Starting phenix.real_space_refine on Fri Mar 6 07:33:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vai_31842/03_2026/7vai_31842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vai_31842/03_2026/7vai_31842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vai_31842/03_2026/7vai_31842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vai_31842/03_2026/7vai_31842.map" model { file = "/net/cci-nas-00/data/ceres_data/7vai_31842/03_2026/7vai_31842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vai_31842/03_2026/7vai_31842.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 18705 2.51 5 N 5116 2.21 5 O 5538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29462 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Time building chain proxies: 6.22, per 1000 atoms: 0.21 Number of scatterers: 29462 At special positions: 0 Unit cell: (147.84, 143.44, 176.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 5538 8.00 N 5116 7.00 C 18705 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: 2.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 28 sheets defined 46.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.560A pdb=" N THR A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.158A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.355A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.991A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.519A pdb=" N TYR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.662A pdb=" N ALA A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.994A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.901A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 531 removed outlier: 3.569A pdb=" N ALA A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.629A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.119A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.667A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.600A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.024A pdb=" N THR B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 5.004A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.578A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.524A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.784A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 472 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 533 removed outlier: 3.648A pdb=" N ALA B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.638A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 550 through 554 removed outlier: 3.508A pdb=" N TYR B 553 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 550 through 554' Processing helix chain 'B' and resid 558 through 576 removed outlier: 3.523A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.505A pdb=" N GLY C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.640A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.256A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 298 through 316 Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.734A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.636A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.006A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.690A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.661A pdb=" N MET D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.726A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.135A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.501A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.980A pdb=" N VAL D 366 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 396 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.581A pdb=" N SER D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 468 through 473 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.632A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.638A pdb=" N ARG E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.679A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.193A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 removed outlier: 3.680A pdb=" N SER E 215 " --> pdb=" O GLY E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 227 through 231 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 259 through 272 removed outlier: 3.670A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.658A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.650A pdb=" N HIS E 344 " --> pdb=" O SER E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.886A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 361 through 366' Processing helix chain 'E' and resid 374 through 399 removed outlier: 3.501A pdb=" N GLY E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.897A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.653A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.550A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.799A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.824A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.747A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 359 through 365 removed outlier: 3.513A pdb=" N MET F 362 " --> pdb=" O SER F 359 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN F 363 " --> pdb=" O ARG F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 4.113A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 removed outlier: 3.581A pdb=" N ARG F 409 " --> pdb=" O THR F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.786A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.740A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 70 removed outlier: 3.896A pdb=" N LEU G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 58 " --> pdb=" O ASP G 54 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 83 Processing helix chain 'G' and resid 122 through 207 removed outlier: 4.040A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE G 130 " --> pdb=" O ALA G 126 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.909A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.535A pdb=" N GLU H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 85 through 98 removed outlier: 3.541A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 105 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 94 removed outlier: 3.925A pdb=" N LEU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 100 through 115 Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.956A pdb=" N ARG J 138 " --> pdb=" O LEU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 186 removed outlier: 5.164A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 4.335A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA K 112 " --> pdb=" O ASP K 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 93 through 97 removed outlier: 3.707A pdb=" N GLN L 96 " --> pdb=" O ALA L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 124 through 132 Proline residue: L 129 - end of helix removed outlier: 3.724A pdb=" N GLU L 132 " --> pdb=" O PRO L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 187 removed outlier: 4.986A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.642A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 6.578A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 35 through 43 removed outlier: 5.928A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.796A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.708A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.805A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.971A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 143 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 143 through 144 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.625A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA9, first strand: chain 'B' and resid 134 through 140 removed outlier: 3.715A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 147 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 204 through 205 removed outlier: 4.748A pdb=" N VAL B 218 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB3, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB4, first strand: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.882A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.763A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.715A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.195A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.565A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.721A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.589A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N GLN E 336 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N LEU E 355 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN E 338 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.726A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.672A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 92 through 94 Processing sheet with id=AC7, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.717A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.667A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 91 through 95 Processing sheet with id=AD1, first strand: chain 'H' and resid 19 through 21 removed outlier: 6.228A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA H 2 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU H 72 " --> pdb=" O VAL H 45 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9622 1.33 - 1.45: 3526 1.45 - 1.57: 16673 1.57 - 1.69: 0 1.69 - 1.80: 194 Bond restraints: 30015 Sorted by residual: bond pdb=" C ILE E 106 " pdb=" N THR E 107 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.44e-02 4.82e+03 5.81e+00 bond pdb=" C GLY B 349 " pdb=" N TYR B 350 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.60e-02 3.91e+03 4.14e+00 bond pdb=" CB GLN B 316 " pdb=" CG GLN B 316 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.08e+00 bond pdb=" CB THR B 285 " pdb=" CG2 THR B 285 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.05e+00 bond pdb=" CB GLN C 316 " pdb=" CG GLN C 316 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.94e+00 ... (remaining 30010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 40022 2.59 - 5.18: 586 5.18 - 7.77: 43 7.77 - 10.36: 6 10.36 - 12.95: 1 Bond angle restraints: 40658 Sorted by residual: angle pdb=" C GLY E 97 " pdb=" N LYS E 98 " pdb=" CA LYS E 98 " ideal model delta sigma weight residual 120.69 107.74 12.95 2.95e+00 1.15e-01 1.93e+01 angle pdb=" N VAL D 76 " pdb=" CA VAL D 76 " pdb=" C VAL D 76 " ideal model delta sigma weight residual 113.53 109.62 3.91 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N VAL E 76 " pdb=" CA VAL E 76 " pdb=" C VAL E 76 " ideal model delta sigma weight residual 111.62 108.59 3.03 7.90e-01 1.60e+00 1.47e+01 angle pdb=" C GLN G 166 " pdb=" N VAL G 167 " pdb=" CA VAL G 167 " ideal model delta sigma weight residual 123.16 119.14 4.02 1.06e+00 8.90e-01 1.44e+01 angle pdb=" C THR D 258 " pdb=" N ASP D 259 " pdb=" CA ASP D 259 " ideal model delta sigma weight residual 122.47 117.36 5.11 1.50e+00 4.44e-01 1.16e+01 ... (remaining 40653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 16481 17.68 - 35.36: 1496 35.36 - 53.04: 251 53.04 - 70.72: 46 70.72 - 88.41: 30 Dihedral angle restraints: 18304 sinusoidal: 7482 harmonic: 10822 Sorted by residual: dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N ASN E 23 " pdb=" CA ASN E 23 " ideal model delta harmonic sigma weight residual -180.00 -138.54 -41.46 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU E 257 " pdb=" C LEU E 257 " pdb=" N THR E 258 " pdb=" CA THR E 258 " ideal model delta harmonic sigma weight residual -180.00 -150.51 -29.49 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2675 0.043 - 0.086: 1367 0.086 - 0.128: 454 0.128 - 0.171: 59 0.171 - 0.214: 5 Chirality restraints: 4560 Sorted by residual: chirality pdb=" CA HIS E 458 " pdb=" N HIS E 458 " pdb=" C HIS E 458 " pdb=" CB HIS E 458 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO C 420 " pdb=" N PRO C 420 " pdb=" C PRO C 420 " pdb=" CB PRO C 420 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4557 not shown) Planarity restraints: 5330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 185 " -0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO E 186 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 186 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 186 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 316 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO F 317 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 317 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 317 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 262 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.56e+00 pdb=" C MET B 262 " -0.037 2.00e-02 2.50e+03 pdb=" O MET B 262 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 263 " 0.012 2.00e-02 2.50e+03 ... (remaining 5327 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 806 2.68 - 3.24: 28944 3.24 - 3.79: 45315 3.79 - 4.35: 60423 4.35 - 4.90: 102986 Nonbonded interactions: 238474 Sorted by model distance: nonbonded pdb=" O ALA I 103 " pdb=" N LEU I 107 " model vdw 2.128 3.120 nonbonded pdb=" OE2 GLU J 110 " pdb=" ND2 ASN J 165 " model vdw 2.137 3.120 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR E 386 " pdb=" OE2 GLU E 419 " model vdw 2.143 3.040 nonbonded pdb=" O ARG C 547 " pdb=" OH TYR C 562 " model vdw 2.147 3.040 ... (remaining 238469 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.520 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 26.030 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 0.011 0.084 30015 Z= 0.479 Angle : 0.822 12.950 40658 Z= 0.461 Chirality : 0.053 0.214 4560 Planarity : 0.005 0.066 5330 Dihedral : 13.981 88.406 11386 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.12), residues: 3764 helix: -1.06 (0.12), residues: 1518 sheet: -1.44 (0.21), residues: 571 loop : -2.06 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 417 TYR 0.028 0.002 TYR F 54 PHE 0.029 0.002 PHE D 60 TRP 0.016 0.002 TRP J 175 HIS 0.008 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.01132 (30015) covalent geometry : angle 0.82172 (40658) hydrogen bonds : bond 0.16258 ( 1247) hydrogen bonds : angle 6.40932 ( 3570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 429 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6803 (tm-30) REVERT: A 154 ARG cc_start: 0.6926 (ptp-110) cc_final: 0.6517 (ptp-110) REVERT: A 156 ARG cc_start: 0.7137 (ttm-80) cc_final: 0.6559 (mtm-85) REVERT: A 481 ARG cc_start: 0.6802 (mtp-110) cc_final: 0.6572 (mtp-110) REVERT: A 491 ARG cc_start: 0.6793 (ttt90) cc_final: 0.6464 (mmt180) REVERT: A 541 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6533 (mt0) REVERT: B 124 LYS cc_start: 0.7297 (ptpp) cc_final: 0.6907 (mttm) REVERT: B 323 MET cc_start: 0.8706 (mtt) cc_final: 0.8480 (mtm) REVERT: B 363 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 408 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7295 (ttm-80) REVERT: B 441 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7530 (tt0) REVERT: B 459 GLN cc_start: 0.8041 (tp40) cc_final: 0.7785 (tp40) REVERT: B 461 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7481 (tt0) REVERT: B 532 ARG cc_start: 0.6464 (ttm110) cc_final: 0.5838 (ttp-110) REVERT: B 548 ILE cc_start: 0.8252 (tt) cc_final: 0.7642 (mt) REVERT: C 93 ARG cc_start: 0.7853 (mmt-90) cc_final: 0.7399 (mmt90) REVERT: C 114 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7211 (mt-10) REVERT: C 130 ARG cc_start: 0.7280 (ptp90) cc_final: 0.6748 (ptt90) REVERT: C 154 ARG cc_start: 0.7021 (mtp-110) cc_final: 0.6672 (mtm-85) REVERT: C 344 MET cc_start: 0.8010 (ttm) cc_final: 0.7609 (ttt) REVERT: C 465 GLN cc_start: 0.6609 (tm-30) cc_final: 0.6233 (tt0) REVERT: C 467 ILE cc_start: 0.7148 (mm) cc_final: 0.6892 (tt) REVERT: C 492 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6890 (mt-10) REVERT: C 500 TYR cc_start: 0.8531 (m-80) cc_final: 0.8331 (m-80) REVERT: C 538 GLU cc_start: 0.6974 (pm20) cc_final: 0.6685 (mp0) REVERT: C 546 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6680 (pt0) REVERT: C 547 ARG cc_start: 0.7521 (tpp-160) cc_final: 0.7161 (tpp-160) REVERT: D 98 LYS cc_start: 0.8274 (mttt) cc_final: 0.7898 (mtmt) REVERT: D 129 GLN cc_start: 0.7863 (mt0) cc_final: 0.7454 (mm-40) REVERT: D 280 ARG cc_start: 0.8015 (ttt-90) cc_final: 0.7733 (ttp80) REVERT: E 232 ILE cc_start: 0.8386 (pt) cc_final: 0.8171 (mt) REVERT: E 353 ASP cc_start: 0.7810 (t0) cc_final: 0.6971 (t0) REVERT: E 420 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.7286 (mtp-110) REVERT: E 450 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6773 (mt-10) REVERT: F 206 GLN cc_start: 0.7558 (mt0) cc_final: 0.7221 (mp10) REVERT: F 373 GLU cc_start: 0.7066 (pm20) cc_final: 0.6697 (pm20) REVERT: F 420 ARG cc_start: 0.7539 (mtm110) cc_final: 0.7327 (mtm110) REVERT: G 13 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7693 (tt0) REVERT: G 53 LEU cc_start: 0.6601 (tp) cc_final: 0.6364 (tp) REVERT: G 132 ARG cc_start: 0.4816 (mtm110) cc_final: 0.4541 (mtm110) REVERT: G 139 ARG cc_start: 0.6600 (mtp-110) cc_final: 0.6295 (mtp180) REVERT: G 185 GLN cc_start: 0.7866 (tp40) cc_final: 0.7409 (tt0) REVERT: H 79 GLU cc_start: 0.4506 (mt-10) cc_final: 0.3874 (mt-10) REVERT: J 78 GLU cc_start: 0.2572 (mm-30) cc_final: 0.2030 (mt-10) REVERT: J 88 ARG cc_start: 0.3079 (mtt180) cc_final: 0.2861 (ttm170) REVERT: J 92 GLU cc_start: 0.3713 (mt-10) cc_final: 0.3467 (mt-10) REVERT: J 148 LEU cc_start: 0.2864 (pt) cc_final: 0.2128 (tp) REVERT: K 93 GLU cc_start: 0.5703 (tp30) cc_final: 0.5107 (mp0) REVERT: L 74 GLN cc_start: 0.6034 (pt0) cc_final: 0.5810 (pt0) REVERT: L 85 ARG cc_start: 0.4696 (tmm160) cc_final: 0.4023 (ttp-170) REVERT: L 160 LYS cc_start: 0.7534 (mtmt) cc_final: 0.6944 (mmtm) outliers start: 4 outliers final: 2 residues processed: 432 average time/residue: 0.2361 time to fit residues: 147.9038 Evaluate side-chains 314 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 312 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain J residue 163 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 283 HIS A 316 GLN B 238 GLN B 316 GLN B 425 ASN B 469 GLN C 290 ASN C 418 HIS D 206 GLN D 222 ASN D 424 ASN E 132 GLN F 23 ASN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN F 448 GLN H 30 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.093456 restraints weight = 43907.385| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.56 r_work: 0.2946 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30015 Z= 0.121 Angle : 0.568 10.274 40658 Z= 0.293 Chirality : 0.044 0.171 4560 Planarity : 0.005 0.047 5330 Dihedral : 4.573 37.710 4182 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.97 % Allowed : 11.55 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 3764 helix: 0.40 (0.13), residues: 1541 sheet: -0.76 (0.23), residues: 511 loop : -1.41 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 106 TYR 0.017 0.001 TYR E 13 PHE 0.015 0.001 PHE D 414 TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00252 (30015) covalent geometry : angle 0.56816 (40658) hydrogen bonds : bond 0.05255 ( 1247) hydrogen bonds : angle 4.88722 ( 3570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 381 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7191 (tm-30) REVERT: A 154 ARG cc_start: 0.7327 (ptp-110) cc_final: 0.6984 (ptp-110) REVERT: A 156 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7313 (mtm-85) REVERT: A 181 LEU cc_start: 0.8677 (mt) cc_final: 0.8414 (mp) REVERT: A 481 ARG cc_start: 0.7404 (mtp-110) cc_final: 0.7075 (mtp85) REVERT: A 491 ARG cc_start: 0.7706 (ttt90) cc_final: 0.7493 (mmt180) REVERT: A 541 GLN cc_start: 0.7517 (mm-40) cc_final: 0.6761 (mt0) REVERT: B 124 LYS cc_start: 0.7682 (ptpp) cc_final: 0.7086 (mttm) REVERT: B 133 MET cc_start: 0.8348 (mtp) cc_final: 0.7812 (mmm) REVERT: B 154 ARG cc_start: 0.7600 (ttt-90) cc_final: 0.7343 (ttt180) REVERT: B 363 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8214 (mm-30) REVERT: B 532 ARG cc_start: 0.6764 (ttm110) cc_final: 0.6226 (ttp80) REVERT: B 550 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7567 (mmm160) REVERT: C 130 ARG cc_start: 0.7655 (ptp90) cc_final: 0.7269 (ptt90) REVERT: C 154 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.7245 (mtm-85) REVERT: C 156 ARG cc_start: 0.8356 (ttm110) cc_final: 0.8132 (ttp-110) REVERT: C 344 MET cc_start: 0.8346 (ttm) cc_final: 0.8144 (ttm) REVERT: C 465 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6656 (tt0) REVERT: C 469 GLN cc_start: 0.7848 (tp40) cc_final: 0.7522 (tt0) REVERT: C 546 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6750 (pt0) REVERT: C 547 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7767 (tpp-160) REVERT: D 22 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8152 (mm-30) REVERT: D 34 ASP cc_start: 0.8397 (p0) cc_final: 0.8193 (p0) REVERT: D 406 GLU cc_start: 0.6613 (tp30) cc_final: 0.6364 (tp30) REVERT: E 259 ASP cc_start: 0.6994 (t0) cc_final: 0.6771 (t0) REVERT: E 334 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: E 420 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.7650 (mtm110) REVERT: F 183 LYS cc_start: 0.7031 (mppt) cc_final: 0.6771 (mtpp) REVERT: F 373 GLU cc_start: 0.7531 (pm20) cc_final: 0.7292 (pm20) REVERT: G 13 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8167 (tt0) REVERT: G 132 ARG cc_start: 0.5591 (mtm110) cc_final: 0.4770 (mtm110) REVERT: G 139 ARG cc_start: 0.6744 (mtp-110) cc_final: 0.6397 (mtp180) REVERT: G 187 GLU cc_start: 0.8429 (tt0) cc_final: 0.8161 (tt0) REVERT: H 34 GLU cc_start: 0.6709 (mm-30) cc_final: 0.5683 (pt0) REVERT: J 78 GLU cc_start: 0.2352 (mm-30) cc_final: 0.1786 (mt-10) REVERT: J 148 LEU cc_start: 0.2910 (pt) cc_final: 0.2011 (tt) REVERT: K 93 GLU cc_start: 0.5898 (tp30) cc_final: 0.5246 (mp0) REVERT: L 74 GLN cc_start: 0.6342 (pt0) cc_final: 0.6040 (pt0) REVERT: L 149 ARG cc_start: 0.5753 (ttp80) cc_final: 0.5478 (ttt-90) REVERT: L 160 LYS cc_start: 0.7654 (mtmt) cc_final: 0.7221 (mmtm) outliers start: 30 outliers final: 19 residues processed: 404 average time/residue: 0.2079 time to fit residues: 127.7527 Evaluate side-chains 337 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 317 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 40 optimal weight: 7.9990 chunk 306 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 541 GLN C 316 GLN D 170 GLN E 222 ASN E 336 GLN F 323 HIS G 175 GLN L 130 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.089329 restraints weight = 44140.237| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.50 r_work: 0.2874 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 30015 Z= 0.239 Angle : 0.652 9.576 40658 Z= 0.337 Chirality : 0.048 0.182 4560 Planarity : 0.006 0.054 5330 Dihedral : 4.891 40.852 4182 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.17 % Allowed : 13.79 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 3764 helix: 0.47 (0.13), residues: 1544 sheet: -0.85 (0.22), residues: 546 loop : -1.20 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 364 TYR 0.015 0.002 TYR D 411 PHE 0.025 0.002 PHE D 60 TRP 0.015 0.002 TRP A 119 HIS 0.005 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00588 (30015) covalent geometry : angle 0.65189 (40658) hydrogen bonds : bond 0.06194 ( 1247) hydrogen bonds : angle 4.87959 ( 3570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 312 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7272 (tm-30) REVERT: A 154 ARG cc_start: 0.7473 (ptp-110) cc_final: 0.6735 (ptm-80) REVERT: A 156 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7462 (mtm-85) REVERT: A 181 LEU cc_start: 0.8665 (mt) cc_final: 0.8363 (mp) REVERT: A 491 ARG cc_start: 0.7695 (ttt90) cc_final: 0.7473 (mmt180) REVERT: A 541 GLN cc_start: 0.7542 (mm-40) cc_final: 0.6771 (mt0) REVERT: B 133 MET cc_start: 0.8494 (mtp) cc_final: 0.8079 (mmm) REVERT: B 154 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.7279 (ttt180) REVERT: B 532 ARG cc_start: 0.6896 (ttm110) cc_final: 0.6300 (ttp80) REVERT: B 550 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7740 (mtp85) REVERT: C 130 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7259 (ptt90) REVERT: C 154 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.7209 (mtm-85) REVERT: C 344 MET cc_start: 0.8346 (ttm) cc_final: 0.8091 (ttt) REVERT: C 465 GLN cc_start: 0.7015 (tm-30) cc_final: 0.6650 (tt0) REVERT: C 546 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6831 (pt0) REVERT: D 388 ASN cc_start: 0.8408 (m-40) cc_final: 0.8013 (t0) REVERT: D 406 GLU cc_start: 0.6851 (tp30) cc_final: 0.6610 (tp30) REVERT: D 413 GLN cc_start: 0.8096 (mp10) cc_final: 0.7821 (mp10) REVERT: E 406 GLU cc_start: 0.6959 (pp20) cc_final: 0.6677 (tp30) REVERT: E 412 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7908 (mp) REVERT: E 420 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7749 (mtm110) REVERT: E 458 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6067 (p-80) REVERT: F 68 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8528 (mp) REVERT: F 183 LYS cc_start: 0.7089 (mppt) cc_final: 0.6874 (mtpp) REVERT: G 13 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8249 (tt0) REVERT: G 132 ARG cc_start: 0.5910 (mtm110) cc_final: 0.5203 (mtm110) REVERT: G 187 GLU cc_start: 0.8423 (tt0) cc_final: 0.8133 (tt0) REVERT: G 190 ASP cc_start: 0.8562 (p0) cc_final: 0.8341 (p0) REVERT: G 207 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.4997 (tm-30) REVERT: H 34 GLU cc_start: 0.6597 (mm-30) cc_final: 0.5698 (pt0) REVERT: H 63 MET cc_start: 0.3936 (OUTLIER) cc_final: 0.3231 (tpt) REVERT: J 78 GLU cc_start: 0.2584 (mm-30) cc_final: 0.2012 (mt-10) REVERT: J 148 LEU cc_start: 0.2993 (pt) cc_final: 0.2127 (tt) REVERT: J 150 LEU cc_start: 0.3788 (OUTLIER) cc_final: 0.3053 (mt) REVERT: K 93 GLU cc_start: 0.6128 (tp30) cc_final: 0.5428 (mp0) REVERT: L 74 GLN cc_start: 0.6518 (pt0) cc_final: 0.6244 (pt0) REVERT: L 149 ARG cc_start: 0.5769 (ttp80) cc_final: 0.5479 (ttt-90) REVERT: L 160 LYS cc_start: 0.7806 (mtmt) cc_final: 0.7395 (mmtm) outliers start: 67 outliers final: 46 residues processed: 365 average time/residue: 0.2005 time to fit residues: 112.6520 Evaluate side-chains 338 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 10 optimal weight: 9.9990 chunk 301 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 338 optimal weight: 0.0570 chunk 17 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.090396 restraints weight = 43661.674| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.55 r_work: 0.2863 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30015 Z= 0.216 Angle : 0.623 10.531 40658 Z= 0.321 Chirality : 0.047 0.183 4560 Planarity : 0.005 0.051 5330 Dihedral : 4.835 40.234 4182 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.85 % Allowed : 14.73 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3764 helix: 0.59 (0.14), residues: 1544 sheet: -0.61 (0.22), residues: 521 loop : -1.14 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 345 TYR 0.013 0.002 TYR D 463 PHE 0.021 0.002 PHE D 60 TRP 0.016 0.002 TRP A 119 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00531 (30015) covalent geometry : angle 0.62304 (40658) hydrogen bonds : bond 0.05814 ( 1247) hydrogen bonds : angle 4.79284 ( 3570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 302 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7210 (tm-30) REVERT: A 154 ARG cc_start: 0.7471 (ptp-110) cc_final: 0.6723 (ptm-80) REVERT: A 156 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7441 (mtm-85) REVERT: A 181 LEU cc_start: 0.8617 (mt) cc_final: 0.8320 (mp) REVERT: A 491 ARG cc_start: 0.7701 (ttt90) cc_final: 0.7495 (mmt180) REVERT: B 133 MET cc_start: 0.8514 (mtp) cc_final: 0.8165 (mmm) REVERT: B 154 ARG cc_start: 0.7617 (ttt-90) cc_final: 0.7274 (ttt180) REVERT: B 532 ARG cc_start: 0.6936 (ttm110) cc_final: 0.6268 (ttp80) REVERT: C 130 ARG cc_start: 0.7728 (ptp90) cc_final: 0.7199 (ptt90) REVERT: C 154 ARG cc_start: 0.7676 (mtp-110) cc_final: 0.7231 (mtm-85) REVERT: C 287 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9017 (mp) REVERT: C 344 MET cc_start: 0.8393 (ttm) cc_final: 0.8142 (ttt) REVERT: C 465 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6608 (tt0) REVERT: C 546 GLU cc_start: 0.7635 (tm-30) cc_final: 0.6876 (pt0) REVERT: D 388 ASN cc_start: 0.8428 (m-40) cc_final: 0.7901 (t0) REVERT: D 406 GLU cc_start: 0.6700 (tp30) cc_final: 0.6478 (tp30) REVERT: E 187 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: E 458 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.5926 (p-80) REVERT: F 68 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8531 (mp) REVERT: F 183 LYS cc_start: 0.6975 (mppt) cc_final: 0.6752 (mtpp) REVERT: F 395 LEU cc_start: 0.8326 (tt) cc_final: 0.8114 (tp) REVERT: G 13 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8301 (tt0) REVERT: G 132 ARG cc_start: 0.5832 (mtm110) cc_final: 0.5199 (mtm110) REVERT: G 190 ASP cc_start: 0.8574 (p0) cc_final: 0.8370 (p0) REVERT: G 207 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.4885 (tm-30) REVERT: H 6 ASP cc_start: 0.4605 (OUTLIER) cc_final: 0.4315 (p0) REVERT: H 34 GLU cc_start: 0.6555 (mm-30) cc_final: 0.5672 (pt0) REVERT: H 63 MET cc_start: 0.3554 (OUTLIER) cc_final: 0.2999 (tpt) REVERT: J 148 LEU cc_start: 0.2936 (pt) cc_final: 0.2114 (tt) REVERT: J 150 LEU cc_start: 0.3700 (OUTLIER) cc_final: 0.2992 (mt) REVERT: K 93 GLU cc_start: 0.6060 (tp30) cc_final: 0.5417 (mp0) REVERT: L 74 GLN cc_start: 0.6486 (pt0) cc_final: 0.6236 (pt0) REVERT: L 149 ARG cc_start: 0.5884 (ttp80) cc_final: 0.5577 (ttt-90) REVERT: L 160 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7409 (mmtm) outliers start: 88 outliers final: 58 residues processed: 373 average time/residue: 0.1940 time to fit residues: 113.2049 Evaluate side-chains 354 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 288 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 139 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 GLN E 170 GLN E 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.092647 restraints weight = 43598.731| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.52 r_work: 0.2911 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30015 Z= 0.130 Angle : 0.539 11.491 40658 Z= 0.275 Chirality : 0.044 0.173 4560 Planarity : 0.005 0.045 5330 Dihedral : 4.432 37.847 4182 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.53 % Allowed : 15.50 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3764 helix: 0.94 (0.14), residues: 1549 sheet: -0.47 (0.23), residues: 514 loop : -0.98 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 106 TYR 0.021 0.001 TYR H 42 PHE 0.014 0.001 PHE D 60 TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00305 (30015) covalent geometry : angle 0.53865 (40658) hydrogen bonds : bond 0.04652 ( 1247) hydrogen bonds : angle 4.52137 ( 3570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 303 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: A 128 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7113 (tm-30) REVERT: A 154 ARG cc_start: 0.7456 (ptp-110) cc_final: 0.6744 (ptm-80) REVERT: A 156 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7436 (mtm-85) REVERT: A 491 ARG cc_start: 0.7629 (ttt90) cc_final: 0.7423 (mmt180) REVERT: B 133 MET cc_start: 0.8524 (mtp) cc_final: 0.8173 (mmm) REVERT: B 154 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.7313 (ttt180) REVERT: B 532 ARG cc_start: 0.7012 (ttm110) cc_final: 0.6325 (ttp80) REVERT: C 130 ARG cc_start: 0.7659 (ptp90) cc_final: 0.7147 (ptt90) REVERT: C 287 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9003 (mp) REVERT: C 342 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7944 (mt-10) REVERT: C 344 MET cc_start: 0.8348 (ttm) cc_final: 0.8103 (ttt) REVERT: C 465 GLN cc_start: 0.7018 (tm-30) cc_final: 0.6570 (tt0) REVERT: C 481 ARG cc_start: 0.6807 (mmm160) cc_final: 0.6515 (mtp-110) REVERT: C 546 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6772 (pt0) REVERT: D 388 ASN cc_start: 0.8377 (m-40) cc_final: 0.7915 (t0) REVERT: D 420 ARG cc_start: 0.8078 (tpm170) cc_final: 0.7745 (ttp-170) REVERT: E 406 GLU cc_start: 0.7244 (tp30) cc_final: 0.6991 (tp30) REVERT: E 458 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.5856 (p-80) REVERT: F 184 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5252 (mt-10) REVERT: G 13 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8233 (tt0) REVERT: G 132 ARG cc_start: 0.5844 (mtm110) cc_final: 0.5189 (mtm110) REVERT: H 6 ASP cc_start: 0.4508 (OUTLIER) cc_final: 0.4291 (p0) REVERT: H 34 GLU cc_start: 0.6542 (mm-30) cc_final: 0.5647 (pt0) REVERT: J 112 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.5100 (mt) REVERT: J 148 LEU cc_start: 0.2840 (OUTLIER) cc_final: 0.2011 (tt) REVERT: J 150 LEU cc_start: 0.3692 (OUTLIER) cc_final: 0.2927 (mt) REVERT: K 93 GLU cc_start: 0.6052 (tp30) cc_final: 0.5389 (mp0) REVERT: L 158 GLU cc_start: 0.5866 (OUTLIER) cc_final: 0.5492 (mp0) REVERT: L 160 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7388 (mmtm) outliers start: 78 outliers final: 51 residues processed: 363 average time/residue: 0.1894 time to fit residues: 107.8343 Evaluate side-chains 342 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 169 optimal weight: 0.4980 chunk 361 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 302 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 254 optimal weight: 7.9990 chunk 168 optimal weight: 0.0270 chunk 145 optimal weight: 5.9990 chunk 206 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN C 418 HIS D 344 HIS E 166 GLN L 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094985 restraints weight = 43552.174| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.45 r_work: 0.2942 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30015 Z= 0.100 Angle : 0.506 11.597 40658 Z= 0.258 Chirality : 0.043 0.177 4560 Planarity : 0.004 0.042 5330 Dihedral : 4.161 35.506 4182 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.21 % Allowed : 16.06 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3764 helix: 1.25 (0.14), residues: 1535 sheet: -0.30 (0.23), residues: 516 loop : -0.80 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 547 TYR 0.015 0.001 TYR H 42 PHE 0.012 0.001 PHE D 60 TRP 0.012 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00214 (30015) covalent geometry : angle 0.50640 (40658) hydrogen bonds : bond 0.04052 ( 1247) hydrogen bonds : angle 4.36670 ( 3570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 300 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7119 (tm-30) REVERT: A 154 ARG cc_start: 0.7521 (ptp-110) cc_final: 0.6813 (ptm-80) REVERT: A 156 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7484 (mtm-85) REVERT: A 491 ARG cc_start: 0.7624 (ttt90) cc_final: 0.7386 (mtt180) REVERT: B 133 MET cc_start: 0.8523 (mtp) cc_final: 0.8173 (mmm) REVERT: B 154 ARG cc_start: 0.7614 (ttt-90) cc_final: 0.7304 (ttt180) REVERT: B 532 ARG cc_start: 0.6907 (ttm110) cc_final: 0.6284 (ttp80) REVERT: C 130 ARG cc_start: 0.7597 (ptp90) cc_final: 0.7150 (ptt90) REVERT: C 342 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7847 (mt-10) REVERT: C 344 MET cc_start: 0.8320 (ttm) cc_final: 0.8081 (ttt) REVERT: C 465 GLN cc_start: 0.7036 (tm-30) cc_final: 0.6591 (tt0) REVERT: C 546 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6675 (pt0) REVERT: D 388 ASN cc_start: 0.8311 (m-40) cc_final: 0.7976 (t0) REVERT: D 413 GLN cc_start: 0.8067 (mp10) cc_final: 0.7789 (mp10) REVERT: D 420 ARG cc_start: 0.8009 (tpm170) cc_final: 0.7655 (ttp-170) REVERT: F 206 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7277 (mt0) REVERT: G 13 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8251 (tt0) REVERT: G 132 ARG cc_start: 0.5838 (mtm110) cc_final: 0.5190 (mtm110) REVERT: G 207 GLU cc_start: 0.5356 (OUTLIER) cc_final: 0.4918 (tm-30) REVERT: H 6 ASP cc_start: 0.4422 (OUTLIER) cc_final: 0.4061 (p0) REVERT: H 34 GLU cc_start: 0.6484 (mm-30) cc_final: 0.5611 (pt0) REVERT: J 112 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.5030 (mt) REVERT: J 148 LEU cc_start: 0.2753 (OUTLIER) cc_final: 0.1908 (tt) REVERT: J 150 LEU cc_start: 0.3707 (OUTLIER) cc_final: 0.2946 (mt) REVERT: J 158 GLU cc_start: 0.6132 (pm20) cc_final: 0.5029 (tp30) REVERT: K 93 GLU cc_start: 0.6095 (tp30) cc_final: 0.5337 (mp0) REVERT: L 158 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.5448 (mp0) REVERT: L 160 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7385 (mmtm) outliers start: 68 outliers final: 45 residues processed: 352 average time/residue: 0.1954 time to fit residues: 106.5011 Evaluate side-chains 340 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 85 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 369 optimal weight: 0.0270 chunk 241 optimal weight: 2.9990 chunk 328 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 365 optimal weight: 0.3980 overall best weight: 0.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.095340 restraints weight = 43676.643| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.58 r_work: 0.2989 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30015 Z= 0.098 Angle : 0.499 11.275 40658 Z= 0.252 Chirality : 0.043 0.199 4560 Planarity : 0.004 0.041 5330 Dihedral : 3.986 32.882 4182 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.85 % Allowed : 15.67 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3764 helix: 1.41 (0.14), residues: 1546 sheet: -0.27 (0.23), residues: 521 loop : -0.66 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 93 TYR 0.013 0.001 TYR H 42 PHE 0.014 0.001 PHE D 60 TRP 0.011 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00215 (30015) covalent geometry : angle 0.49903 (40658) hydrogen bonds : bond 0.03788 ( 1247) hydrogen bonds : angle 4.23816 ( 3570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 310 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: A 128 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7168 (tm-30) REVERT: A 154 ARG cc_start: 0.7489 (ptp-110) cc_final: 0.6820 (ptm-80) REVERT: A 156 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7507 (mtm-85) REVERT: B 124 LYS cc_start: 0.7630 (ptpp) cc_final: 0.7261 (mttm) REVERT: B 133 MET cc_start: 0.8523 (mtp) cc_final: 0.8174 (mmm) REVERT: B 154 ARG cc_start: 0.7593 (ttt-90) cc_final: 0.7317 (ttt180) REVERT: B 470 LEU cc_start: 0.6964 (tp) cc_final: 0.6609 (tt) REVERT: B 532 ARG cc_start: 0.6880 (ttm110) cc_final: 0.6237 (ttp80) REVERT: C 130 ARG cc_start: 0.7597 (ptp90) cc_final: 0.7182 (ptt90) REVERT: C 287 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8900 (mp) REVERT: C 342 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7902 (mt-10) REVERT: C 344 MET cc_start: 0.8355 (ttm) cc_final: 0.8114 (ttt) REVERT: C 465 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6552 (tt0) REVERT: C 481 ARG cc_start: 0.6738 (mmm160) cc_final: 0.6503 (mtp-110) REVERT: C 546 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6656 (pt0) REVERT: D 388 ASN cc_start: 0.8304 (m-40) cc_final: 0.8042 (t0) REVERT: D 413 GLN cc_start: 0.8139 (mp10) cc_final: 0.7870 (mp10) REVERT: E 458 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.5859 (p-80) REVERT: F 184 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5127 (mt-10) REVERT: F 206 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7216 (mt0) REVERT: G 13 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8099 (tt0) REVERT: G 132 ARG cc_start: 0.5810 (mtm110) cc_final: 0.5160 (mtm110) REVERT: G 207 GLU cc_start: 0.5164 (OUTLIER) cc_final: 0.4759 (tm-30) REVERT: H 34 GLU cc_start: 0.6433 (mm-30) cc_final: 0.5580 (pt0) REVERT: J 148 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.1836 (tt) REVERT: J 150 LEU cc_start: 0.3746 (OUTLIER) cc_final: 0.2991 (mt) REVERT: J 158 GLU cc_start: 0.6141 (pm20) cc_final: 0.5072 (tp30) REVERT: K 93 GLU cc_start: 0.6060 (tp30) cc_final: 0.5264 (mp0) REVERT: L 158 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5384 (mp0) REVERT: L 160 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7361 (mmtm) outliers start: 88 outliers final: 59 residues processed: 379 average time/residue: 0.1888 time to fit residues: 111.6940 Evaluate side-chains 364 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 296 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 26 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 294 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 238 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN L 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092564 restraints weight = 43733.994| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.56 r_work: 0.2906 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30015 Z= 0.179 Angle : 0.570 10.732 40658 Z= 0.291 Chirality : 0.046 0.187 4560 Planarity : 0.005 0.042 5330 Dihedral : 4.374 33.033 4182 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.95 % Allowed : 15.89 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3764 helix: 1.18 (0.14), residues: 1551 sheet: -0.20 (0.23), residues: 516 loop : -0.75 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 420 TYR 0.018 0.001 TYR H 42 PHE 0.021 0.002 PHE D 60 TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS F 458 Details of bonding type rmsd covalent geometry : bond 0.00440 (30015) covalent geometry : angle 0.56983 (40658) hydrogen bonds : bond 0.04902 ( 1247) hydrogen bonds : angle 4.41372 ( 3570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 290 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: A 128 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7182 (tm-30) REVERT: A 154 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.6811 (ptm-80) REVERT: A 156 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7379 (mtm-85) REVERT: B 124 LYS cc_start: 0.7626 (ptpp) cc_final: 0.7265 (mttm) REVERT: B 133 MET cc_start: 0.8567 (mtp) cc_final: 0.8248 (mmm) REVERT: B 154 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7333 (ttt180) REVERT: B 532 ARG cc_start: 0.7009 (ttm110) cc_final: 0.6338 (ttp80) REVERT: B 547 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7546 (tpp80) REVERT: C 130 ARG cc_start: 0.7657 (ptp90) cc_final: 0.7168 (ptt90) REVERT: C 287 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8970 (mp) REVERT: C 342 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7870 (mt-10) REVERT: C 344 MET cc_start: 0.8346 (ttm) cc_final: 0.8104 (ttt) REVERT: C 465 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6626 (tt0) REVERT: C 481 ARG cc_start: 0.6882 (mmm160) cc_final: 0.6619 (mtp-110) REVERT: C 546 GLU cc_start: 0.7528 (tm-30) cc_final: 0.6745 (pt0) REVERT: D 88 MET cc_start: 0.8969 (mtp) cc_final: 0.8584 (mtt) REVERT: D 388 ASN cc_start: 0.8378 (m-40) cc_final: 0.8032 (t0) REVERT: E 458 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6046 (p-80) REVERT: F 184 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5178 (mt-10) REVERT: F 206 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7190 (mt0) REVERT: G 13 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8098 (tt0) REVERT: G 132 ARG cc_start: 0.5860 (mtm110) cc_final: 0.5185 (mtm110) REVERT: G 207 GLU cc_start: 0.5213 (OUTLIER) cc_final: 0.4838 (tm-30) REVERT: H 34 GLU cc_start: 0.6436 (mm-30) cc_final: 0.5576 (pt0) REVERT: J 121 LEU cc_start: 0.5654 (tt) cc_final: 0.5381 (mt) REVERT: J 148 LEU cc_start: 0.2818 (OUTLIER) cc_final: 0.2056 (tt) REVERT: J 150 LEU cc_start: 0.3818 (OUTLIER) cc_final: 0.3130 (mt) REVERT: J 158 GLU cc_start: 0.6092 (pm20) cc_final: 0.5049 (tp30) REVERT: K 93 GLU cc_start: 0.6100 (tp30) cc_final: 0.5346 (mp0) REVERT: L 158 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.5174 (mp0) REVERT: L 160 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7430 (mmtm) outliers start: 91 outliers final: 65 residues processed: 367 average time/residue: 0.1859 time to fit residues: 107.7589 Evaluate side-chains 360 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 285 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 144 optimal weight: 2.9990 chunk 322 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 362 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 317 optimal weight: 0.6980 chunk 366 optimal weight: 3.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094345 restraints weight = 43509.428| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.54 r_work: 0.2956 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30015 Z= 0.109 Angle : 0.509 11.016 40658 Z= 0.259 Chirality : 0.043 0.201 4560 Planarity : 0.004 0.041 5330 Dihedral : 4.108 31.265 4182 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.63 % Allowed : 16.35 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3764 helix: 1.39 (0.14), residues: 1548 sheet: -0.21 (0.23), residues: 526 loop : -0.67 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 106 TYR 0.013 0.001 TYR H 42 PHE 0.013 0.001 PHE D 60 TRP 0.012 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00248 (30015) covalent geometry : angle 0.50900 (40658) hydrogen bonds : bond 0.04017 ( 1247) hydrogen bonds : angle 4.25348 ( 3570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 298 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: A 128 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7087 (tm-30) REVERT: A 154 ARG cc_start: 0.7523 (ptp-110) cc_final: 0.6848 (ptm-80) REVERT: A 156 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7485 (mtm-85) REVERT: A 466 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: B 124 LYS cc_start: 0.7718 (ptpp) cc_final: 0.7284 (mttm) REVERT: B 133 MET cc_start: 0.8553 (mtp) cc_final: 0.8225 (mmm) REVERT: B 154 ARG cc_start: 0.7645 (ttt-90) cc_final: 0.7314 (ttt180) REVERT: B 547 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7692 (ttm170) REVERT: C 130 ARG cc_start: 0.7621 (ptp90) cc_final: 0.7153 (ptt90) REVERT: C 287 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8916 (mp) REVERT: C 342 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7884 (mt-10) REVERT: C 344 MET cc_start: 0.8366 (ttm) cc_final: 0.8124 (ttt) REVERT: C 465 GLN cc_start: 0.7025 (tm-30) cc_final: 0.6568 (tt0) REVERT: C 481 ARG cc_start: 0.6854 (mmm160) cc_final: 0.6458 (mtp-110) REVERT: C 492 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7654 (mt-10) REVERT: C 546 GLU cc_start: 0.7586 (tm-30) cc_final: 0.6658 (pt0) REVERT: D 88 MET cc_start: 0.8984 (mtp) cc_final: 0.8623 (mtt) REVERT: D 388 ASN cc_start: 0.8323 (m-40) cc_final: 0.7995 (t0) REVERT: E 211 THR cc_start: 0.8004 (m) cc_final: 0.7723 (t) REVERT: E 458 HIS cc_start: 0.7013 (OUTLIER) cc_final: 0.5855 (p-80) REVERT: F 68 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8434 (mp) REVERT: F 184 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5153 (mt-10) REVERT: F 206 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7096 (mt0) REVERT: G 13 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8264 (tt0) REVERT: G 132 ARG cc_start: 0.5807 (mtm110) cc_final: 0.5172 (mtm110) REVERT: G 207 GLU cc_start: 0.5277 (OUTLIER) cc_final: 0.4922 (tm-30) REVERT: H 34 GLU cc_start: 0.6374 (mm-30) cc_final: 0.5505 (pt0) REVERT: J 121 LEU cc_start: 0.5687 (tt) cc_final: 0.5486 (mt) REVERT: J 148 LEU cc_start: 0.2721 (OUTLIER) cc_final: 0.1977 (tt) REVERT: J 150 LEU cc_start: 0.3810 (OUTLIER) cc_final: 0.3065 (mt) REVERT: J 158 GLU cc_start: 0.6022 (pm20) cc_final: 0.5020 (tp30) REVERT: K 93 GLU cc_start: 0.6120 (tp30) cc_final: 0.5361 (mp0) REVERT: L 158 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5154 (mp0) REVERT: L 160 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7366 (mmtm) outliers start: 81 outliers final: 60 residues processed: 364 average time/residue: 0.2044 time to fit residues: 116.6561 Evaluate side-chains 355 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 284 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 147 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.093344 restraints weight = 43559.624| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.53 r_work: 0.2913 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30015 Z= 0.143 Angle : 0.542 10.906 40658 Z= 0.275 Chirality : 0.044 0.200 4560 Planarity : 0.005 0.042 5330 Dihedral : 4.239 31.711 4182 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.56 % Allowed : 16.70 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3764 helix: 1.30 (0.14), residues: 1557 sheet: -0.23 (0.23), residues: 532 loop : -0.70 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 106 TYR 0.015 0.001 TYR H 42 PHE 0.018 0.001 PHE D 60 TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00346 (30015) covalent geometry : angle 0.54235 (40658) hydrogen bonds : bond 0.04477 ( 1247) hydrogen bonds : angle 4.30565 ( 3570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 288 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: A 128 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7051 (tm-30) REVERT: A 154 ARG cc_start: 0.7507 (ptp-110) cc_final: 0.6822 (ptm-80) REVERT: A 156 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7304 (mtm-85) REVERT: A 466 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: B 124 LYS cc_start: 0.7696 (ptpp) cc_final: 0.7266 (mttm) REVERT: B 133 MET cc_start: 0.8553 (mtp) cc_final: 0.8225 (mmm) REVERT: B 154 ARG cc_start: 0.7604 (ttt-90) cc_final: 0.7294 (ttt180) REVERT: B 532 ARG cc_start: 0.6939 (ttm110) cc_final: 0.6298 (ttp80) REVERT: B 547 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7678 (ttm170) REVERT: C 130 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7109 (ptt90) REVERT: C 287 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8970 (mp) REVERT: C 342 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7848 (mt-10) REVERT: C 344 MET cc_start: 0.8338 (ttm) cc_final: 0.8094 (ttt) REVERT: C 465 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6549 (tt0) REVERT: C 481 ARG cc_start: 0.6844 (mmm160) cc_final: 0.6444 (mtp-110) REVERT: C 492 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 546 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6687 (pt0) REVERT: D 88 MET cc_start: 0.8995 (mtp) cc_final: 0.8647 (mtt) REVERT: D 388 ASN cc_start: 0.8304 (m-40) cc_final: 0.7917 (t0) REVERT: E 211 THR cc_start: 0.8030 (m) cc_final: 0.7749 (t) REVERT: E 458 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.5896 (p-80) REVERT: F 68 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8463 (mp) REVERT: F 184 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5184 (mt-10) REVERT: F 206 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7065 (mt0) REVERT: G 13 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8239 (tt0) REVERT: G 53 LEU cc_start: 0.6574 (tp) cc_final: 0.6326 (tp) REVERT: G 132 ARG cc_start: 0.5820 (mtm110) cc_final: 0.5146 (mtm110) REVERT: G 207 GLU cc_start: 0.5223 (OUTLIER) cc_final: 0.4878 (tm-30) REVERT: H 34 GLU cc_start: 0.6382 (mm-30) cc_final: 0.5551 (pt0) REVERT: J 82 GLU cc_start: 0.4313 (OUTLIER) cc_final: 0.4031 (mm-30) REVERT: J 121 LEU cc_start: 0.5670 (tt) cc_final: 0.5462 (mt) REVERT: J 148 LEU cc_start: 0.2522 (OUTLIER) cc_final: 0.1889 (tt) REVERT: J 150 LEU cc_start: 0.3925 (OUTLIER) cc_final: 0.3259 (mt) REVERT: J 158 GLU cc_start: 0.6003 (pm20) cc_final: 0.4973 (tp30) REVERT: K 93 GLU cc_start: 0.6021 (tp30) cc_final: 0.5346 (mp0) REVERT: L 158 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.5033 (mp0) REVERT: L 160 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7360 (mmtm) REVERT: L 161 THR cc_start: 0.8342 (m) cc_final: 0.8140 (m) outliers start: 79 outliers final: 63 residues processed: 351 average time/residue: 0.1883 time to fit residues: 104.9045 Evaluate side-chains 359 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 284 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 458 HIS Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 158 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 330 optimal weight: 6.9990 chunk 100 optimal weight: 0.0570 chunk 63 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 266 optimal weight: 0.0770 chunk 348 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.2660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.095426 restraints weight = 43708.003| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.61 r_work: 0.2952 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30015 Z= 0.108 Angle : 0.512 11.000 40658 Z= 0.259 Chirality : 0.043 0.202 4560 Planarity : 0.004 0.041 5330 Dihedral : 4.059 30.585 4182 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.47 % Allowed : 16.80 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3764 helix: 1.45 (0.14), residues: 1559 sheet: -0.12 (0.23), residues: 521 loop : -0.63 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 106 TYR 0.012 0.001 TYR H 42 PHE 0.014 0.001 PHE D 60 TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00249 (30015) covalent geometry : angle 0.51170 (40658) hydrogen bonds : bond 0.03936 ( 1247) hydrogen bonds : angle 4.19452 ( 3570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8007.30 seconds wall clock time: 137 minutes 7.05 seconds (8227.05 seconds total)