Starting phenix.real_space_refine on Sun Sep 13 07:52:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m1d_30041/09_2026/6m1d_30041.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m1d_30041/09_2026/6m1d_30041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m1d_30041/09_2026/6m1d_30041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m1d_30041/09_2026/6m1d_30041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m1d_30041/09_2026/6m1d_30041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m1d_30041/09_2026/6m1d_30041.map" } resolution = 4.5 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= 0.003 sd= 0.054 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 128 5.16 5 C 14154 2.51 5 N 3524 2.21 5 O 3970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21776 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "B" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6089 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 35, 'TRANS': 712} Chain: "C" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "D" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6089 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 35, 'TRANS': 712} Time building chain proxies: 5.06, per 1000 atoms: 0.23 Number of scatterers: 21776 At special positions: 0 Unit cell: (109.787, 130.44, 184.79, 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 128 16.00 O 3970 8.00 N 3524 7.00 C 14154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.04 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 383 " distance=2.02 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.83 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 10 sheets defined 58.5% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.888A pdb=" N MET A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS A 45 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 46 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 49 " --> pdb=" O CYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 removed outlier: 4.097A pdb=" N GLN A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 97 removed outlier: 3.806A pdb=" N PHE A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 3.885A pdb=" N TYR A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.738A pdb=" N TRP A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 142 removed outlier: 4.590A pdb=" N MET A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.663A pdb=" N PHE A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.688A pdb=" N ALA A 204 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 207 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 3.646A pdb=" N THR A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 244 removed outlier: 3.525A pdb=" N VAL A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.672A pdb=" N LEU A 262 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.019A pdb=" N TRP A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.691A pdb=" N SER A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 348 removed outlier: 3.767A pdb=" N SER A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.548A pdb=" N PHE A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.869A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 431 removed outlier: 3.530A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.615A pdb=" N VAL A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.593A pdb=" N CYS A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.597A pdb=" N PHE A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 472 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.678A pdb=" N TRP A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 4.414A pdb=" N ILE A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 497 " --> pdb=" O PRO A 493 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 504 " --> pdb=" O CYS A 500 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 removed outlier: 3.691A pdb=" N ASP A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 519 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 4.078A pdb=" N GLN A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP A 534 " --> pdb=" O TRP A 530 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.729A pdb=" N MET A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 608 removed outlier: 4.109A pdb=" N ALA A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.136A pdb=" N THR A 596 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 4.871A pdb=" N ALA A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 32 Processing helix chain 'B' and resid 36 through 49 removed outlier: 4.423A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 77 removed outlier: 4.557A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.992A pdb=" N ILE B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 157 through 170 removed outlier: 3.775A pdb=" N ARG B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.539A pdb=" N LYS B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.654A pdb=" N ARG B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 208 Processing helix chain 'B' and resid 229 through 252 removed outlier: 3.506A pdb=" N ILE B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.743A pdb=" N MET B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 305 through 317 removed outlier: 4.031A pdb=" N LYS B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 317 " --> pdb=" O LYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.270A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 434 through 447 removed outlier: 4.085A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 removed outlier: 3.579A pdb=" N TYR B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.709A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 481 " --> pdb=" O TRP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.852A pdb=" N SER B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.939A pdb=" N THR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 521 " --> pdb=" O THR B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 removed outlier: 3.597A pdb=" N GLN B 526 " --> pdb=" O GLN B 522 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 528 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 533 No H-bonds generated for 'chain 'B' and resid 531 through 533' Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.572A pdb=" N GLN B 552 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 575 removed outlier: 3.903A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 593 removed outlier: 3.695A pdb=" N THR B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 636 through 658 removed outlier: 3.654A pdb=" N SER B 645 " --> pdb=" O TYR B 641 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 651 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 656 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.670A pdb=" N VAL B 700 " --> pdb=" O PRO B 696 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 712 removed outlier: 3.872A pdb=" N ILE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN B 712 " --> pdb=" O ARG B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 712' Processing helix chain 'B' and resid 741 through 767 removed outlier: 3.621A pdb=" N VAL B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 749 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY B 751 " --> pdb=" O GLY B 747 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 753 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 754 " --> pdb=" O MET B 750 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 758 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 760 " --> pdb=" O GLY B 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.890A pdb=" N MET C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS C 45 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 46 " --> pdb=" O MET C 42 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 49 " --> pdb=" O CYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.098A pdb=" N GLN C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 97 removed outlier: 3.807A pdb=" N PHE C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.884A pdb=" N TYR C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.739A pdb=" N TRP C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 142 removed outlier: 4.590A pdb=" N MET C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.650A pdb=" N PHE C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 removed outlier: 3.688A pdb=" N ALA C 204 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 207 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 removed outlier: 3.646A pdb=" N THR C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 244 removed outlier: 5.156A pdb=" N LEU C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.672A pdb=" N LEU C 262 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 279 removed outlier: 4.018A pdb=" N TRP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.691A pdb=" N SER C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 348 removed outlier: 3.767A pdb=" N SER C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN C 310 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE C 337 " --> pdb=" O TYR C 333 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 Processing helix chain 'C' and resid 373 through 377 Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.548A pdb=" N PHE C 400 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.869A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 431 removed outlier: 3.530A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 422 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.615A pdb=" N VAL C 440 " --> pdb=" O MET C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 464 removed outlier: 3.593A pdb=" N CYS C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.596A pdb=" N PHE C 471 " --> pdb=" O LEU C 468 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 472 " --> pdb=" O ILE C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 488 removed outlier: 3.677A pdb=" N TRP C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 484 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 removed outlier: 4.414A pdb=" N ILE C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE C 497 " --> pdb=" O PRO C 493 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 498 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 503 " --> pdb=" O PHE C 499 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 504 " --> pdb=" O CYS C 500 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 522 removed outlier: 3.691A pdb=" N ASP C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU C 519 " --> pdb=" O ASN C 515 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 536 removed outlier: 4.077A pdb=" N GLN C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP C 534 " --> pdb=" O TRP C 530 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 535 " --> pdb=" O GLN C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.729A pdb=" N MET C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 546 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 608 removed outlier: 4.110A pdb=" N ALA C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Proline residue: C 593 - end of helix removed outlier: 4.136A pdb=" N THR C 596 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE C 597 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Proline residue: C 598 - end of helix removed outlier: 4.870A pdb=" N ALA C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 36 through 49 removed outlier: 4.423A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.096A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.691A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 3.993A pdb=" N ILE D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 148 through 154 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.776A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 180 through 194 removed outlier: 3.539A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.654A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 229 through 252 removed outlier: 3.506A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.744A pdb=" N MET D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 305 through 317 removed outlier: 4.030A pdb=" N LYS D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 removed outlier: 4.269A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N HIS D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 407 removed outlier: 3.567A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 434 through 447 removed outlier: 4.084A pdb=" N LEU D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU D 440 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 removed outlier: 3.580A pdb=" N TYR D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.709A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.852A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 530 removed outlier: 4.101A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS D 530 " --> pdb=" O GLN D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 533 No H-bonds generated for 'chain 'D' and resid 531 through 533' Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.572A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.694A pdb=" N THR D 593 " --> pdb=" O GLU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 597 Processing helix chain 'D' and resid 613 through 617 Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.654A pdb=" N SER D 645 " --> pdb=" O TYR D 641 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 651 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 656 " --> pdb=" O ARG D 652 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.671A pdb=" N VAL D 700 " --> pdb=" O PRO D 696 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 712 removed outlier: 3.873A pdb=" N ILE D 711 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN D 712 " --> pdb=" O ARG D 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 707 through 712' Processing helix chain 'D' and resid 741 through 767 removed outlier: 3.621A pdb=" N VAL D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 749 " --> pdb=" O VAL D 745 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY D 751 " --> pdb=" O GLY D 747 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 753 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL D 754 " --> pdb=" O MET D 750 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL D 755 " --> pdb=" O GLY D 751 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 756 " --> pdb=" O VAL D 752 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE D 757 " --> pdb=" O ILE D 753 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL D 758 " --> pdb=" O VAL D 754 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 760 " --> pdb=" O GLY D 756 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.650A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA5, first strand: chain 'B' and resid 618 through 621 removed outlier: 6.841A pdb=" N SER B 680 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU B 675 " --> pdb=" O SER B 680 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 560 through 562 Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.650A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 347 through 348 Processing sheet with id=AB1, first strand: chain 'D' and resid 618 through 620 removed outlier: 6.841A pdb=" N SER D 680 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU D 675 " --> pdb=" O SER D 680 " (cutoff:3.500A) 749 hydrogen bonds defined for protein. 2133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6741 1.34 - 1.46: 5643 1.46 - 1.58: 9790 1.58 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 22384 Sorted by residual: bond pdb=" C GLU D 145 " pdb=" N PRO D 146 " ideal model delta sigma weight residual 1.332 1.375 -0.043 8.20e-03 1.49e+04 2.69e+01 bond pdb=" C GLU B 145 " pdb=" N PRO B 146 " ideal model delta sigma weight residual 1.332 1.374 -0.042 8.20e-03 1.49e+04 2.65e+01 bond pdb=" N PRO B 677 " pdb=" CD PRO B 677 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" N PRO B 565 " pdb=" CD PRO B 565 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" N PRO A 147 " pdb=" CD PRO A 147 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.79e+01 ... (remaining 22379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 29215 2.71 - 5.42: 1040 5.42 - 8.13: 178 8.13 - 10.84: 34 10.84 - 13.55: 5 Bond angle restraints: 30472 Sorted by residual: angle pdb=" N ASN D 51 " pdb=" CA ASN D 51 " pdb=" C ASN D 51 " ideal model delta sigma weight residual 113.16 123.29 -10.13 1.24e+00 6.50e-01 6.68e+01 angle pdb=" N LYS B 363 " pdb=" CA LYS B 363 " pdb=" C LYS B 363 " ideal model delta sigma weight residual 113.20 102.67 10.53 1.36e+00 5.41e-01 6.00e+01 angle pdb=" N ILE B 421 " pdb=" CA ILE B 421 " pdb=" C ILE B 421 " ideal model delta sigma weight residual 113.20 106.25 6.95 9.60e-01 1.09e+00 5.24e+01 angle pdb=" N ILE D 421 " pdb=" CA ILE D 421 " pdb=" C ILE D 421 " ideal model delta sigma weight residual 113.20 106.25 6.95 9.60e-01 1.09e+00 5.24e+01 angle pdb=" O GLY D 395 " pdb=" C GLY D 395 " pdb=" N ALA D 396 " ideal model delta sigma weight residual 122.71 127.63 -4.92 7.80e-01 1.64e+00 3.98e+01 ... (remaining 30467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 11274 17.89 - 35.78: 1322 35.78 - 53.67: 365 53.67 - 71.56: 129 71.56 - 89.45: 40 Dihedral angle restraints: 13130 sinusoidal: 5230 harmonic: 7900 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual -86.00 -161.21 75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 383 " pdb=" CB CYS C 383 " ideal model delta sinusoidal sigma weight residual -86.00 -161.21 75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CA ASN D 432 " pdb=" C ASN D 432 " pdb=" N GLU D 433 " pdb=" CA GLU D 433 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 13127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2840 0.081 - 0.161: 443 0.161 - 0.242: 36 0.242 - 0.323: 8 0.323 - 0.403: 5 Chirality restraints: 3332 Sorted by residual: chirality pdb=" CA ASN D 51 " pdb=" N ASN D 51 " pdb=" C ASN D 51 " pdb=" CB ASN D 51 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA CYS D 344 " pdb=" N CYS D 344 " pdb=" C CYS D 344 " pdb=" CB CYS D 344 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CG LEU B 423 " pdb=" CB LEU B 423 " pdb=" CD1 LEU B 423 " pdb=" CD2 LEU B 423 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 3329 not shown) Planarity restraints: 3870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 649 " 0.028 2.00e-02 2.50e+03 2.70e-02 1.46e+01 pdb=" CG TYR D 649 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR D 649 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 649 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR D 649 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR D 649 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 649 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 649 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 649 " -0.028 2.00e-02 2.50e+03 2.68e-02 1.44e+01 pdb=" CG TYR B 649 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR B 649 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 649 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR B 649 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 649 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 649 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 649 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " 0.051 5.00e-02 4.00e+02 7.87e-02 9.91e+00 pdb=" N PRO D 346 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " 0.043 5.00e-02 4.00e+02 ... (remaining 3867 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 532 2.61 - 3.19: 19442 3.19 - 3.76: 38615 3.76 - 4.33: 52003 4.33 - 4.90: 77587 Nonbonded interactions: 188179 Sorted by model distance: nonbonded pdb=" O CYS D 361 " pdb=" OG1 THR D 362 " model vdw 2.043 3.040 nonbonded pdb=" O PHE A 144 " pdb=" CG GLN A 145 " model vdw 2.074 3.440 nonbonded pdb=" O THR A 212 " pdb=" OG1 THR A 212 " model vdw 2.165 3.040 nonbonded pdb=" O THR C 212 " pdb=" OG1 THR C 212 " model vdw 2.165 3.040 nonbonded pdb=" O VAL D 343 " pdb=" CB CYS D 344 " model vdw 2.175 3.440 ... (remaining 188174 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.260 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.008 0.797 22394 Z= 0.382 Angle : 1.205 20.534 30492 Z= 0.710 Chirality : 0.060 0.403 3332 Planarity : 0.008 0.079 3870 Dihedral : 18.157 89.453 8020 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.30 % Favored : 89.84 % Rotamer: Outliers : 9.51 % Allowed : 8.21 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.09 (0.12), residues: 2698 helix: -3.75 (0.09), residues: 1296 sheet: -2.30 (0.62), residues: 64 loop : -3.01 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 393 TYR 0.065 0.003 TYR D 649 PHE 0.028 0.002 PHE D 523 TRP 0.021 0.002 TRP B 635 HIS 0.008 0.002 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.27 (22384) covalent geometry : angle 1.19803 / 0.71 (30472) SS BOND : bond 0.25215 / 21.37 ( 10) SS BOND : angle 5.30358 / 4.59 ( 20) hydrogen bonds : bond 0.32309 / 20.81 ( 749) hydrogen bonds : angle 10.81963 / 7.31 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 30 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 CYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9271 (t) REVERT: A 137 MET cc_start: 0.9806 (OUTLIER) cc_final: 0.9484 (ptp) REVERT: A 231 TYR cc_start: 0.8719 (m-80) cc_final: 0.8435 (m-80) REVERT: A 355 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9159 (m) REVERT: A 365 GLN cc_start: 0.9553 (OUTLIER) cc_final: 0.9231 (mm110) REVERT: A 436 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9055 (tmm) outliers start: 39 outliers final: 4 residues processed: 63 average time/residue: 0.0443 time to fit residues: 4.2190 Evaluate side-chains 29 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.195 Evaluate side-chains 154 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 79 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 SER cc_start: 0.5801 (OUTLIER) cc_final: 0.5214 (p) REVERT: B 64 ASN cc_start: 0.9398 (m-40) cc_final: 0.8996 (m-40) REVERT: B 113 SER cc_start: 0.6761 (OUTLIER) cc_final: 0.6484 (p) REVERT: B 152 MET cc_start: 0.8817 (mmt) cc_final: 0.8469 (mmp) REVERT: B 180 TYR cc_start: 0.9007 (m-10) cc_final: 0.8690 (m-80) REVERT: B 190 MET cc_start: 0.9205 (ttm) cc_final: 0.8865 (tmm) REVERT: B 203 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8955 (m-10) REVERT: B 249 MET cc_start: 0.8891 (mmm) cc_final: 0.8532 (tpp) REVERT: B 270 MET cc_start: 0.8934 (tpp) cc_final: 0.8286 (tpp) REVERT: B 462 MET cc_start: 0.9197 (mtm) cc_final: 0.8979 (ttm) REVERT: B 505 HIS cc_start: 0.8541 (m-70) cc_final: 0.8309 (m90) REVERT: B 545 SER cc_start: 0.4614 (OUTLIER) cc_final: 0.4057 (p) REVERT: B 623 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7223 (p) REVERT: B 655 PHE cc_start: 0.9079 (m-10) cc_final: 0.8647 (m-10) REVERT: B 664 LEU cc_start: 0.8697 (mt) cc_final: 0.8432 (tp) REVERT: B 707 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.7887 (p) REVERT: B 750 MET cc_start: 0.9316 (ptt) cc_final: 0.9057 (ptt) outliers start: 75 outliers final: 16 residues processed: 143 average time/residue: 0.0803 time to fit residues: 15.2176 Evaluate side-chains 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 1.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS A 130 ASN A 194 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN A 340 ASN A 357 GLN A 377 GLN A 574 GLN B 33 ASN B 42 GLN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 139 GLN B 241 HIS B 300 GLN B 305 GLN B 322 ASN B 524 GLN B 531 GLN B 556 ASN B 616 GLN B 653 GLN B 660 ASN B 735 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037018 restraints weight = 66723.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.037818 restraints weight = 41198.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.038344 restraints weight = 29225.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.038658 restraints weight = 22545.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.038942 restraints weight = 19003.713| |-----------------------------------------------------------------------------| r_work (final): 0.2900 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.050578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.038331 restraints weight = 73001.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.039383 restraints weight = 53914.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.040207 restraints weight = 43226.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.040761 restraints weight = 36609.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.041162 restraints weight = 32373.137| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22394 Z= 0.163 Angle : 0.796 11.529 30492 Z= 0.427 Chirality : 0.047 0.212 3332 Planarity : 0.006 0.062 3870 Dihedral : 7.301 31.682 2914 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.38 % Favored : 90.73 % Rotamer: Outliers : 0.50 % Allowed : 4.69 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.04 (0.14), residues: 2698 helix: -2.64 (0.11), residues: 1438 sheet: -1.57 (0.78), residues: 40 loop : -2.68 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 678 TYR 0.019 0.002 TYR B 41 PHE 0.013 0.002 PHE B 327 TRP 0.019 0.002 TRP B 48 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (22384) covalent geometry : angle 0.79385 / 0.43 (30472) SS BOND : bond 0.00797 / 0.52 ( 10) SS BOND : angle 2.63519 / 1.84 ( 20) hydrogen bonds : bond 0.06469 / 4.26 ( 749) hydrogen bonds : angle 6.86263 / 4.64 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9749 (mtm) cc_final: 0.9503 (ptp) REVERT: A 231 TYR cc_start: 0.8428 (m-80) cc_final: 0.8111 (m-80) REVERT: A 312 PHE cc_start: 0.9504 (m-80) cc_final: 0.9278 (m-80) REVERT: A 432 MET cc_start: 0.9112 (mmm) cc_final: 0.8693 (tpp) REVERT: A 488 TYR cc_start: 0.7919 (t80) cc_final: 0.7403 (t80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0535 time to fit residues: 2.3975 Evaluate side-chains 21 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.195 Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASN cc_start: 0.9552 (m-40) cc_final: 0.9254 (m-40) REVERT: B 190 MET cc_start: 0.9272 (ttm) cc_final: 0.8865 (tmm) REVERT: B 249 MET cc_start: 0.9168 (mmm) cc_final: 0.8930 (tpp) REVERT: B 270 MET cc_start: 0.8713 (tpp) cc_final: 0.8075 (tpp) REVERT: B 462 MET cc_start: 0.9316 (mtm) cc_final: 0.9095 (ttm) REVERT: B 640 MET cc_start: 0.9410 (mmp) cc_final: 0.9039 (mmm) REVERT: B 643 PHE cc_start: 0.9377 (t80) cc_final: 0.9165 (t80) REVERT: B 655 PHE cc_start: 0.8877 (m-10) cc_final: 0.8608 (m-10) REVERT: B 664 LEU cc_start: 0.8439 (mt) cc_final: 0.8113 (tp) REVERT: B 722 LEU cc_start: 0.8770 (mp) cc_final: 0.8510 (mt) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.0886 time to fit residues: 7.8679 Evaluate side-chains 45 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 177 optimal weight: 0.1980 chunk 142 optimal weight: 9.9990 chunk 214 optimal weight: 0.0000 chunk 52 optimal weight: 0.0030 chunk 252 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 ASN B 51 ASN B 305 GLN B 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.031947 restraints weight = 66580.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032509 restraints weight = 47349.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.033039 restraints weight = 37921.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.033325 restraints weight = 31640.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.033637 restraints weight = 27583.213| |-----------------------------------------------------------------------------| r_work (final): 0.2856 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.051037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.038778 restraints weight = 72433.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.039812 restraints weight = 53994.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.040571 restraints weight = 43733.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.041134 restraints weight = 37185.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.041463 restraints weight = 32913.864| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22394 Z= 0.137 Angle : 0.711 9.051 30492 Z= 0.376 Chirality : 0.046 0.222 3332 Planarity : 0.005 0.066 3870 Dihedral : 6.663 34.741 2914 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.60 % Favored : 91.03 % Rotamer: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.31 (0.15), residues: 2698 helix: -1.87 (0.12), residues: 1456 sheet: -2.65 (0.53), residues: 64 loop : -2.50 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 678 TYR 0.022 0.002 TYR B 521 PHE 0.019 0.002 PHE D 327 TRP 0.017 0.001 TRP B 165 HIS 0.008 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (22384) covalent geometry : angle 0.71081 / 0.38 (30472) SS BOND : bond 0.02166 / 1.48 ( 10) SS BOND : angle 1.19840 / 0.75 ( 20) hydrogen bonds : bond 0.04853 / 3.12 ( 749) hydrogen bonds : angle 6.12270 / 4.12 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9724 (mtm) cc_final: 0.9486 (mtm) REVERT: A 231 TYR cc_start: 0.8701 (m-80) cc_final: 0.8348 (m-80) REVERT: A 312 PHE cc_start: 0.9563 (m-80) cc_final: 0.9322 (m-10) REVERT: A 423 MET cc_start: 0.8874 (mtp) cc_final: 0.8389 (mmm) REVERT: A 432 MET cc_start: 0.9388 (mmm) cc_final: 0.8993 (tpp) REVERT: A 488 TYR cc_start: 0.8094 (t80) cc_final: 0.7628 (t80) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.0417 time to fit residues: 1.8365 Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.170 Evaluate side-chains 55 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 MET cc_start: 0.9320 (ttm) cc_final: 0.8927 (tmm) REVERT: B 270 MET cc_start: 0.8770 (tpp) cc_final: 0.8031 (tpp) REVERT: B 462 MET cc_start: 0.9354 (mtm) cc_final: 0.8965 (ttp) REVERT: B 640 MET cc_start: 0.9501 (mmp) cc_final: 0.9066 (mmm) REVERT: B 643 PHE cc_start: 0.9468 (t80) cc_final: 0.9204 (t80) REVERT: B 655 PHE cc_start: 0.9072 (m-10) cc_final: 0.8731 (m-10) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0837 time to fit residues: 6.2444 Evaluate side-chains 42 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 43 optimal weight: 0.0010 chunk 141 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 155 optimal weight: 0.0070 chunk 61 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 0.0000 chunk 247 optimal weight: 20.0000 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 94 GLN B 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.039617 restraints weight = 68771.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.040440 restraints weight = 42982.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041009 restraints weight = 31045.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.041411 restraints weight = 24141.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041630 restraints weight = 19919.015| |-----------------------------------------------------------------------------| r_work (final): 0.2931 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.052320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.039466 restraints weight = 70995.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.040546 restraints weight = 52899.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.041339 restraints weight = 42531.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.041944 restraints weight = 36115.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.042367 restraints weight = 31976.768| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22394 Z= 0.125 Angle : 0.692 8.630 30492 Z= 0.364 Chirality : 0.045 0.222 3332 Planarity : 0.005 0.063 3870 Dihedral : 6.238 35.099 2914 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.45 % Favored : 91.18 % Rotamer: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.89 (0.16), residues: 2698 helix: -1.48 (0.13), residues: 1458 sheet: -1.96 (0.66), residues: 40 loop : -2.41 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 678 TYR 0.026 0.001 TYR D 180 PHE 0.028 0.001 PHE C 175 TRP 0.017 0.001 TRP B 165 HIS 0.004 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (22384) covalent geometry : angle 0.69064 / 0.36 (30472) SS BOND : bond 0.00968 / 0.55 ( 10) SS BOND : angle 1.86175 / 1.24 ( 20) hydrogen bonds : bond 0.04264 / 2.78 ( 749) hydrogen bonds : angle 5.67725 / 3.81 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9345 (ttt) cc_final: 0.9123 (ttt) REVERT: A 231 TYR cc_start: 0.8585 (m-80) cc_final: 0.8208 (m-80) REVERT: A 312 PHE cc_start: 0.9483 (m-80) cc_final: 0.9228 (m-10) REVERT: A 423 MET cc_start: 0.8970 (mtp) cc_final: 0.8617 (mmm) REVERT: A 432 MET cc_start: 0.9317 (mmm) cc_final: 0.8383 (tpp) REVERT: A 488 TYR cc_start: 0.7896 (t80) cc_final: 0.7430 (t80) REVERT: A 542 MET cc_start: 0.9330 (ttt) cc_final: 0.9095 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0472 time to fit residues: 2.1170 Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.135 Evaluate side-chains 55 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 MET cc_start: 0.9316 (ttm) cc_final: 0.9085 (tmm) REVERT: B 270 MET cc_start: 0.8832 (tpp) cc_final: 0.8183 (tpp) REVERT: B 455 MET cc_start: 0.9264 (ttp) cc_final: 0.8940 (ttp) REVERT: B 462 MET cc_start: 0.9296 (mtm) cc_final: 0.8937 (ttp) REVERT: B 481 LYS cc_start: 0.9515 (mtpt) cc_final: 0.9313 (mtmt) REVERT: B 640 MET cc_start: 0.9521 (mmp) cc_final: 0.8989 (mmm) REVERT: B 643 PHE cc_start: 0.9408 (t80) cc_final: 0.9016 (t80) REVERT: B 651 MET cc_start: 0.9444 (mmp) cc_final: 0.9219 (mmm) REVERT: B 655 PHE cc_start: 0.9067 (m-10) cc_final: 0.8590 (m-10) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.0807 time to fit residues: 5.9846 Evaluate side-chains 41 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 chunk 133 optimal weight: 0.9990 chunk 118 optimal weight: 0.0030 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 218 optimal weight: 0.0770 chunk 41 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.040078 restraints weight = 67517.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040884 restraints weight = 42682.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.041458 restraints weight = 30859.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.041842 restraints weight = 24230.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.042070 restraints weight = 20017.350| |-----------------------------------------------------------------------------| r_work (final): 0.2944 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.052802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.039658 restraints weight = 71786.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.040781 restraints weight = 53301.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.041621 restraints weight = 42928.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.042161 restraints weight = 36393.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.042618 restraints weight = 32345.581| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22394 Z= 0.120 Angle : 0.688 9.465 30492 Z= 0.356 Chirality : 0.045 0.206 3332 Planarity : 0.005 0.063 3870 Dihedral : 5.954 33.220 2914 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.67 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.67 (0.16), residues: 2698 helix: -1.27 (0.13), residues: 1464 sheet: -2.50 (0.51), residues: 64 loop : -2.32 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 678 TYR 0.022 0.001 TYR B 180 PHE 0.012 0.001 PHE D 230 TRP 0.030 0.001 TRP A 56 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (22384) covalent geometry : angle 0.68743 / 0.36 (30472) SS BOND : bond 0.00722 / 0.49 ( 10) SS BOND : angle 1.22182 / 0.79 ( 20) hydrogen bonds : bond 0.03988 / 2.59 ( 749) hydrogen bonds : angle 5.41751 / 3.63 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.9337 (ttt) cc_final: 0.9116 (ttt) REVERT: A 137 MET cc_start: 0.9761 (mtm) cc_final: 0.9397 (ptp) REVERT: A 231 TYR cc_start: 0.8711 (m-80) cc_final: 0.8321 (m-80) REVERT: A 312 PHE cc_start: 0.9550 (m-80) cc_final: 0.9257 (m-10) REVERT: A 423 MET cc_start: 0.9257 (mtp) cc_final: 0.8941 (mmm) REVERT: A 488 TYR cc_start: 0.7926 (t80) cc_final: 0.7350 (t80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0530 time to fit residues: 2.2985 Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.225 Evaluate side-chains 54 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.9122 (tp-100) cc_final: 0.8856 (tp-100) REVERT: B 64 ASN cc_start: 0.9345 (m110) cc_final: 0.8981 (p0) REVERT: B 270 MET cc_start: 0.8830 (tpp) cc_final: 0.8329 (tpp) REVERT: B 376 MET cc_start: 0.5891 (mmp) cc_final: 0.5613 (mmp) REVERT: B 462 MET cc_start: 0.9298 (mtm) cc_final: 0.9072 (ttm) REVERT: B 474 MET cc_start: 0.7790 (ttm) cc_final: 0.7561 (ttm) REVERT: B 640 MET cc_start: 0.9411 (mmp) cc_final: 0.8937 (mmm) REVERT: B 643 PHE cc_start: 0.9333 (t80) cc_final: 0.8969 (t80) REVERT: B 651 MET cc_start: 0.9317 (mmp) cc_final: 0.9094 (mmm) REVERT: B 655 PHE cc_start: 0.8965 (m-10) cc_final: 0.8478 (m-10) REVERT: B 662 MET cc_start: 0.8502 (tpp) cc_final: 0.8043 (tpt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0671 time to fit residues: 5.1353 Evaluate side-chains 41 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 16 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 264 optimal weight: 0.0670 chunk 154 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS A 444 GLN A 527 ASN B 86 GLN B 380 GLN B 417 HIS B 546 ASN B 578 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.043749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035149 restraints weight = 65663.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036148 restraints weight = 41677.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036962 restraints weight = 30180.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.037518 restraints weight = 24049.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037925 restraints weight = 20184.881| |-----------------------------------------------------------------------------| r_work (final): 0.2918 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.053006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.039974 restraints weight = 72182.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.041087 restraints weight = 53673.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.041901 restraints weight = 43432.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.042489 restraints weight = 37030.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.042946 restraints weight = 32783.898| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22394 Z= 0.118 Angle : 0.677 9.891 30492 Z= 0.349 Chirality : 0.044 0.185 3332 Planarity : 0.005 0.057 3870 Dihedral : 5.783 33.164 2914 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.78 % Favored : 91.85 % Rotamer: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.54 (0.16), residues: 2698 helix: -1.15 (0.13), residues: 1470 sheet: -2.20 (0.52), residues: 60 loop : -2.30 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 678 TYR 0.018 0.001 TYR D 180 PHE 0.027 0.001 PHE C 403 TRP 0.022 0.001 TRP C 56 HIS 0.003 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (22384) covalent geometry : angle 0.67600 / 0.35 (30472) SS BOND : bond 0.00938 / 0.59 ( 10) SS BOND : angle 1.66083 / 1.09 ( 20) hydrogen bonds : bond 0.03826 / 2.47 ( 749) hydrogen bonds : angle 5.30246 / 3.55 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.9264 (mtm) cc_final: 0.8989 (mtm) REVERT: A 423 MET cc_start: 0.8865 (mtp) cc_final: 0.8619 (mmm) REVERT: A 488 TYR cc_start: 0.6760 (t80) cc_final: 0.6540 (t80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0579 time to fit residues: 2.5383 Evaluate side-chains 23 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.183 Evaluate side-chains 52 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8882 (tp-100) REVERT: B 64 ASN cc_start: 0.9353 (m110) cc_final: 0.8975 (p0) REVERT: B 270 MET cc_start: 0.8879 (tpp) cc_final: 0.8348 (tpp) REVERT: B 462 MET cc_start: 0.9275 (mtm) cc_final: 0.8913 (ttp) REVERT: B 474 MET cc_start: 0.7738 (ttm) cc_final: 0.7376 (ttm) REVERT: B 578 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8471 (t0) REVERT: B 640 MET cc_start: 0.9352 (mmm) cc_final: 0.8909 (mmm) REVERT: B 643 PHE cc_start: 0.9416 (t80) cc_final: 0.9008 (t80) REVERT: B 651 MET cc_start: 0.9353 (mmp) cc_final: 0.9103 (mmm) REVERT: B 655 PHE cc_start: 0.9032 (m-10) cc_final: 0.8516 (m-10) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0712 time to fit residues: 5.2833 Evaluate side-chains 42 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 173 optimal weight: 8.9990 chunk 5 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN B 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.042206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034655 restraints weight = 64746.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035377 restraints weight = 47635.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.035888 restraints weight = 37916.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.036272 restraints weight = 32011.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.036564 restraints weight = 28062.419| |-----------------------------------------------------------------------------| r_work (final): 0.3058 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.052818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.039803 restraints weight = 71783.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.040770 restraints weight = 54609.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.041577 restraints weight = 44859.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.041915 restraints weight = 38601.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.042476 restraints weight = 35062.932| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22394 Z= 0.116 Angle : 0.672 9.696 30492 Z= 0.348 Chirality : 0.044 0.230 3332 Planarity : 0.004 0.049 3870 Dihedral : 5.741 31.190 2914 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.38 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.16), residues: 2698 helix: -1.01 (0.13), residues: 1472 sheet: -2.11 (0.54), residues: 60 loop : -2.28 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 678 TYR 0.017 0.001 TYR D 180 PHE 0.019 0.001 PHE D 512 TRP 0.017 0.001 TRP C 56 HIS 0.003 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (22384) covalent geometry : angle 0.67061 / 0.35 (30472) SS BOND : bond 0.00576 / 0.38 ( 10) SS BOND : angle 1.57547 / 1.00 ( 20) hydrogen bonds : bond 0.03756 / 2.44 ( 749) hydrogen bonds : angle 5.32300 / 3.57 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.188 Fit side-chains REVERT: C 502 MET cc_start: 0.7506 (mmp) cc_final: 0.6898 (mmt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0647 time to fit residues: 3.2174 Evaluate side-chains 21 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.186 Evaluate side-chains 47 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 60 GLN cc_start: 0.9208 (tp-100) cc_final: 0.8892 (tp-100) REVERT: B 64 ASN cc_start: 0.9362 (m110) cc_final: 0.8926 (p0) REVERT: B 123 MET cc_start: 0.8741 (mmt) cc_final: 0.8538 (mmt) REVERT: B 270 MET cc_start: 0.8895 (tpp) cc_final: 0.8447 (tpp) REVERT: B 455 MET cc_start: 0.9388 (tmm) cc_final: 0.9016 (tmm) REVERT: B 462 MET cc_start: 0.9318 (mtm) cc_final: 0.9037 (ttm) REVERT: B 474 MET cc_start: 0.7741 (ttm) cc_final: 0.7325 (ttm) REVERT: B 640 MET cc_start: 0.9350 (mmm) cc_final: 0.8930 (mmm) REVERT: B 643 PHE cc_start: 0.9447 (t80) cc_final: 0.9150 (t80) REVERT: B 647 VAL cc_start: 0.9606 (t) cc_final: 0.9387 (p) REVERT: B 651 MET cc_start: 0.9392 (mmp) cc_final: 0.9130 (mmm) REVERT: B 655 PHE cc_start: 0.9070 (m-10) cc_final: 0.8524 (m-10) REVERT: B 662 MET cc_start: 0.8430 (tpp) cc_final: 0.7942 (tpt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0669 time to fit residues: 4.5640 Evaluate side-chains 42 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 146 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 73 optimal weight: 0.0670 chunk 36 optimal weight: 9.9990 chunk 246 optimal weight: 30.0000 chunk 118 optimal weight: 0.0170 chunk 40 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 250 optimal weight: 7.9990 overall best weight: 2.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 ASN B 690 ASN B 720 ASN C 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.039168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032701 restraints weight = 64388.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.033297 restraints weight = 47614.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.033759 restraints weight = 38159.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.034017 restraints weight = 32361.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034315 restraints weight = 29098.080| |-----------------------------------------------------------------------------| r_work (final): 0.3066 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.051504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.039043 restraints weight = 73274.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.040010 restraints weight = 56203.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.040717 restraints weight = 46175.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.041267 restraints weight = 39849.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.041634 restraints weight = 35655.141| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22394 Z= 0.127 Angle : 0.693 9.776 30492 Z= 0.358 Chirality : 0.045 0.227 3332 Planarity : 0.004 0.048 3870 Dihedral : 5.775 31.782 2914 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.23 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.27 (0.16), residues: 2698 helix: -0.86 (0.14), residues: 1460 sheet: -1.74 (0.59), residues: 60 loop : -2.30 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 621 TYR 0.016 0.001 TYR B 516 PHE 0.014 0.001 PHE B 512 TRP 0.014 0.001 TRP C 56 HIS 0.003 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (22384) covalent geometry : angle 0.69224 / 0.36 (30472) SS BOND : bond 0.00640 / 0.42 ( 10) SS BOND : angle 1.49935 / 1.00 ( 20) hydrogen bonds : bond 0.03803 / 2.49 ( 749) hydrogen bonds : angle 5.40588 / 3.62 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9532 (mtm) cc_final: 0.9070 (mtm) REVERT: A 423 MET cc_start: 0.8919 (mmm) cc_final: 0.8559 (mmt) REVERT: A 432 MET cc_start: 0.9503 (mmp) cc_final: 0.8933 (mmm) REVERT: A 488 TYR cc_start: 0.8074 (t80) cc_final: 0.7560 (t80) REVERT: A 542 MET cc_start: 0.8925 (ppp) cc_final: 0.8577 (ppp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0453 time to fit residues: 2.3334 Evaluate side-chains 22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.186 Evaluate side-chains 51 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: B 60 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8886 (tp-100) REVERT: B 64 ASN cc_start: 0.9287 (m110) cc_final: 0.8842 (p0) REVERT: B 455 MET cc_start: 0.9296 (tmm) cc_final: 0.8692 (ppp) REVERT: B 462 MET cc_start: 0.9303 (mtm) cc_final: 0.9092 (ttp) REVERT: B 640 MET cc_start: 0.9315 (mmm) cc_final: 0.8914 (mmm) REVERT: B 643 PHE cc_start: 0.9441 (t80) cc_final: 0.9226 (t80) REVERT: B 655 PHE cc_start: 0.9073 (m-10) cc_final: 0.8634 (m-10) REVERT: B 662 MET cc_start: 0.8439 (tpp) cc_final: 0.8209 (tpt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0603 time to fit residues: 4.5721 Evaluate side-chains 37 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 21 optimal weight: 7.9990 chunk 245 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 139 optimal weight: 0.0070 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 overall best weight: 3.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.039182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.032859 restraints weight = 65895.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.033462 restraints weight = 47904.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.033917 restraints weight = 38398.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034257 restraints weight = 32558.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034502 restraints weight = 28664.713| |-----------------------------------------------------------------------------| r_work (final): 0.2870 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.052070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.038466 restraints weight = 69030.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.039612 restraints weight = 51096.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.040446 restraints weight = 41100.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.041065 restraints weight = 34878.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.041422 restraints weight = 30810.890| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22394 Z= 0.134 Angle : 0.698 10.956 30492 Z= 0.361 Chirality : 0.045 0.209 3332 Planarity : 0.004 0.048 3870 Dihedral : 5.828 32.554 2914 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.97 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.18 (0.16), residues: 2698 helix: -0.80 (0.14), residues: 1460 sheet: -1.64 (0.61), residues: 60 loop : -2.24 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 621 TYR 0.022 0.002 TYR A 139 PHE 0.015 0.001 PHE C 403 TRP 0.034 0.001 TRP D 163 HIS 0.004 0.001 HIS B 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (22384) covalent geometry : angle 0.69670 / 0.36 (30472) SS BOND : bond 0.00860 / 0.56 ( 10) SS BOND : angle 1.54235 / 1.05 ( 20) hydrogen bonds : bond 0.03759 / 2.45 ( 749) hydrogen bonds : angle 5.38994 / 3.61 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.9678 (mtm) cc_final: 0.9230 (mtm) REVERT: A 231 TYR cc_start: 0.9377 (m-10) cc_final: 0.9017 (m-80) REVERT: A 423 MET cc_start: 0.8793 (mmm) cc_final: 0.8588 (mmt) REVERT: A 488 TYR cc_start: 0.8126 (t80) cc_final: 0.7641 (t80) REVERT: A 542 MET cc_start: 0.8969 (ppp) cc_final: 0.8706 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0531 time to fit residues: 2.3745 Evaluate side-chains 21 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.197 Evaluate side-chains 48 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8825 (mmp) cc_final: 0.8266 (mmm) REVERT: B 270 MET cc_start: 0.9378 (tpt) cc_final: 0.9040 (tpp) REVERT: B 462 MET cc_start: 0.9289 (mtm) cc_final: 0.9055 (ttm) REVERT: B 474 MET cc_start: 0.8025 (ttm) cc_final: 0.7772 (ttm) REVERT: B 643 PHE cc_start: 0.9578 (t80) cc_final: 0.9261 (t80) REVERT: B 655 PHE cc_start: 0.9115 (m-10) cc_final: 0.8726 (m-10) REVERT: B 662 MET cc_start: 0.8586 (tpp) cc_final: 0.8374 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0629 time to fit residues: 4.4397 Evaluate side-chains 40 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 51 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 212 optimal weight: 0.0050 chunk 241 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 120 optimal weight: 0.2980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.032054 restraints weight = 64977.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033084 restraints weight = 38512.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.033875 restraints weight = 26988.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.034413 restraints weight = 20868.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.034673 restraints weight = 17225.574| |-----------------------------------------------------------------------------| r_work (final): 0.2930 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.053531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.040563 restraints weight = 72037.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.041623 restraints weight = 55160.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.042408 restraints weight = 45130.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.043004 restraints weight = 38824.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.043383 restraints weight = 34556.722| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22394 Z= 0.122 Angle : 0.685 10.480 30492 Z= 0.352 Chirality : 0.045 0.196 3332 Planarity : 0.004 0.052 3870 Dihedral : 5.629 31.922 2914 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.23 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.13 (0.16), residues: 2698 helix: -0.77 (0.14), residues: 1476 sheet: -1.48 (0.62), residues: 60 loop : -2.22 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 621 TYR 0.020 0.001 TYR A 139 PHE 0.023 0.001 PHE C 514 TRP 0.020 0.001 TRP D 163 HIS 0.004 0.001 HIS B 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (22384) covalent geometry : angle 0.68367 / 0.35 (30472) SS BOND : bond 0.00602 / 0.41 ( 10) SS BOND : angle 1.55251 / 1.06 ( 20) hydrogen bonds : bond 0.03731 / 2.41 ( 749) hydrogen bonds : angle 5.25943 / 3.52 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.8937 (mtm) cc_final: 0.8696 (mtm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0513 time to fit residues: 2.3666 Evaluate side-chains 22 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.229 Evaluate side-chains 51 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8817 (mmp) cc_final: 0.8376 (mmm) REVERT: B 474 MET cc_start: 0.8021 (ttm) cc_final: 0.7780 (ttm) REVERT: B 640 MET cc_start: 0.9359 (mmm) cc_final: 0.8952 (mmm) REVERT: B 643 PHE cc_start: 0.9470 (t80) cc_final: 0.9156 (t80) REVERT: B 655 PHE cc_start: 0.9042 (m-10) cc_final: 0.8622 (m-10) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0697 time to fit residues: 5.1485 Evaluate side-chains 40 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 99 optimal weight: 0.0050 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 134 optimal weight: 50.0000 chunk 177 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.041955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034398 restraints weight = 64892.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035080 restraints weight = 47236.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035583 restraints weight = 37897.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035952 restraints weight = 32041.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036231 restraints weight = 28151.614| |-----------------------------------------------------------------------------| r_work (final): 0.3035 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.052782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.040118 restraints weight = 73240.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.041117 restraints weight = 56125.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.041889 restraints weight = 46061.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.042487 restraints weight = 39624.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.042880 restraints weight = 35268.248| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22394 Z= 0.121 Angle : 0.680 10.139 30492 Z= 0.350 Chirality : 0.045 0.187 3332 Planarity : 0.004 0.050 3870 Dihedral : 5.621 31.861 2914 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.15 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.10 (0.16), residues: 2698 helix: -0.76 (0.14), residues: 1484 sheet: -1.52 (0.61), residues: 60 loop : -2.19 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 621 TYR 0.016 0.001 TYR D 516 PHE 0.014 0.001 PHE D 512 TRP 0.021 0.001 TRP D 163 HIS 0.004 0.001 HIS B 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22384) covalent geometry : angle 0.67858 / 0.35 (30472) SS BOND : bond 0.00564 / 0.38 ( 10) SS BOND : angle 1.62854 / 1.13 ( 20) hydrogen bonds : bond 0.03643 / 2.42 ( 749) hydrogen bonds : angle 5.23156 / 3.50 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.60 seconds wall clock time: 43 minutes 8.68 seconds (2588.68 seconds total)