Starting phenix.real_space_refine on Sun Sep 13 05:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6e2g_8962/09_2026/6e2g_8962.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e2g_8962/09_2026/6e2g_8962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6e2g_8962/09_2026/6e2g_8962.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6e2g_8962/09_2026/6e2g_8962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e2g_8962/09_2026/6e2g_8962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e2g_8962/09_2026/6e2g_8962.map" model { file = "/net/cci-nas-00/data/ceres_data/6e2g_8962/09_2026/6e2g_8962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e2g_8962/09_2026/6e2g_8962.cif" } resolution = 3.6 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= 0.006 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 149 5.16 5 C 13616 2.51 5 N 3553 2.21 5 O 3784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s 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: 21108 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4885 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 25, 'TRANS': 585} Chain: "B" Number of atoms: 4979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4979 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 25, 'TRANS': 595} Chain: "C" Number of atoms: 5172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5172 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 25, 'TRANS': 618} Chain breaks: 1 Chain: "D" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4901 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 25, 'TRANS': 587} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.93, per 1000 atoms: 0.23 Number of scatterers: 21108 At special positions: 0 Unit cell: (133.56, 130.38, 131.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 149 16.00 O 3784 8.00 N 3553 7.00 C 13616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 890.2 milliseconds 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4946 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 8 sheets defined 58.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 4.470A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.753A pdb=" N LEU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.545A pdb=" N TYR A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.653A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.738A pdb=" N PHE A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.094A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.595A pdb=" N PHE A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.871A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.565A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.823A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.564A pdb=" N VAL A 234 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.533A pdb=" N MET A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 4.238A pdb=" N VAL A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.597A pdb=" N ARG A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 308 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.693A pdb=" N TRP A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 347 removed outlier: 3.544A pdb=" N PHE A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.779A pdb=" N GLY A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.004A pdb=" N ILE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 442 removed outlier: 3.922A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.691A pdb=" N PHE A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.731A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 removed outlier: 3.647A pdb=" N VAL A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.548A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.555A pdb=" N THR A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 569 removed outlier: 4.078A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 582 removed outlier: 4.279A pdb=" N ALA A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 removed outlier: 3.605A pdb=" N LEU A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.719A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.978A pdb=" N LEU B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.873A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.203A pdb=" N PHE B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 4.240A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.824A pdb=" N ALA B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.763A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.533A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.992A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.819A pdb=" N GLY B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.770A pdb=" N VAL B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.905A pdb=" N ALA B 303 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 305 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 307 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 4.030A pdb=" N TRP B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.555A pdb=" N TYR B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 403 removed outlier: 3.774A pdb=" N VAL B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.578A pdb=" N ARG B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 442 removed outlier: 3.634A pdb=" N ILE B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.594A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.748A pdb=" N GLY B 470 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.813A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 removed outlier: 4.184A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 537 removed outlier: 3.584A pdb=" N LEU B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.859A pdb=" N SER B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 556 " --> pdb=" O PHE B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.113A pdb=" N ALA B 575 " --> pdb=" O ASN B 571 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 605 removed outlier: 3.557A pdb=" N ARG B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 3.832A pdb=" N ILE B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.701A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.807A pdb=" N LEU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.518A pdb=" N LEU C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.520A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.673A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.818A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.590A pdb=" N ALA C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.584A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.608A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.504A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 204' Processing helix chain 'C' and resid 211 through 223 removed outlier: 4.151A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.792A pdb=" N GLY C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.556A pdb=" N GLN C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.894A pdb=" N VAL C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 4.290A pdb=" N GLN C 305 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 307 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 removed outlier: 3.734A pdb=" N TRP C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 347 removed outlier: 3.631A pdb=" N TYR C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 407 removed outlier: 3.568A pdb=" N LEU C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix removed outlier: 3.877A pdb=" N PHE C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 Processing helix chain 'C' and resid 426 through 442 removed outlier: 4.164A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 438 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.517A pdb=" N VAL C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 removed outlier: 3.592A pdb=" N TYR C 466 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 489 removed outlier: 3.801A pdb=" N THR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY C 487 " --> pdb=" O LYS C 483 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 511 removed outlier: 4.914A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 498 " --> pdb=" O TRP C 494 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 524 through 534 removed outlier: 4.381A pdb=" N PHE C 530 " --> pdb=" O PRO C 526 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 566 removed outlier: 3.978A pdb=" N SER C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 556 " --> pdb=" O PHE C 552 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 582 removed outlier: 4.126A pdb=" N ALA C 575 " --> pdb=" O ASN C 571 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP C 582 " --> pdb=" O GLY C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.535A pdb=" N LEU C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 651 removed outlier: 3.654A pdb=" N ALA C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 705 removed outlier: 3.658A pdb=" N ASN C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 3.684A pdb=" N SER D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.649A pdb=" N LEU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.647A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.516A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 removed outlier: 3.530A pdb=" N ALA D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.517A pdb=" N ALA D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.548A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.832A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 221 removed outlier: 3.763A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.745A pdb=" N GLY D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 removed outlier: 3.550A pdb=" N GLN D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.759A pdb=" N VAL D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.888A pdb=" N ARG D 304 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 305 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE D 306 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 307 " --> pdb=" O ARG D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.802A pdb=" N LEU D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 345 removed outlier: 3.721A pdb=" N TYR D 327 " --> pdb=" O TYR D 323 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 407 removed outlier: 3.524A pdb=" N VAL D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 396 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'D' and resid 422 through 425 removed outlier: 3.559A pdb=" N HIS D 425 " --> pdb=" O GLY D 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 422 through 425' Processing helix chain 'D' and resid 426 through 442 removed outlier: 3.635A pdb=" N THR D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 437 " --> pdb=" O PHE D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 461 removed outlier: 4.107A pdb=" N MET D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 474 through 486 removed outlier: 3.805A pdb=" N THR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET D 480 " --> pdb=" O PRO D 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 511 removed outlier: 4.016A pdb=" N VAL D 498 " --> pdb=" O TRP D 494 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 510 " --> pdb=" O ALA D 506 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 511 " --> pdb=" O PHE D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 537 removed outlier: 4.064A pdb=" N PHE D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D 534 " --> pdb=" O PHE D 530 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 537 " --> pdb=" O PHE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 567 removed outlier: 4.155A pdb=" N SER D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE D 556 " --> pdb=" O PHE D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 583 removed outlier: 4.483A pdb=" N ALA D 575 " --> pdb=" O ASN D 571 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP D 582 " --> pdb=" O GLY D 578 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 605 removed outlier: 3.948A pdb=" N ARG D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 603 " --> pdb=" O THR D 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.621A pdb=" N ILE E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU E 11 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.918A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.581A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.731A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.875A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.527A pdb=" N ARG E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 removed outlier: 3.608A pdb=" N ASP E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.727A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 269 removed outlier: 7.295A pdb=" N SER A 274 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR A 268 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 269 removed outlier: 6.916A pdb=" N SER B 274 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR B 268 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 353 Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 269 removed outlier: 5.065A pdb=" N ILE C 265 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 276 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 267 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 351 through 352 Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 269 removed outlier: 6.956A pdb=" N SER D 274 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR D 268 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 273 " --> pdb=" O ASP D 634 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 630 " --> pdb=" O TYR D 277 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 351 through 353 795 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6165 1.33 - 1.45: 3815 1.45 - 1.57: 11336 1.57 - 1.69: 0 1.69 - 1.81: 254 Bond restraints: 21570 Sorted by residual: bond pdb=" C LYS A 606 " pdb=" N LEU A 607 " ideal model delta sigma weight residual 1.331 1.230 0.101 2.83e-02 1.25e+03 1.28e+01 bond pdb=" C GLU A 164 " pdb=" N HIS A 165 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.83e-02 1.25e+03 9.31e+00 bond pdb=" C ILE A 403 " pdb=" N PRO A 404 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.39e+00 bond pdb=" CB ARG D 469 " pdb=" CG ARG D 469 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.72e+00 bond pdb=" C VAL D 451 " pdb=" N PRO D 452 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.20e-02 6.94e+03 4.44e+00 ... (remaining 21565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 28522 3.27 - 6.54: 638 6.54 - 9.82: 75 9.82 - 13.09: 19 13.09 - 16.36: 8 Bond angle restraints: 29262 Sorted by residual: angle pdb=" C ASP B 637 " pdb=" N LEU B 638 " pdb=" CA LEU B 638 " ideal model delta sigma weight residual 121.54 134.79 -13.25 1.91e+00 2.74e-01 4.81e+01 angle pdb=" C LYS C 209 " pdb=" N THR C 210 " pdb=" CA THR C 210 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" C PHE A 211 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" N PHE D 211 " pdb=" CA PHE D 211 " pdb=" C PHE D 211 " ideal model delta sigma weight residual 114.75 108.24 6.51 1.26e+00 6.30e-01 2.67e+01 angle pdb=" N THR B 310 " pdb=" CA THR B 310 " pdb=" C THR B 310 " ideal model delta sigma weight residual 109.81 121.13 -11.32 2.21e+00 2.05e-01 2.62e+01 ... (remaining 29257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 11986 17.49 - 34.99: 719 34.99 - 52.48: 141 52.48 - 69.97: 11 69.97 - 87.47: 12 Dihedral angle restraints: 12869 sinusoidal: 5192 harmonic: 7677 Sorted by residual: dihedral pdb=" CA GLY B 286 " pdb=" C GLY B 286 " pdb=" N ASP B 287 " pdb=" CA ASP B 287 " ideal model delta harmonic sigma weight residual 180.00 -131.18 -48.82 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" CA ARG C 362 " pdb=" C ARG C 362 " pdb=" N ASP C 363 " pdb=" CA ASP C 363 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.25e+01 dihedral pdb=" CA LYS C 209 " pdb=" C LYS C 209 " pdb=" N THR C 210 " pdb=" CA THR C 210 " ideal model delta harmonic sigma weight residual 180.00 141.98 38.02 0 5.00e+00 4.00e-02 5.78e+01 ... (remaining 12866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2713 0.079 - 0.157: 539 0.157 - 0.235: 58 0.235 - 0.314: 10 0.314 - 0.392: 1 Chirality restraints: 3321 Sorted by residual: chirality pdb=" CB ILE E 100 " pdb=" CA ILE E 100 " pdb=" CG1 ILE E 100 " pdb=" CG2 ILE E 100 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA THR B 310 " pdb=" N THR B 310 " pdb=" C THR B 310 " pdb=" CB THR B 310 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE A 355 " pdb=" CA ILE A 355 " pdb=" CG1 ILE A 355 " pdb=" CG2 ILE A 355 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3318 not shown) Planarity restraints: 3721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 286 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLY B 286 " 0.067 2.00e-02 2.50e+03 pdb=" O GLY B 286 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B 287 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 612 " -0.021 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP C 612 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 612 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 612 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 612 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 612 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 612 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 612 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 612 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 612 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 403 " 0.048 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO D 404 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " 0.040 5.00e-02 4.00e+02 ... (remaining 3718 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5219 2.78 - 3.31: 19522 3.31 - 3.84: 33101 3.84 - 4.37: 38798 4.37 - 4.90: 64150 Nonbonded interactions: 160790 Sorted by model distance: nonbonded pdb=" OG SER D 505 " pdb=" OH TYR D 525 " model vdw 2.249 3.040 nonbonded pdb=" O VAL B 151 " pdb=" ND2 ASN B 158 " model vdw 2.270 3.120 nonbonded pdb=" NH1 ARG B 469 " pdb=" OE1 GLN B 595 " model vdw 2.283 3.120 nonbonded pdb=" O VAL A 440 " pdb=" OG1 THR A 444 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASP A 34 " pdb=" NH1 ARG D 631 " model vdw 2.298 3.120 ... (remaining 160785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 637) selection = (chain 'B' and resid 27 through 637) selection = (chain 'C' and resid 27 through 637) selection = (chain 'D' and resid 27 through 637) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.680 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.010 0.106 21570 Z= 0.426 Angle : 1.212 16.361 29262 Z= 0.629 Chirality : 0.064 0.392 3321 Planarity : 0.007 0.071 3721 Dihedral : 11.958 87.467 7923 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.38 % Favored : 87.20 % Rotamer: Outliers : 1.05 % Allowed : 7.42 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -5.78 (0.12), residues: 2625 helix: -4.05 (0.07), residues: 1393 sheet: -1.74 (0.61), residues: 80 loop : -3.60 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 631 TYR 0.028 0.003 TYR D 523 PHE 0.026 0.004 PHE B 552 TRP 0.055 0.004 TRP C 612 HIS 0.013 0.002 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00973 / 0.43 (21570) covalent geometry : angle 1.21228 / 0.63 (29262) hydrogen bonds : bond 0.32427 / 21.05 ( 795) hydrogen bonds : angle 9.54556 / 6.61 ( 2268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 497 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8572 (mtm) cc_final: 0.8135 (mtm) REVERT: A 219 LEU cc_start: 0.9388 (mm) cc_final: 0.8976 (mp) REVERT: A 278 ASP cc_start: 0.8132 (t0) cc_final: 0.7884 (t0) REVERT: A 289 GLN cc_start: 0.8727 (mt0) cc_final: 0.8378 (pm20) REVERT: A 344 MET cc_start: 0.8057 (mtt) cc_final: 0.7651 (mmp) REVERT: A 455 PHE cc_start: 0.8619 (m-10) cc_final: 0.8080 (m-80) REVERT: A 484 MET cc_start: 0.7996 (mmt) cc_final: 0.7665 (mmt) REVERT: A 494 TRP cc_start: 0.8442 (m100) cc_final: 0.8094 (m100) REVERT: A 590 GLU cc_start: 0.8101 (tp30) cc_final: 0.7676 (tp30) REVERT: B 301 ARG cc_start: 0.8697 (ttt-90) cc_final: 0.8428 (tpt90) REVERT: B 434 MET cc_start: 0.8979 (mmt) cc_final: 0.8123 (mmm) REVERT: B 484 MET cc_start: 0.8600 (mmt) cc_final: 0.8170 (mmt) REVERT: B 547 ASP cc_start: 0.8488 (m-30) cc_final: 0.8203 (t0) REVERT: B 572 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8823 (tm) REVERT: B 602 MET cc_start: 0.8261 (tmm) cc_final: 0.7941 (tmm) REVERT: B 641 GLN cc_start: 0.8701 (tt0) cc_final: 0.8181 (tm-30) REVERT: C 110 MET cc_start: 0.9287 (mtt) cc_final: 0.9006 (mtp) REVERT: C 113 GLU cc_start: 0.9133 (tp30) cc_final: 0.8907 (tm-30) REVERT: C 237 ASN cc_start: 0.8894 (t160) cc_final: 0.8638 (m110) REVERT: C 281 GLU cc_start: 0.8170 (tp30) cc_final: 0.7959 (tm-30) REVERT: C 283 ASP cc_start: 0.7737 (t0) cc_final: 0.6907 (t0) REVERT: C 300 LYS cc_start: 0.9027 (mtpm) cc_final: 0.8816 (ttmt) REVERT: C 301 ARG cc_start: 0.8131 (ttt-90) cc_final: 0.7814 (tpt90) REVERT: C 441 MET cc_start: 0.8828 (mmt) cc_final: 0.8544 (mmm) REVERT: C 473 MET cc_start: 0.8696 (ttt) cc_final: 0.7632 (ptp) REVERT: C 576 MET cc_start: 0.9221 (tpt) cc_final: 0.8758 (tpp) REVERT: C 595 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8456 (mm-40) REVERT: D 78 MET cc_start: 0.8740 (mpt) cc_final: 0.8053 (mpt) REVERT: D 176 GLU cc_start: 0.8588 (pt0) cc_final: 0.8375 (pp20) REVERT: D 233 LEU cc_start: 0.8796 (mm) cc_final: 0.8450 (mp) REVERT: D 293 GLU cc_start: 0.8929 (tp30) cc_final: 0.8541 (tp30) REVERT: D 301 ARG cc_start: 0.8987 (tpp-160) cc_final: 0.8724 (tpp80) REVERT: D 322 ARG cc_start: 0.9025 (mtm180) cc_final: 0.8337 (tpt170) REVERT: D 389 LEU cc_start: 0.9471 (mm) cc_final: 0.9157 (mm) REVERT: E 14 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8533 (mm-30) REVERT: E 34 THR cc_start: 0.7952 (p) cc_final: 0.7714 (t) REVERT: E 39 LEU cc_start: 0.8842 (tt) cc_final: 0.8580 (tt) REVERT: E 77 LYS cc_start: 0.6736 (mmpt) cc_final: 0.5907 (mmtt) REVERT: E 144 MET cc_start: 0.8332 (mmm) cc_final: 0.8037 (mmt) outliers start: 24 outliers final: 7 residues processed: 516 average time/residue: 0.1624 time to fit residues: 127.0907 Evaluate side-chains 300 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 292 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 74 GLN A 217 ASN A 237 ASN A 251 ASN A 364 ASN A 571 ASN ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS B 237 ASN B 251 ASN B 364 ASN B 368 GLN B 581 HIS B 586 HIS C 37 ASN C 118 GLN C 237 ASN C 251 ASN C 256 GLN C 309 GLN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS C 641 GLN D 74 GLN D 118 GLN D 237 ASN D 251 ASN D 445 ASN D 482 GLN D 571 ASN D 581 HIS E 8 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.112384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091236 restraints weight = 49341.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094287 restraints weight = 22645.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096300 restraints weight = 13697.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097602 restraints weight = 9828.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098432 restraints weight = 7912.638| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21570 Z= 0.153 Angle : 0.772 16.772 29262 Z= 0.390 Chirality : 0.044 0.203 3321 Planarity : 0.005 0.051 3721 Dihedral : 6.861 53.016 2893 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.10 % Favored : 89.75 % Rotamer: Outliers : 3.16 % Allowed : 12.51 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.92 (0.14), residues: 2625 helix: -2.15 (0.11), residues: 1439 sheet: -1.64 (0.57), residues: 85 loop : -3.24 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 349 TYR 0.016 0.001 TYR C 216 PHE 0.024 0.002 PHE E 65 TRP 0.025 0.002 TRP C 612 HIS 0.010 0.001 HIS C 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21570) covalent geometry : angle 0.77182 / 0.39 (29262) hydrogen bonds : bond 0.04836 / 3.13 ( 795) hydrogen bonds : angle 4.94482 / 3.43 ( 2268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 372 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.7890 (t80) cc_final: 0.7433 (t80) REVERT: A 275 THR cc_start: 0.9023 (m) cc_final: 0.8712 (p) REVERT: A 278 ASP cc_start: 0.8137 (t0) cc_final: 0.7277 (t0) REVERT: A 344 MET cc_start: 0.8135 (mtt) cc_final: 0.7647 (mmt) REVERT: A 388 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8018 (tt0) REVERT: A 473 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8285 (ppp) REVERT: A 500 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 576 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8071 (ttt) REVERT: B 96 MET cc_start: 0.8385 (tmm) cc_final: 0.8079 (tmm) REVERT: B 110 MET cc_start: 0.9033 (mtp) cc_final: 0.8647 (mtp) REVERT: B 479 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8956 (mp) REVERT: B 490 MET cc_start: 0.7893 (mmm) cc_final: 0.7655 (mmm) REVERT: B 547 ASP cc_start: 0.8184 (m-30) cc_final: 0.7982 (t0) REVERT: B 590 GLU cc_start: 0.8653 (tp30) cc_final: 0.8253 (tp30) REVERT: B 595 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8288 (mm-40) REVERT: B 602 MET cc_start: 0.8287 (tmm) cc_final: 0.8002 (tmm) REVERT: B 611 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8623 (pp) REVERT: B 641 GLN cc_start: 0.8496 (tt0) cc_final: 0.8191 (tp40) REVERT: C 215 MET cc_start: 0.8459 (tpp) cc_final: 0.8236 (tpp) REVERT: C 237 ASN cc_start: 0.8832 (t0) cc_final: 0.8587 (m110) REVERT: C 283 ASP cc_start: 0.7485 (t0) cc_final: 0.6678 (t0) REVERT: C 288 ASP cc_start: 0.8258 (m-30) cc_final: 0.8005 (t0) REVERT: C 304 ARG cc_start: 0.8663 (ttp-170) cc_final: 0.8340 (mtp-110) REVERT: C 473 MET cc_start: 0.8702 (ttt) cc_final: 0.7612 (ptp) REVERT: C 576 MET cc_start: 0.8995 (tpt) cc_final: 0.8665 (tpp) REVERT: C 589 ASP cc_start: 0.8441 (m-30) cc_final: 0.8200 (p0) REVERT: D 78 MET cc_start: 0.8701 (mpt) cc_final: 0.7979 (mpt) REVERT: D 99 MET cc_start: 0.9011 (mtm) cc_final: 0.8545 (mtm) REVERT: D 293 GLU cc_start: 0.8835 (tp30) cc_final: 0.8563 (tp30) REVERT: D 308 ASP cc_start: 0.8223 (m-30) cc_final: 0.7919 (m-30) REVERT: D 315 LEU cc_start: 0.9129 (mp) cc_final: 0.8811 (mp) REVERT: D 322 ARG cc_start: 0.8893 (mtm180) cc_final: 0.8423 (tpt170) REVERT: D 482 GLN cc_start: 0.8680 (tm-30) cc_final: 0.7782 (mm-40) REVERT: D 571 ASN cc_start: 0.8940 (m-40) cc_final: 0.8636 (m110) REVERT: E 34 THR cc_start: 0.7966 (p) cc_final: 0.7684 (t) REVERT: E 49 GLN cc_start: 0.7501 (pm20) cc_final: 0.7255 (pm20) REVERT: E 51 MET cc_start: 0.8841 (ttm) cc_final: 0.8152 (ttm) REVERT: E 144 MET cc_start: 0.8231 (mmm) cc_final: 0.7841 (mmm) outliers start: 72 outliers final: 33 residues processed: 426 average time/residue: 0.1382 time to fit residues: 93.5853 Evaluate side-chains 324 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 247 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 184 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 586 HIS C 463 ASN C 482 GLN ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN E 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.114898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093045 restraints weight = 53855.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096056 restraints weight = 25135.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.098016 restraints weight = 15386.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099301 restraints weight = 11174.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.100093 restraints weight = 9081.389| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21570 Z= 0.155 Angle : 0.729 16.582 29262 Z= 0.362 Chirality : 0.043 0.202 3321 Planarity : 0.004 0.045 3721 Dihedral : 6.228 49.875 2890 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.63 % Favored : 89.26 % Rotamer: Outliers : 3.38 % Allowed : 14.97 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.91 (0.15), residues: 2625 helix: -1.10 (0.13), residues: 1450 sheet: -1.46 (0.57), residues: 83 loop : -3.12 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 37 TYR 0.018 0.001 TYR B 338 PHE 0.015 0.001 PHE D 67 TRP 0.041 0.001 TRP B 612 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (21570) covalent geometry : angle 0.72895 / 0.36 (29262) hydrogen bonds : bond 0.04144 / 2.69 ( 795) hydrogen bonds : angle 4.47607 / 3.10 ( 2268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 269 TYR cc_start: 0.8048 (t80) cc_final: 0.7528 (t80) REVERT: A 275 THR cc_start: 0.9025 (m) cc_final: 0.8726 (p) REVERT: A 344 MET cc_start: 0.7977 (mtt) cc_final: 0.7657 (mmt) REVERT: A 453 MET cc_start: 0.8202 (ttm) cc_final: 0.7905 (ttm) REVERT: A 473 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8442 (ppp) REVERT: A 500 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8941 (tt) REVERT: A 576 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8269 (ttt) REVERT: A 633 GLU cc_start: 0.8488 (pm20) cc_final: 0.7921 (pt0) REVERT: B 96 MET cc_start: 0.8402 (tmm) cc_final: 0.8107 (tmm) REVERT: B 110 MET cc_start: 0.8931 (mtp) cc_final: 0.8584 (mtp) REVERT: B 259 MET cc_start: 0.8953 (tpp) cc_final: 0.8536 (tpp) REVERT: B 275 THR cc_start: 0.8832 (m) cc_final: 0.8387 (p) REVERT: B 399 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9011 (mm) REVERT: B 590 GLU cc_start: 0.8633 (tp30) cc_final: 0.8217 (tp30) REVERT: B 634 ASP cc_start: 0.8316 (m-30) cc_final: 0.7721 (p0) REVERT: B 641 GLN cc_start: 0.8493 (tt0) cc_final: 0.8230 (tp40) REVERT: C 283 ASP cc_start: 0.7487 (t0) cc_final: 0.6824 (t0) REVERT: C 289 GLN cc_start: 0.8898 (mt0) cc_final: 0.8660 (mt0) REVERT: C 331 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8830 (mm) REVERT: C 473 MET cc_start: 0.8681 (ttt) cc_final: 0.7681 (ptp) REVERT: C 579 ASP cc_start: 0.8734 (t0) cc_final: 0.8533 (t0) REVERT: D 78 MET cc_start: 0.8630 (mpt) cc_final: 0.8092 (mpp) REVERT: D 308 ASP cc_start: 0.8314 (m-30) cc_final: 0.7997 (m-30) REVERT: D 322 ARG cc_start: 0.8906 (mtm180) cc_final: 0.8437 (tpt170) REVERT: D 602 MET cc_start: 0.7918 (ppp) cc_final: 0.7669 (ppp) REVERT: E 8 GLN cc_start: 0.8137 (mt0) cc_final: 0.7915 (mt0) REVERT: E 49 GLN cc_start: 0.7470 (pm20) cc_final: 0.7211 (pm20) REVERT: E 84 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7884 (tm-30) REVERT: E 144 MET cc_start: 0.8244 (mmm) cc_final: 0.7978 (mmm) outliers start: 77 outliers final: 44 residues processed: 368 average time/residue: 0.1395 time to fit residues: 82.3975 Evaluate side-chains 320 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 78 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 HIS B 586 HIS C 238 GLN C 425 HIS ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS C 651 GLN D 122 HIS D 256 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.116324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095144 restraints weight = 52854.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098222 restraints weight = 24441.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100206 restraints weight = 14844.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.101508 restraints weight = 10666.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.102250 restraints weight = 8595.027| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21570 Z= 0.115 Angle : 0.679 14.975 29262 Z= 0.337 Chirality : 0.042 0.195 3321 Planarity : 0.003 0.040 3721 Dihedral : 5.654 50.923 2886 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.33 % Favored : 90.55 % Rotamer: Outliers : 3.29 % Allowed : 16.42 % Favored : 80.29 % 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: -2.31 (0.16), residues: 2625 helix: -0.52 (0.13), residues: 1454 sheet: -1.28 (0.58), residues: 83 loop : -3.01 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 469 TYR 0.015 0.001 TYR D 269 PHE 0.016 0.001 PHE B 530 TRP 0.033 0.001 TRP B 612 HIS 0.006 0.001 HIS C 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (21570) covalent geometry : angle 0.67931 / 0.34 (29262) hydrogen bonds : bond 0.03415 / 2.20 ( 795) hydrogen bonds : angle 4.13356 / 2.87 ( 2268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 316 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 269 TYR cc_start: 0.7998 (t80) cc_final: 0.7563 (t80) REVERT: A 275 THR cc_start: 0.8986 (m) cc_final: 0.8780 (p) REVERT: A 299 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8612 (mmtt) REVERT: A 453 MET cc_start: 0.8193 (ttm) cc_final: 0.7873 (ttm) REVERT: A 500 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8916 (tt) REVERT: A 501 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8451 (mm) REVERT: A 576 MET cc_start: 0.8867 (mmm) cc_final: 0.8646 (ttt) REVERT: A 602 MET cc_start: 0.8362 (tmm) cc_final: 0.8152 (tmm) REVERT: B 96 MET cc_start: 0.8480 (tmm) cc_final: 0.8220 (tmm) REVERT: B 110 MET cc_start: 0.8865 (mtp) cc_final: 0.8561 (mtp) REVERT: B 259 MET cc_start: 0.8949 (tpp) cc_final: 0.8542 (tpp) REVERT: B 275 THR cc_start: 0.8700 (m) cc_final: 0.8346 (p) REVERT: B 399 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8988 (mm) REVERT: B 434 MET cc_start: 0.9040 (mmt) cc_final: 0.8188 (mmm) REVERT: B 590 GLU cc_start: 0.8554 (tp30) cc_final: 0.8342 (tp30) REVERT: B 593 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8113 (mtm-85) REVERT: B 634 ASP cc_start: 0.8276 (m-30) cc_final: 0.7630 (p0) REVERT: B 641 GLN cc_start: 0.8435 (tt0) cc_final: 0.8138 (tp40) REVERT: C 283 ASP cc_start: 0.7478 (t0) cc_final: 0.6948 (t0) REVERT: C 302 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7875 (mm-30) REVERT: C 473 MET cc_start: 0.8708 (ttt) cc_final: 0.7680 (ptp) REVERT: C 576 MET cc_start: 0.8785 (tpp) cc_final: 0.8486 (tpp) REVERT: C 586 HIS cc_start: 0.7284 (t70) cc_final: 0.7063 (t-170) REVERT: D 78 MET cc_start: 0.8546 (mpt) cc_final: 0.8111 (mpp) REVERT: D 96 MET cc_start: 0.9319 (mtm) cc_final: 0.9088 (mtm) REVERT: D 99 MET cc_start: 0.8919 (mtm) cc_final: 0.8224 (mtm) REVERT: D 293 GLU cc_start: 0.8998 (tp30) cc_final: 0.8506 (tp30) REVERT: D 308 ASP cc_start: 0.8359 (m-30) cc_final: 0.8051 (m-30) REVERT: D 322 ARG cc_start: 0.8901 (mtm180) cc_final: 0.8422 (tpt170) REVERT: D 391 SER cc_start: 0.9306 (t) cc_final: 0.8905 (p) REVERT: D 576 MET cc_start: 0.8632 (ttm) cc_final: 0.8394 (ttt) REVERT: D 602 MET cc_start: 0.7995 (ppp) cc_final: 0.7750 (ppp) REVERT: E 49 GLN cc_start: 0.7530 (pm20) cc_final: 0.7239 (pm20) REVERT: E 84 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8110 (tm-30) REVERT: E 123 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8743 (mm-30) REVERT: E 144 MET cc_start: 0.8298 (mmm) cc_final: 0.7856 (mmm) outliers start: 75 outliers final: 38 residues processed: 373 average time/residue: 0.1415 time to fit residues: 84.7887 Evaluate side-chains 316 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 64 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 153 optimal weight: 0.3980 chunk 246 optimal weight: 0.0470 chunk 258 optimal weight: 0.3980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS C 238 GLN ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN D 463 ASN D 512 GLN E 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.114947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093163 restraints weight = 52632.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096258 restraints weight = 24576.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098279 restraints weight = 15054.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099576 restraints weight = 10891.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.100333 restraints weight = 8840.472| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21570 Z= 0.111 Angle : 0.675 16.081 29262 Z= 0.329 Chirality : 0.041 0.187 3321 Planarity : 0.003 0.036 3721 Dihedral : 5.394 52.245 2886 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.60 % Favored : 90.29 % Rotamer: Outliers : 2.81 % Allowed : 17.43 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.16), residues: 2625 helix: -0.20 (0.14), residues: 1453 sheet: -1.07 (0.58), residues: 83 loop : -2.92 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 469 TYR 0.015 0.001 TYR C 466 PHE 0.016 0.001 PHE E 65 TRP 0.032 0.001 TRP B 612 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (21570) covalent geometry : angle 0.67452 / 0.33 (29262) hydrogen bonds : bond 0.03283 / 2.12 ( 795) hydrogen bonds : angle 4.02380 / 2.80 ( 2268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7962 (mmm) REVERT: A 269 TYR cc_start: 0.8038 (t80) cc_final: 0.7539 (t80) REVERT: A 275 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8768 (p) REVERT: A 299 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8591 (mmtt) REVERT: A 453 MET cc_start: 0.8210 (ttm) cc_final: 0.7996 (ttm) REVERT: A 500 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8921 (tt) REVERT: A 501 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 569 MET cc_start: 0.8876 (mmt) cc_final: 0.8667 (mmt) REVERT: A 602 MET cc_start: 0.8312 (tmm) cc_final: 0.8096 (tmm) REVERT: B 96 MET cc_start: 0.8451 (tmm) cc_final: 0.8246 (tmm) REVERT: B 259 MET cc_start: 0.8848 (tpp) cc_final: 0.8474 (tpp) REVERT: B 275 THR cc_start: 0.8783 (m) cc_final: 0.8441 (p) REVERT: B 399 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8978 (mm) REVERT: B 434 MET cc_start: 0.9018 (mmt) cc_final: 0.8195 (mmm) REVERT: B 634 ASP cc_start: 0.8204 (m-30) cc_final: 0.7577 (p0) REVERT: B 641 GLN cc_start: 0.8348 (tt0) cc_final: 0.8073 (tp40) REVERT: C 283 ASP cc_start: 0.7273 (t0) cc_final: 0.6847 (t0) REVERT: C 473 MET cc_start: 0.8683 (ttt) cc_final: 0.7737 (ptp) REVERT: C 576 MET cc_start: 0.8706 (tpp) cc_final: 0.8396 (tpp) REVERT: C 586 HIS cc_start: 0.7112 (t70) cc_final: 0.6823 (t70) REVERT: D 40 GLN cc_start: 0.9159 (tt0) cc_final: 0.8214 (tt0) REVERT: D 78 MET cc_start: 0.8528 (mpt) cc_final: 0.8106 (mpt) REVERT: D 293 GLU cc_start: 0.8973 (tp30) cc_final: 0.8542 (tp30) REVERT: D 308 ASP cc_start: 0.8297 (m-30) cc_final: 0.7999 (m-30) REVERT: D 322 ARG cc_start: 0.8873 (mtm180) cc_final: 0.8380 (tpt170) REVERT: D 391 SER cc_start: 0.9269 (t) cc_final: 0.8860 (p) REVERT: D 576 MET cc_start: 0.8620 (ttm) cc_final: 0.8381 (ttt) REVERT: D 602 MET cc_start: 0.8017 (ppp) cc_final: 0.7793 (ppp) REVERT: E 49 GLN cc_start: 0.7523 (pm20) cc_final: 0.7238 (pm20) REVERT: E 84 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8103 (tm-30) REVERT: E 126 ARG cc_start: 0.7652 (ptp90) cc_final: 0.7274 (mtm110) REVERT: E 144 MET cc_start: 0.8220 (mmm) cc_final: 0.7952 (mmm) outliers start: 64 outliers final: 32 residues processed: 350 average time/residue: 0.1427 time to fit residues: 79.2712 Evaluate side-chains 311 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 234 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 187 optimal weight: 0.0370 chunk 218 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 chunk 232 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 463 ASN B 586 HIS C 238 GLN C 581 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.120302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099111 restraints weight = 51832.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102157 restraints weight = 23864.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104131 restraints weight = 14305.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.105402 restraints weight = 10251.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.106136 restraints weight = 8229.777| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21570 Z= 0.111 Angle : 0.668 14.245 29262 Z= 0.326 Chirality : 0.041 0.180 3321 Planarity : 0.003 0.035 3721 Dihedral : 5.211 53.072 2885 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.37 % Favored : 90.51 % Rotamer: Outliers : 2.85 % Allowed : 18.88 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.17), residues: 2625 helix: 0.05 (0.14), residues: 1451 sheet: -1.00 (0.58), residues: 83 loop : -2.88 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 469 TYR 0.014 0.001 TYR D 269 PHE 0.023 0.001 PHE D 511 TRP 0.013 0.001 TRP C 45 HIS 0.003 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (21570) covalent geometry : angle 0.66767 / 0.33 (29262) hydrogen bonds : bond 0.03112 / 2.00 ( 795) hydrogen bonds : angle 3.93736 / 2.74 ( 2268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 301 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7916 (mmm) REVERT: A 275 THR cc_start: 0.8940 (m) cc_final: 0.8727 (p) REVERT: A 299 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8526 (mmtt) REVERT: A 453 MET cc_start: 0.8187 (ttm) cc_final: 0.7962 (ttm) REVERT: A 500 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8920 (tt) REVERT: A 501 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8377 (mm) REVERT: A 569 MET cc_start: 0.8900 (mmt) cc_final: 0.8670 (mmt) REVERT: A 590 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 602 MET cc_start: 0.8292 (tmm) cc_final: 0.8061 (tmm) REVERT: B 96 MET cc_start: 0.8466 (tmm) cc_final: 0.8239 (tmm) REVERT: B 110 MET cc_start: 0.8781 (mtm) cc_final: 0.8128 (mtm) REVERT: B 137 LEU cc_start: 0.9248 (mm) cc_final: 0.8905 (pp) REVERT: B 259 MET cc_start: 0.8817 (tpp) cc_final: 0.8435 (tpp) REVERT: B 275 THR cc_start: 0.8745 (m) cc_final: 0.8423 (p) REVERT: B 399 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8960 (mm) REVERT: B 434 MET cc_start: 0.9015 (mmt) cc_final: 0.8196 (mmm) REVERT: B 634 ASP cc_start: 0.8213 (m-30) cc_final: 0.7609 (p0) REVERT: B 637 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7808 (t0) REVERT: C 283 ASP cc_start: 0.7173 (t0) cc_final: 0.6800 (t0) REVERT: C 473 MET cc_start: 0.8670 (ttt) cc_final: 0.7758 (ptp) REVERT: C 576 MET cc_start: 0.8706 (tpp) cc_final: 0.8391 (tpp) REVERT: C 577 MET cc_start: 0.8806 (mmm) cc_final: 0.8529 (mtt) REVERT: C 586 HIS cc_start: 0.7141 (t70) cc_final: 0.6882 (t70) REVERT: D 40 GLN cc_start: 0.9132 (tt0) cc_final: 0.8221 (tt0) REVERT: D 78 MET cc_start: 0.8519 (mpt) cc_final: 0.8170 (mpt) REVERT: D 99 MET cc_start: 0.8857 (mtm) cc_final: 0.8242 (mtm) REVERT: D 293 GLU cc_start: 0.8989 (tp30) cc_final: 0.8474 (tp30) REVERT: D 308 ASP cc_start: 0.8324 (m-30) cc_final: 0.8024 (m-30) REVERT: D 322 ARG cc_start: 0.8812 (mtm180) cc_final: 0.8360 (tpt170) REVERT: D 331 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9308 (tt) REVERT: D 391 SER cc_start: 0.9209 (t) cc_final: 0.8814 (p) REVERT: D 602 MET cc_start: 0.7942 (ppp) cc_final: 0.7691 (ppp) REVERT: E 49 GLN cc_start: 0.7487 (pm20) cc_final: 0.7225 (pm20) REVERT: E 126 ARG cc_start: 0.7547 (ptp90) cc_final: 0.7341 (mtm110) REVERT: E 144 MET cc_start: 0.8230 (mmm) cc_final: 0.7848 (mmm) outliers start: 65 outliers final: 38 residues processed: 349 average time/residue: 0.1464 time to fit residues: 80.6080 Evaluate side-chains 324 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 161 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS C 73 HIS C 238 GLN D 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091556 restraints weight = 51613.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094662 restraints weight = 24297.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.096662 restraints weight = 14935.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.097993 restraints weight = 10843.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098881 restraints weight = 8776.158| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21570 Z= 0.127 Angle : 0.672 14.718 29262 Z= 0.328 Chirality : 0.042 0.177 3321 Planarity : 0.003 0.039 3721 Dihedral : 5.152 55.112 2885 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.98 % Favored : 89.90 % Rotamer: Outliers : 3.20 % Allowed : 18.61 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2625 helix: 0.22 (0.14), residues: 1460 sheet: -0.88 (0.59), residues: 83 loop : -2.85 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 469 TYR 0.013 0.001 TYR D 269 PHE 0.016 0.001 PHE B 530 TRP 0.008 0.001 TRP C 45 HIS 0.004 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21570) covalent geometry : angle 0.67246 / 0.33 (29262) hydrogen bonds : bond 0.03184 / 2.07 ( 795) hydrogen bonds : angle 3.91986 / 2.72 ( 2268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 290 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7888 (mmm) REVERT: A 275 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8766 (p) REVERT: A 299 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8513 (mmtt) REVERT: A 453 MET cc_start: 0.8219 (ttm) cc_final: 0.7959 (ttm) REVERT: A 500 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8955 (tt) REVERT: A 501 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 602 MET cc_start: 0.8166 (tmm) cc_final: 0.7911 (tmm) REVERT: B 96 MET cc_start: 0.8595 (tmm) cc_final: 0.8317 (tmm) REVERT: B 137 LEU cc_start: 0.9222 (mm) cc_final: 0.8893 (pp) REVERT: B 259 MET cc_start: 0.8857 (tpp) cc_final: 0.8449 (tpp) REVERT: B 275 THR cc_start: 0.8766 (m) cc_final: 0.8426 (p) REVERT: B 399 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8959 (mm) REVERT: B 434 MET cc_start: 0.9032 (mmt) cc_final: 0.8233 (mmm) REVERT: B 634 ASP cc_start: 0.8211 (m-30) cc_final: 0.7590 (p0) REVERT: B 637 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7816 (t0) REVERT: C 64 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8665 (tt) REVERT: C 283 ASP cc_start: 0.7189 (t0) cc_final: 0.6800 (t0) REVERT: C 473 MET cc_start: 0.8700 (ttt) cc_final: 0.7755 (ptp) REVERT: C 576 MET cc_start: 0.8750 (tpp) cc_final: 0.8452 (tpp) REVERT: C 586 HIS cc_start: 0.7119 (t70) cc_final: 0.6886 (t70) REVERT: D 40 GLN cc_start: 0.9143 (tt0) cc_final: 0.8200 (tt0) REVERT: D 78 MET cc_start: 0.8616 (mpt) cc_final: 0.8167 (mpt) REVERT: D 80 GLU cc_start: 0.8781 (pm20) cc_final: 0.8509 (pm20) REVERT: D 96 MET cc_start: 0.9136 (mtp) cc_final: 0.8753 (mtm) REVERT: D 99 MET cc_start: 0.8898 (mtm) cc_final: 0.8271 (mtm) REVERT: D 293 GLU cc_start: 0.8999 (tp30) cc_final: 0.8479 (tp30) REVERT: D 308 ASP cc_start: 0.8319 (m-30) cc_final: 0.8003 (m-30) REVERT: D 322 ARG cc_start: 0.8835 (mtm180) cc_final: 0.8404 (tpt170) REVERT: D 472 GLN cc_start: 0.6098 (OUTLIER) cc_final: 0.5501 (pm20) REVERT: D 602 MET cc_start: 0.7983 (ppp) cc_final: 0.7733 (ppp) REVERT: E 49 GLN cc_start: 0.7609 (pm20) cc_final: 0.7368 (pm20) REVERT: E 144 MET cc_start: 0.8284 (mmm) cc_final: 0.7875 (mmm) outliers start: 73 outliers final: 45 residues processed: 340 average time/residue: 0.1403 time to fit residues: 75.5017 Evaluate side-chains 324 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 116 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS C 256 GLN C 309 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089621 restraints weight = 50056.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092612 restraints weight = 23754.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094561 restraints weight = 14655.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095861 restraints weight = 10699.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096716 restraints weight = 8704.312| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21570 Z= 0.164 Angle : 0.716 15.383 29262 Z= 0.348 Chirality : 0.044 0.249 3321 Planarity : 0.003 0.039 3721 Dihedral : 5.252 55.098 2885 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.36 % Favored : 89.52 % Rotamer: Outliers : 3.20 % Allowed : 18.96 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2625 helix: 0.32 (0.14), residues: 1457 sheet: -0.96 (0.59), residues: 85 loop : -2.79 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 469 TYR 0.012 0.001 TYR B 338 PHE 0.025 0.001 PHE C 433 TRP 0.007 0.001 TRP D 320 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (21570) covalent geometry : angle 0.71558 / 0.35 (29262) hydrogen bonds : bond 0.03491 / 2.26 ( 795) hydrogen bonds : angle 4.07229 / 2.83 ( 2268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 272 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7961 (tmm) REVERT: A 275 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8822 (p) REVERT: A 299 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8410 (mmtt) REVERT: A 439 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7589 (mmt) REVERT: A 453 MET cc_start: 0.8295 (ttm) cc_final: 0.8071 (ttm) REVERT: A 500 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.9003 (tt) REVERT: A 501 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 602 MET cc_start: 0.8070 (tmm) cc_final: 0.7811 (tmm) REVERT: A 633 GLU cc_start: 0.8394 (pm20) cc_final: 0.8135 (mp0) REVERT: B 96 MET cc_start: 0.8690 (tmm) cc_final: 0.8418 (tmm) REVERT: B 137 LEU cc_start: 0.9216 (mm) cc_final: 0.8837 (pp) REVERT: B 259 MET cc_start: 0.8863 (tpp) cc_final: 0.8439 (tpp) REVERT: B 275 THR cc_start: 0.8772 (m) cc_final: 0.8431 (p) REVERT: B 399 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8971 (mm) REVERT: B 434 MET cc_start: 0.9057 (mmt) cc_final: 0.8250 (mmm) REVERT: B 602 MET cc_start: 0.8226 (tmm) cc_final: 0.8000 (tmm) REVERT: B 634 ASP cc_start: 0.8265 (m-30) cc_final: 0.7632 (p0) REVERT: B 637 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7803 (t0) REVERT: C 64 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8757 (tt) REVERT: C 283 ASP cc_start: 0.7366 (t0) cc_final: 0.6918 (t0) REVERT: C 473 MET cc_start: 0.8714 (ttt) cc_final: 0.7720 (ptp) REVERT: C 576 MET cc_start: 0.8803 (tpp) cc_final: 0.8546 (tpp) REVERT: C 586 HIS cc_start: 0.7239 (t70) cc_final: 0.7010 (t70) REVERT: D 78 MET cc_start: 0.8629 (mpt) cc_final: 0.8415 (mpp) REVERT: D 96 MET cc_start: 0.9166 (mtp) cc_final: 0.8771 (mtm) REVERT: D 99 MET cc_start: 0.8963 (mtm) cc_final: 0.8337 (mtm) REVERT: D 229 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8605 (mmmm) REVERT: D 293 GLU cc_start: 0.9015 (tp30) cc_final: 0.8709 (tp30) REVERT: D 308 ASP cc_start: 0.8387 (m-30) cc_final: 0.8069 (m-30) REVERT: D 441 MET cc_start: 0.9001 (tpp) cc_final: 0.8645 (ttm) REVERT: D 472 GLN cc_start: 0.6145 (OUTLIER) cc_final: 0.5338 (pm20) REVERT: D 602 MET cc_start: 0.8038 (ppp) cc_final: 0.7776 (ppp) REVERT: E 49 GLN cc_start: 0.7593 (pm20) cc_final: 0.7350 (pm20) REVERT: E 144 MET cc_start: 0.8417 (mmm) cc_final: 0.7986 (mmm) outliers start: 73 outliers final: 45 residues processed: 320 average time/residue: 0.1459 time to fit residues: 73.4610 Evaluate side-chains 317 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 42 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 202 optimal weight: 0.0980 chunk 154 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS C 238 GLN D 256 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.113176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090993 restraints weight = 50342.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.094116 restraints weight = 23495.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096180 restraints weight = 14337.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097507 restraints weight = 10360.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098372 restraints weight = 8384.545| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21570 Z= 0.124 Angle : 0.703 18.751 29262 Z= 0.336 Chirality : 0.043 0.279 3321 Planarity : 0.003 0.041 3721 Dihedral : 5.116 50.083 2885 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.45 % Favored : 90.44 % Rotamer: Outliers : 2.94 % Allowed : 19.36 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2625 helix: 0.45 (0.14), residues: 1455 sheet: -0.90 (0.59), residues: 83 loop : -2.77 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 627 TYR 0.021 0.001 TYR B 162 PHE 0.014 0.001 PHE A 67 TRP 0.007 0.001 TRP C 45 HIS 0.004 0.001 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (21570) covalent geometry : angle 0.70315 / 0.34 (29262) hydrogen bonds : bond 0.03174 / 2.06 ( 795) hydrogen bonds : angle 3.96060 / 2.76 ( 2268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8012 (tmm) REVERT: A 275 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8786 (p) REVERT: A 299 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8413 (mmtt) REVERT: A 453 MET cc_start: 0.8251 (ttm) cc_final: 0.8033 (ttm) REVERT: A 500 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8876 (tt) REVERT: A 501 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 569 MET cc_start: 0.9035 (mmt) cc_final: 0.8788 (mmt) REVERT: A 602 MET cc_start: 0.8066 (tmm) cc_final: 0.7809 (tmm) REVERT: B 96 MET cc_start: 0.8714 (tmm) cc_final: 0.8443 (tmm) REVERT: B 137 LEU cc_start: 0.9186 (mm) cc_final: 0.8827 (pp) REVERT: B 259 MET cc_start: 0.8881 (tpp) cc_final: 0.8442 (tpp) REVERT: B 275 THR cc_start: 0.8828 (m) cc_final: 0.8502 (p) REVERT: B 399 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8946 (mm) REVERT: B 434 MET cc_start: 0.9037 (mmt) cc_final: 0.8236 (mmm) REVERT: B 602 MET cc_start: 0.8191 (tmm) cc_final: 0.7974 (tmm) REVERT: B 634 ASP cc_start: 0.8196 (m-30) cc_final: 0.7525 (p0) REVERT: B 637 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7809 (t0) REVERT: C 64 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8775 (tt) REVERT: C 283 ASP cc_start: 0.7358 (t0) cc_final: 0.6957 (t0) REVERT: C 473 MET cc_start: 0.8772 (ttt) cc_final: 0.7743 (ptp) REVERT: C 576 MET cc_start: 0.8784 (tpp) cc_final: 0.8522 (tpp) REVERT: C 586 HIS cc_start: 0.7211 (t70) cc_final: 0.7003 (t70) REVERT: D 96 MET cc_start: 0.9174 (mtp) cc_final: 0.8769 (mtm) REVERT: D 99 MET cc_start: 0.9002 (mtm) cc_final: 0.8357 (mtm) REVERT: D 229 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8606 (mmmm) REVERT: D 293 GLU cc_start: 0.9009 (tp30) cc_final: 0.8358 (tp30) REVERT: D 297 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8378 (m) REVERT: D 308 ASP cc_start: 0.8416 (m-30) cc_final: 0.8102 (m-30) REVERT: D 441 MET cc_start: 0.8916 (tpp) cc_final: 0.8626 (ttm) REVERT: D 472 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.5509 (pm20) REVERT: D 602 MET cc_start: 0.8043 (ppp) cc_final: 0.7767 (ppp) REVERT: E 126 ARG cc_start: 0.6685 (mtm110) cc_final: 0.6468 (mtm110) REVERT: E 144 MET cc_start: 0.8392 (mmm) cc_final: 0.7859 (mmm) outliers start: 67 outliers final: 41 residues processed: 321 average time/residue: 0.1378 time to fit residues: 71.1034 Evaluate side-chains 319 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 240 optimal weight: 1.9990 chunk 215 optimal weight: 0.0060 chunk 167 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 120 optimal weight: 0.0170 chunk 15 optimal weight: 2.9990 overall best weight: 0.5034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 586 HIS B 639 ASN C 238 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.115777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.093709 restraints weight = 50245.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096873 restraints weight = 23328.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.098927 restraints weight = 14197.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100279 restraints weight = 10242.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101175 restraints weight = 8299.052| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21570 Z= 0.113 Angle : 0.690 17.834 29262 Z= 0.332 Chirality : 0.042 0.272 3321 Planarity : 0.003 0.041 3721 Dihedral : 4.937 47.085 2885 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.14 % Favored : 90.78 % Rotamer: Outliers : 2.55 % Allowed : 19.97 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2625 helix: 0.54 (0.14), residues: 1455 sheet: -0.88 (0.60), residues: 83 loop : -2.69 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 627 TYR 0.012 0.001 TYR B 162 PHE 0.027 0.001 PHE C 433 TRP 0.009 0.001 TRP C 45 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (21570) covalent geometry : angle 0.68995 / 0.33 (29262) hydrogen bonds : bond 0.02917 / 1.90 ( 795) hydrogen bonds : angle 3.88883 / 2.72 ( 2268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8054 (t80) cc_final: 0.7516 (t80) REVERT: A 275 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 299 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8326 (mmtt) REVERT: A 500 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8863 (tt) REVERT: A 501 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8348 (mm) REVERT: A 569 MET cc_start: 0.8976 (mmt) cc_final: 0.8744 (mmt) REVERT: A 602 MET cc_start: 0.8082 (tmm) cc_final: 0.7825 (tmm) REVERT: B 96 MET cc_start: 0.8696 (tmm) cc_final: 0.8447 (tmm) REVERT: B 137 LEU cc_start: 0.9105 (mm) cc_final: 0.8772 (pp) REVERT: B 259 MET cc_start: 0.8863 (tpp) cc_final: 0.8437 (tpp) REVERT: B 275 THR cc_start: 0.8726 (m) cc_final: 0.8436 (p) REVERT: B 399 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8935 (mm) REVERT: B 434 MET cc_start: 0.8981 (mmt) cc_final: 0.8206 (mmm) REVERT: B 527 MET cc_start: 0.8399 (tpp) cc_final: 0.8052 (tpt) REVERT: B 634 ASP cc_start: 0.8183 (m-30) cc_final: 0.7481 (p0) REVERT: B 637 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7863 (t0) REVERT: C 64 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8751 (tt) REVERT: C 283 ASP cc_start: 0.7336 (t0) cc_final: 0.7014 (t0) REVERT: C 473 MET cc_start: 0.8762 (ttt) cc_final: 0.7791 (ptp) REVERT: C 553 MET cc_start: 0.7546 (tpt) cc_final: 0.7086 (tpp) REVERT: C 576 MET cc_start: 0.8680 (tpp) cc_final: 0.8396 (tpp) REVERT: C 586 HIS cc_start: 0.7195 (t70) cc_final: 0.6986 (t70) REVERT: D 96 MET cc_start: 0.9171 (mtp) cc_final: 0.8768 (mtm) REVERT: D 99 MET cc_start: 0.8988 (mtm) cc_final: 0.8340 (mtm) REVERT: D 293 GLU cc_start: 0.8979 (tp30) cc_final: 0.8542 (tp30) REVERT: D 308 ASP cc_start: 0.8431 (m-30) cc_final: 0.8118 (m-30) REVERT: D 490 MET cc_start: 0.8013 (mmm) cc_final: 0.7712 (mmm) REVERT: D 602 MET cc_start: 0.8102 (ppp) cc_final: 0.7802 (ppp) REVERT: E 109 MET cc_start: 0.8659 (mmt) cc_final: 0.7634 (tpp) REVERT: E 144 MET cc_start: 0.8289 (mmm) cc_final: 0.7975 (mtp) outliers start: 58 outliers final: 36 residues processed: 330 average time/residue: 0.1417 time to fit residues: 74.7897 Evaluate side-chains 310 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 49 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 201 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 189 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 215 optimal weight: 0.0370 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS C 238 GLN ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 256 GLN D 463 ASN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.116727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094561 restraints weight = 49759.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097747 restraints weight = 23087.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099824 restraints weight = 14053.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101183 restraints weight = 10161.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102056 restraints weight = 8224.609| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21570 Z= 0.114 Angle : 0.694 16.737 29262 Z= 0.333 Chirality : 0.042 0.262 3321 Planarity : 0.003 0.046 3721 Dihedral : 4.853 47.140 2885 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.33 % Favored : 90.55 % Rotamer: Outliers : 2.15 % Allowed : 20.59 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.17), residues: 2625 helix: 0.60 (0.14), residues: 1463 sheet: -0.93 (0.58), residues: 85 loop : -2.66 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 627 TYR 0.011 0.001 TYR B 162 PHE 0.015 0.001 PHE A 67 TRP 0.007 0.001 TRP C 45 HIS 0.003 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (21570) covalent geometry : angle 0.69431 / 0.33 (29262) hydrogen bonds : bond 0.02947 / 1.94 ( 795) hydrogen bonds : angle 3.90004 / 2.73 ( 2268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3547.40 seconds wall clock time: 62 minutes 25.41 seconds (3745.41 seconds total)