc_start: 0.8607 (mmm) cc_final: 0.7889 (mmm) REVERT: E 46 MET cc_start: 0.7518 (mtp) cc_final: 0.7206 (mtp) REVERT: E 88 MET cc_start: 0.8725 (mmp) cc_final: 0.8231 (mmm) REVERT: E 124 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8343 (mtp85) REVERT: E 174 LEU cc_start: 0.9019 (mt) cc_final: 0.8805 (mt) REVERT: E 191 ASP cc_start: 0.7508 (m-30) cc_final: 0.6715 (m-30) REVERT: F 88 MET cc_start: 0.8179 (mmp) cc_final: 0.7861 (mmm) REVERT: F 162 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7653 (p) REVERT: F 300 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8295 (mm-30) REVERT: G 523 LEU cc_start: 0.7769 (mm) cc_final: 0.7196 (tp) REVERT: G 563 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7095 (mtp180) REVERT: G 582 TRP cc_start: 0.7795 (m100) cc_final: 0.7517 (m100) REVERT: G 593 PHE cc_start: 0.7444 (m-80) cc_final: 0.6886 (m-80) REVERT: G 641 PHE cc_start: 0.8255 (m-80) cc_final: 0.7968 (m-80) REVERT: G 658 LYS cc_start: 0.7296 (pttm) cc_final: 0.6670 (pttm) REVERT: G 684 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7251 (tp) REVERT: G 745 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.4169 (ttt180) REVERT: G 759 ILE cc_start: 0.7624 (mp) cc_final: 0.7304 (tp) REVERT: G 880 LYS cc_start: 0.8608 (mttt) cc_final: 0.8251 (mmtt) REVERT: G 901 MET cc_start: 0.8776 (tpp) cc_final: 0.8492 (tpp) REVERT: G 1027 ASN cc_start: 0.8500 (t0) cc_final: 0.7752 (t0) REVERT: G 1123 TYR cc_start: 0.8371 (m-80) cc_final: 0.7810 (m-80) REVERT: H 272 MET cc_start: 0.8909 (mmm) cc_final: 0.8396 (mmm) REVERT: I 139 ARG cc_start: 0.4142 (mtt180) cc_final: 0.3712 (tpm170) REVERT: J 65 CYS cc_start: 0.4560 (OUTLIER) cc_final: 0.4205 (m) REVERT: J 93 MET cc_start: 0.4602 (tpt) cc_final: 0.4361 (tpp) REVERT: J 142 LEU cc_start: 0.8994 (mt) cc_final: 0.8498 (pt) REVERT: J 263 TRP cc_start: 0.8794 (m100) cc_final: 0.8108 (m100) REVERT: J 268 TYR cc_start: 0.9311 (t80) cc_final: 0.9047 (t80) REVERT: J 276 MET cc_start: 0.1802 (mmp) cc_final: 0.1359 (mmp) REVERT: J 481 LYS cc_start: 0.8652 (pptt) cc_final: 0.8175 (tptp) REVERT: J 540 TRP cc_start: 0.9002 (t60) cc_final: 0.8627 (t60) REVERT: M 51 ILE cc_start: 0.7767 (mm) cc_final: 0.7277 (mt) REVERT: N 55 ARG cc_start: 0.6146 (mtt180) cc_final: 0.5883 (mtt-85) REVERT: N 58 LEU cc_start: 0.8465 (tt) cc_final: 0.8093 (mp) REVERT: Q 62 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6343 (mt) REVERT: Q 115 LYS cc_start: 0.8015 (tppt) cc_final: 0.7116 (tttt) REVERT: Q 134 ARG cc_start: 0.6423 (ttm170) cc_final: 0.5947 (ttm-80) REVERT: R 51 TYR cc_start: 0.8431 (t80) cc_final: 0.8171 (t80) REVERT: R 52 GLU cc_start: 0.7754 (pm20) cc_final: 0.7469 (pm20) REVERT: R 84 MET cc_start: 0.6645 (pmm) cc_final: 0.6071 (mmm) REVERT: S 25 PHE cc_start: 0.7464 (m-80) cc_final: 0.7189 (m-80) REVERT: T 76 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7653 (pt0) REVERT: T 113 GLU cc_start: 0.7958 (tp30) cc_final: 0.7492 (tp30) outliers start: 89 outliers final: 65 residues processed: 576 average time/residue: 0.2613 time to fit residues: 244.5731 Evaluate side-chains 540 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 466 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 677 LEU Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 745 ARG Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 436 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 340 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 325 optimal weight: 0.9980 chunk 334 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 429 optimal weight: 8.9990 chunk 272 optimal weight: 30.0000 chunk 304 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS E 344 HIS ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 766 GLN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN T 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078709 restraints weight = 95588.236| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.68 r_work: 0.3089 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 41156 Z= 0.303 Angle : 0.781 14.217 56544 Z= 0.397 Chirality : 0.047 0.239 6419 Planarity : 0.005 0.058 6443 Dihedral : 21.335 179.778 7470 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 2.60 % Allowed : 20.27 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4415 helix: 0.23 (0.12), residues: 1999 sheet: -0.73 (0.19), residues: 675 loop : -0.80 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 208 TYR 0.041 0.002 TYR J 439 PHE 0.076 0.002 PHE M 67 TRP 0.018 0.002 TRP G 582 HIS 0.012 0.001 HIS G 583 Details of bonding type rmsd covalent geometry : bond 0.00703 (41156) covalent geometry : angle 0.78139 (56544) hydrogen bonds : bond 0.04929 ( 1696) hydrogen bonds : angle 4.69465 ( 4619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13258.47 seconds wall clock time: 227 minutes 6.65 seconds (13626.65 seconds total)