Starting phenix.real_space_refine on Sat Jul 4 04:56:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v44_64766/07_2026/9v44_64766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v44_64766/07_2026/9v44_64766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v44_64766/07_2026/9v44_64766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v44_64766/07_2026/9v44_64766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v44_64766/07_2026/9v44_64766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v44_64766/07_2026/9v44_64766.map" } resolution = 2.97 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 209 atoms to isotropic. 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 P 38 5.49 5 S 132 5.16 5 C 11079 2.51 5 N 3121 2.21 5 O 3465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17835 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5722 Classifications: {'peptide': 705} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 674} Chain breaks: 1 Chain: "B" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 5874 Classifications: {'peptide': 736} Link IDs: {'PTRANS': 32, 'TRANS': 703} Chain breaks: 1 Chain: "C" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2002 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "D" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3434 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 2 Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 6, 'rna3p': 7} Chain: "F" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 515 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 18} Time building chain proxies: 3.37, per 1000 atoms: 0.19 Number of scatterers: 17835 At special positions: 0 Unit cell: (134.4, 156.48, 122.88, 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) S 132 16.00 P 38 15.00 O 3465 8.00 N 3121 7.00 C 11079 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: 1.42 Conformation dependent library (CDL) restraints added in 833.8 milliseconds 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3994 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 18 sheets defined 50.1% alpha, 9.3% beta 7 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.705A pdb=" N LYS A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 83 through 96 removed outlier: 4.215A pdb=" N THR A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.802A pdb=" N GLU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.141A pdb=" N ALA A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 165 through 186 removed outlier: 4.122A pdb=" N ALA A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.777A pdb=" N ARG A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.584A pdb=" N GLY A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.822A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.124A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.691A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 removed outlier: 3.628A pdb=" N TYR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 removed outlier: 4.013A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.935A pdb=" N LEU A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 579 removed outlier: 3.608A pdb=" N MET A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 600 removed outlier: 4.119A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 removed outlier: 3.832A pdb=" N PHE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.679A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.573A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 667 " --> pdb=" O ARG A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 3.564A pdb=" N TYR A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.748A pdb=" N LEU A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 21 removed outlier: 3.736A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.559A pdb=" N ASN B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.503A pdb=" N ARG B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 124 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 152 removed outlier: 4.182A pdb=" N ASN B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.729A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.658A pdb=" N PHE B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.609A pdb=" N LYS B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.032A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.762A pdb=" N LEU B 373 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.953A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.625A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.749A pdb=" N LYS B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 471 removed outlier: 4.445A pdb=" N GLN B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 4.458A pdb=" N GLU B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 520 through 536 removed outlier: 3.866A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 582 removed outlier: 3.878A pdb=" N LYS B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.507A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS B 605 " --> pdb=" O ARG B 602 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 606 " --> pdb=" O ASN B 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 606' Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 680 through 694 removed outlier: 3.688A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 700 removed outlier: 3.563A pdb=" N LYS B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.637A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 729 removed outlier: 3.572A pdb=" N ASP B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 754 removed outlier: 4.154A pdb=" N SER B 741 " --> pdb=" O LYS B 737 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 754 " --> pdb=" O ILE B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.600A pdb=" N ILE C 31 " --> pdb=" O HIS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.911A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 126 removed outlier: 4.389A pdb=" N LYS C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.906A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.758A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.564A pdb=" N ILE C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 230' Processing helix chain 'D' and resid 22 through 48 Processing helix chain 'D' and resid 50 through 55 Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 72 through 82 removed outlier: 3.572A pdb=" N HIS D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 removed outlier: 3.743A pdb=" N ILE D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 148 Processing helix chain 'D' and resid 150 through 157 removed outlier: 3.833A pdb=" N LEU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 removed outlier: 4.294A pdb=" N THR D 171 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 172 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'D' and resid 185 through 203 Processing helix chain 'D' and resid 211 through 230 removed outlier: 3.613A pdb=" N PHE D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.893A pdb=" N ALA D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 265 Processing helix chain 'D' and resid 277 through 288 Proline residue: D 283 - end of helix removed outlier: 3.677A pdb=" N GLY D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 removed outlier: 4.595A pdb=" N PHE D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'D' and resid 340 through 348 removed outlier: 4.586A pdb=" N PHE D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 421 through 427 Processing helix chain 'D' and resid 441 through 450 removed outlier: 3.757A pdb=" N GLY D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.686A pdb=" N PHE A 53 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 61 " --> pdb=" O PHE A 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 removed outlier: 3.779A pdb=" N TYR A 110 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.957A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 525 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 546 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.841A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.897A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 364 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.377A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680 removed outlier: 3.934A pdb=" N ILE B 484 " --> pdb=" O GLY A 679 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY B 304 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 446 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.745A pdb=" N LYS B 54 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.789A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.510A pdb=" N THR C 129 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 131 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB8, first strand: chain 'D' and resid 96 through 99 removed outlier: 3.513A pdb=" N ILE D 96 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 313 through 316 725 hydrogen bonds defined for protein. 2031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3013 1.32 - 1.44: 4934 1.44 - 1.57: 10011 1.57 - 1.69: 75 1.69 - 1.81: 229 Bond restraints: 18262 Sorted by residual: bond pdb=" CA ARG D 65 " pdb=" C ARG D 65 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.28e-02 6.10e+03 2.77e+01 bond pdb=" CA PHE B 574 " pdb=" C PHE B 574 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.35e-02 5.49e+03 2.47e+01 bond pdb=" CA ILE D 138 " pdb=" C ILE D 138 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.27e-02 6.20e+03 2.31e+01 bond pdb=" CA SER B 443 " pdb=" C SER B 443 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.21e-02 6.83e+03 2.07e+01 bond pdb=" CA ARG D 38 " pdb=" C ARG D 38 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.27e-02 6.20e+03 2.01e+01 ... (remaining 18257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 24051 2.58 - 5.16: 622 5.16 - 7.74: 93 7.74 - 10.32: 18 10.32 - 12.90: 3 Bond angle restraints: 24787 Sorted by residual: angle pdb=" N ASP D 101 " pdb=" CA ASP D 101 " pdb=" C ASP D 101 " ideal model delta sigma weight residual 114.62 101.72 12.90 1.14e+00 7.69e-01 1.28e+02 angle pdb=" N ARG B 572 " pdb=" CA ARG B 572 " pdb=" C ARG B 572 " ideal model delta sigma weight residual 112.92 102.49 10.43 1.23e+00 6.61e-01 7.19e+01 angle pdb=" N ALA D 284 " pdb=" CA ALA D 284 " pdb=" C ALA D 284 " ideal model delta sigma weight residual 111.33 103.09 8.24 1.21e+00 6.83e-01 4.64e+01 angle pdb=" N PHE D 258 " pdb=" CA PHE D 258 " pdb=" C PHE D 258 " ideal model delta sigma weight residual 111.14 104.22 6.92 1.08e+00 8.57e-01 4.11e+01 angle pdb=" N GLU D 465 " pdb=" CA GLU D 465 " pdb=" C GLU D 465 " ideal model delta sigma weight residual 108.90 98.56 10.34 1.63e+00 3.76e-01 4.02e+01 ... (remaining 24782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 10676 34.64 - 69.29: 521 69.29 - 103.93: 37 103.93 - 138.57: 5 138.57 - 173.21: 1 Dihedral angle restraints: 11240 sinusoidal: 5065 harmonic: 6175 Sorted by residual: dihedral pdb=" C4' A F 23 " pdb=" C3' A F 23 " pdb=" C2' A F 23 " pdb=" C1' A F 23 " ideal model delta sinusoidal sigma weight residual -35.00 29.16 -64.16 1 8.00e+00 1.56e-02 8.46e+01 dihedral pdb=" C5' A F 23 " pdb=" C4' A F 23 " pdb=" C3' A F 23 " pdb=" O3' A F 23 " ideal model delta sinusoidal sigma weight residual 147.00 83.58 63.42 1 8.00e+00 1.56e-02 8.29e+01 dihedral pdb=" O4' A F 23 " pdb=" C4' A F 23 " pdb=" C3' A F 23 " pdb=" C2' A F 23 " ideal model delta sinusoidal sigma weight residual 24.00 -37.75 61.75 1 8.00e+00 1.56e-02 7.90e+01 ... (remaining 11237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2460 0.088 - 0.176: 244 0.176 - 0.263: 22 0.263 - 0.351: 1 0.351 - 0.439: 1 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CG LEU D 266 " pdb=" CB LEU D 266 " pdb=" CD1 LEU D 266 " pdb=" CD2 LEU D 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" C2' U F 21 " pdb=" C3' U F 21 " pdb=" O2' U F 21 " pdb=" C1' U F 21 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ILE D 138 " pdb=" N ILE D 138 " pdb=" C ILE D 138 " pdb=" CB ILE D 138 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2725 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 147 " 0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ILE A 147 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE A 147 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE A 148 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 351 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LYS D 351 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS D 351 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL D 352 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 106 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ARG D 106 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG D 106 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU D 107 " -0.019 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 855 2.70 - 3.25: 17953 3.25 - 3.80: 27721 3.80 - 4.35: 36291 4.35 - 4.90: 58170 Nonbonded interactions: 140990 Sorted by model distance: nonbonded pdb=" O LEU D 110 " pdb=" CD1 LEU D 110 " model vdw 2.145 3.460 nonbonded pdb=" OD1 ASN B 77 " pdb=" OH TYR B 467 " model vdw 2.197 3.040 nonbonded pdb=" ND2 ASN A 96 " pdb=" OD1 ASN C 170 " model vdw 2.214 3.120 nonbonded pdb=" O GLN C 182 " pdb=" OG1 THR C 186 " model vdw 2.226 3.040 nonbonded pdb=" O LEU B 579 " pdb=" OG1 THR B 583 " model vdw 2.227 3.040 ... (remaining 140985 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 0.007 0.067 18262 Z= 0.447 Angle : 0.984 12.904 24787 Z= 0.653 Chirality : 0.055 0.439 2728 Planarity : 0.006 0.080 3066 Dihedral : 18.572 173.213 7246 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.40 % Favored : 91.36 % Rotamer: Outliers : 7.84 % Allowed : 8.00 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.14), residues: 2106 helix: -2.65 (0.13), residues: 951 sheet: -1.64 (0.33), residues: 199 loop : -3.59 (0.16), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 459 TYR 0.026 0.002 TYR A 564 PHE 0.021 0.002 PHE B 495 TRP 0.024 0.002 TRP B 438 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.45 (18262) covalent geometry : angle 0.98389 / 0.65 (24787) hydrogen bonds : bond 0.16835 / 11.11 ( 740) hydrogen bonds : angle 7.24388 / 4.98 ( 2069) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 430 time to evaluate : 0.538 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 47 MET cc_start: 0.5928 (tpt) cc_final: 0.5404 (tpt) REVERT: A 73 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.5450 (tttm) REVERT: A 125 ARG cc_start: 0.4424 (OUTLIER) cc_final: 0.4181 (ppt170) REVERT: A 133 GLU cc_start: 0.4064 (OUTLIER) cc_final: 0.3730 (mp0) REVERT: A 141 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5739 (pp20) REVERT: A 187 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5674 (pp) REVERT: A 286 ASP cc_start: 0.6584 (t0) cc_final: 0.6097 (t0) REVERT: A 321 TYR cc_start: 0.6942 (p90) cc_final: 0.6638 (p90) REVERT: A 396 ASP cc_start: 0.7073 (m-30) cc_final: 0.6788 (m-30) REVERT: B 8 LEU cc_start: 0.8250 (mt) cc_final: 0.8037 (mt) REVERT: B 118 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7728 (mtt90) REVERT: B 327 LYS cc_start: 0.7862 (ttmm) cc_final: 0.7492 (ttpp) REVERT: B 391 LYS cc_start: 0.7836 (tttt) cc_final: 0.7607 (tttm) REVERT: B 455 ASN cc_start: 0.7558 (t0) cc_final: 0.7265 (t0) REVERT: B 502 VAL cc_start: 0.8445 (t) cc_final: 0.8193 (m) REVERT: B 537 ASN cc_start: 0.7304 (t0) cc_final: 0.7077 (t0) REVERT: C 187 LYS cc_start: 0.7979 (ptpt) cc_final: 0.7758 (ptpt) REVERT: C 197 LYS cc_start: 0.6407 (pmtt) cc_final: 0.5930 (pttt) REVERT: D 55 ARG cc_start: 0.3567 (OUTLIER) cc_final: 0.2801 (mmm-85) REVERT: D 110 LEU cc_start: 0.6780 (pp) cc_final: 0.6573 (pp) REVERT: D 119 ILE cc_start: 0.2471 (OUTLIER) cc_final: 0.2033 (tp) REVERT: D 125 ASN cc_start: 0.2787 (OUTLIER) cc_final: 0.1962 (m-40) REVERT: D 166 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4096 (tp) REVERT: D 167 MET cc_start: 0.6024 (mtm) cc_final: 0.5773 (mtm) REVERT: D 184 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6248 (mttm) REVERT: D 193 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7939 (tp) REVERT: D 194 ILE cc_start: 0.7335 (mm) cc_final: 0.6845 (mp) REVERT: D 198 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7428 (ttpt) REVERT: D 214 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5715 (pttp) REVERT: D 225 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7704 (mm) REVERT: D 235 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.6258 (mm-40) REVERT: D 242 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6680 (m) REVERT: D 245 SER cc_start: 0.8154 (t) cc_final: 0.7284 (p) REVERT: D 257 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7801 (mp) REVERT: D 258 PHE cc_start: 0.7553 (m-10) cc_final: 0.7349 (m-10) REVERT: D 259 SER cc_start: 0.7832 (OUTLIER) cc_final: 0.7415 (m) REVERT: D 304 PHE cc_start: -0.0539 (OUTLIER) cc_final: -0.1289 (m-80) REVERT: D 339 GLU cc_start: 0.3945 (OUTLIER) cc_final: 0.1088 (tm-30) REVERT: D 360 THR cc_start: 0.2012 (OUTLIER) cc_final: 0.1745 (t) REVERT: D 415 GLN cc_start: 0.3645 (OUTLIER) cc_final: 0.3274 (mp10) REVERT: D 416 ARG cc_start: 0.5006 (OUTLIER) cc_final: 0.4759 (mmp-170) REVERT: D 422 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.5924 (mppt) REVERT: D 443 GLU cc_start: 0.5921 (tp30) cc_final: 0.5348 (tp30) REVERT: D 455 GLU cc_start: 0.2441 (OUTLIER) cc_final: 0.1369 (mm-30) REVERT: D 479 PHE cc_start: -0.1440 (OUTLIER) cc_final: -0.3337 (m-80) outliers start: 147 outliers final: 52 residues processed: 543 average time/residue: 0.6461 time to fit residues: 386.3528 Evaluate side-chains 461 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 383 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 229 LYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.0770 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 92 ASN A 128 HIS ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 359 ASN A 409 ASN A 452 HIS A 466 ASN A 471 ASN A 591 GLN A 703 ASN A 708 ASN B 16 ASN B 58 ASN B 145 ASN B 247 GLN B 276 ASN B 310 ASN B 328 ASN B 485 ASN B 533 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 642 ASN B 679 GLN B 687 GLN C 110 HIS C 160 GLN C 236 GLN D 124 ASN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN D 241 GLN D 308 GLN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145988 restraints weight = 25278.870| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.20 r_work: 0.3672 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18262 Z= 0.178 Angle : 0.725 16.578 24787 Z= 0.389 Chirality : 0.045 0.270 2728 Planarity : 0.006 0.073 3066 Dihedral : 16.278 177.725 3115 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.59 % Rotamer: Outliers : 5.82 % Allowed : 16.76 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.16), residues: 2106 helix: -1.02 (0.16), residues: 963 sheet: -1.16 (0.35), residues: 196 loop : -3.14 (0.17), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 727 TYR 0.019 0.002 TYR A 131 PHE 0.035 0.002 PHE A 46 TRP 0.025 0.002 TRP D 139 HIS 0.016 0.002 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (18262) covalent geometry : angle 0.72483 / 0.39 (24787) hydrogen bonds : bond 0.06041 / 3.99 ( 740) hydrogen bonds : angle 5.10149 / 3.54 ( 2069) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 378 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.7802 (t-170) cc_final: 0.7559 (t-90) REVERT: A 47 MET cc_start: 0.6251 (tpt) cc_final: 0.5699 (tpt) REVERT: A 116 ARG cc_start: 0.6436 (mtp-110) cc_final: 0.6234 (mtm-85) REVERT: A 133 GLU cc_start: 0.4184 (OUTLIER) cc_final: 0.3727 (mp0) REVERT: A 187 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6201 (pp) REVERT: A 286 ASP cc_start: 0.6951 (t0) cc_final: 0.6649 (t0) REVERT: A 321 TYR cc_start: 0.7423 (p90) cc_final: 0.7100 (p90) REVERT: A 396 ASP cc_start: 0.7648 (m-30) cc_final: 0.7386 (m-30) REVERT: A 430 GLU cc_start: 0.7775 (pm20) cc_final: 0.7490 (mp0) REVERT: A 623 GLU cc_start: 0.7707 (pt0) cc_final: 0.7504 (pt0) REVERT: B 8 LEU cc_start: 0.8446 (mt) cc_final: 0.8222 (mt) REVERT: B 311 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7104 (mp0) REVERT: B 391 LYS cc_start: 0.8538 (tttt) cc_final: 0.7990 (tmmt) REVERT: B 502 VAL cc_start: 0.8536 (t) cc_final: 0.8299 (m) REVERT: B 506 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7843 (m) REVERT: B 716 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7432 (tt0) REVERT: B 750 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6349 (tp) REVERT: C 102 ASN cc_start: 0.7100 (p0) cc_final: 0.6862 (p0) REVERT: C 122 VAL cc_start: 0.7571 (p) cc_final: 0.7244 (t) REVERT: C 186 THR cc_start: 0.8219 (m) cc_final: 0.7957 (p) REVERT: C 187 LYS cc_start: 0.8167 (ptpt) cc_final: 0.7894 (ptpt) REVERT: C 197 LYS cc_start: 0.6549 (pmtt) cc_final: 0.5851 (pttt) REVERT: D 119 ILE cc_start: -0.0357 (OUTLIER) cc_final: -0.0976 (tt) REVERT: D 127 ASP cc_start: -0.0545 (OUTLIER) cc_final: -0.0777 (m-30) REVERT: D 156 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6653 (mtp180) REVERT: D 163 MET cc_start: 0.5090 (ttt) cc_final: 0.3776 (mpt) REVERT: D 166 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.4500 (tp) REVERT: D 194 ILE cc_start: 0.7505 (mm) cc_final: 0.7285 (mp) REVERT: D 220 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6955 (mm-30) REVERT: D 243 ARG cc_start: 0.6955 (ttp-110) cc_final: 0.6733 (ttp80) REVERT: D 264 LEU cc_start: 0.5580 (OUTLIER) cc_final: 0.5313 (tp) REVERT: D 308 GLN cc_start: 0.2341 (OUTLIER) cc_final: 0.1383 (mt0) REVERT: D 339 GLU cc_start: 0.2666 (OUTLIER) cc_final: 0.1300 (tm-30) REVERT: D 416 ARG cc_start: 0.3655 (OUTLIER) cc_final: 0.2994 (mmm160) REVERT: D 422 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6358 (mppt) REVERT: D 455 GLU cc_start: 0.3562 (OUTLIER) cc_final: 0.2037 (mp0) REVERT: D 479 PHE cc_start: -0.2235 (OUTLIER) cc_final: -0.4066 (m-80) outliers start: 109 outliers final: 46 residues processed: 449 average time/residue: 0.6941 time to fit residues: 343.1871 Evaluate side-chains 426 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 365 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 687 GLN Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 66 optimal weight: 0.0980 chunk 159 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 340 GLN A 359 ASN A 519 ASN B 276 ASN B 603 ASN B 642 ASN B 687 GLN C 110 HIS C 236 GLN D 76 ASN D 125 ASN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 324 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.182034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144119 restraints weight = 25492.154| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.40 r_work: 0.3622 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18262 Z= 0.176 Angle : 0.670 17.215 24787 Z= 0.357 Chirality : 0.044 0.227 2728 Planarity : 0.006 0.074 3066 Dihedral : 15.050 178.044 3018 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 6.24 % Allowed : 18.41 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.17), residues: 2106 helix: -0.44 (0.16), residues: 961 sheet: -0.87 (0.36), residues: 194 loop : -2.87 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 496 TYR 0.017 0.002 TYR A 131 PHE 0.035 0.002 PHE A 46 TRP 0.030 0.002 TRP D 139 HIS 0.010 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (18262) covalent geometry : angle 0.67042 / 0.36 (24787) hydrogen bonds : bond 0.05802 / 3.82 ( 740) hydrogen bonds : angle 4.86146 / 3.39 ( 2069) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 386 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7763 (pm20) cc_final: 0.7517 (pm20) REVERT: A 41 HIS cc_start: 0.7677 (t-170) cc_final: 0.7435 (t70) REVERT: A 47 MET cc_start: 0.6087 (tpt) cc_final: 0.5540 (tpt) REVERT: A 97 THR cc_start: 0.7052 (OUTLIER) cc_final: 0.6600 (p) REVERT: A 133 GLU cc_start: 0.4148 (OUTLIER) cc_final: 0.3681 (mp0) REVERT: A 187 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6213 (pp) REVERT: A 286 ASP cc_start: 0.6717 (t0) cc_final: 0.6359 (t0) REVERT: A 321 TYR cc_start: 0.7272 (p90) cc_final: 0.6998 (p90) REVERT: A 396 ASP cc_start: 0.7496 (m-30) cc_final: 0.7237 (m-30) REVERT: A 430 GLU cc_start: 0.7420 (pm20) cc_final: 0.7137 (mp0) REVERT: A 548 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6951 (ttp) REVERT: B 8 LEU cc_start: 0.8392 (mt) cc_final: 0.8142 (mt) REVERT: B 92 MET cc_start: 0.7543 (mmt) cc_final: 0.6075 (mmt) REVERT: B 311 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6850 (mm-30) REVERT: B 391 LYS cc_start: 0.8326 (tttt) cc_final: 0.7908 (tttm) REVERT: B 571 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7175 (tpp-160) REVERT: B 667 ILE cc_start: 0.8451 (mt) cc_final: 0.8143 (mp) REVERT: B 716 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7073 (tt0) REVERT: B 750 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6299 (tp) REVERT: C 102 ASN cc_start: 0.6884 (p0) cc_final: 0.6660 (p0) REVERT: C 122 VAL cc_start: 0.7397 (p) cc_final: 0.7165 (t) REVERT: C 186 THR cc_start: 0.8127 (m) cc_final: 0.7913 (p) REVERT: C 197 LYS cc_start: 0.6450 (pmtt) cc_final: 0.5685 (pttt) REVERT: D 107 GLU cc_start: 0.2595 (OUTLIER) cc_final: 0.2258 (pm20) REVERT: D 110 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6865 (pp) REVERT: D 119 ILE cc_start: -0.0259 (OUTLIER) cc_final: -0.0872 (tt) REVERT: D 166 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.4809 (tp) REVERT: D 194 ILE cc_start: 0.7588 (mm) cc_final: 0.7327 (mp) REVERT: D 220 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6773 (mm-30) REVERT: D 222 MET cc_start: 0.7655 (mtt) cc_final: 0.7129 (mtm) REVERT: D 243 ARG cc_start: 0.6981 (ttp-110) cc_final: 0.6728 (ttp80) REVERT: D 257 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7296 (mp) REVERT: D 264 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5464 (tp) REVERT: D 339 GLU cc_start: 0.2413 (OUTLIER) cc_final: 0.0821 (tm-30) REVERT: D 416 ARG cc_start: 0.4014 (OUTLIER) cc_final: 0.3229 (mmm160) REVERT: D 422 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.5972 (mttt) REVERT: D 455 GLU cc_start: 0.2795 (OUTLIER) cc_final: 0.0873 (tt0) REVERT: D 479 PHE cc_start: -0.2249 (OUTLIER) cc_final: -0.3998 (m-80) outliers start: 117 outliers final: 55 residues processed: 457 average time/residue: 0.6739 time to fit residues: 339.2792 Evaluate side-chains 444 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 372 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 138 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN A 519 ASN B 247 GLN B 276 ASN B 485 ASN B 603 ASN B 642 ASN B 679 GLN C 110 HIS D 125 ASN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.181721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143769 restraints weight = 25385.724| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.30 r_work: 0.3635 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 18262 Z= 0.191 Angle : 0.677 18.023 24787 Z= 0.356 Chirality : 0.044 0.223 2728 Planarity : 0.005 0.069 3066 Dihedral : 14.694 179.251 3002 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.35 % Rotamer: Outliers : 5.92 % Allowed : 19.90 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.17), residues: 2106 helix: -0.24 (0.17), residues: 968 sheet: -0.78 (0.36), residues: 198 loop : -2.82 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 116 TYR 0.017 0.002 TYR A 540 PHE 0.027 0.002 PHE A 46 TRP 0.034 0.002 TRP D 139 HIS 0.009 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (18262) covalent geometry : angle 0.67654 / 0.36 (24787) hydrogen bonds : bond 0.05739 / 3.76 ( 740) hydrogen bonds : angle 4.77054 / 3.33 ( 2069) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 373 time to evaluate : 0.630 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 18 GLU cc_start: 0.7907 (pm20) cc_final: 0.7573 (pm20) REVERT: A 26 GLU cc_start: 0.4157 (OUTLIER) cc_final: 0.3619 (mm-30) REVERT: A 47 MET cc_start: 0.6220 (tpt) cc_final: 0.5645 (tpt) REVERT: A 97 THR cc_start: 0.7179 (OUTLIER) cc_final: 0.6712 (p) REVERT: A 133 GLU cc_start: 0.4233 (OUTLIER) cc_final: 0.3729 (mp0) REVERT: A 187 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6271 (pp) REVERT: A 286 ASP cc_start: 0.6963 (t0) cc_final: 0.6572 (t0) REVERT: A 321 TYR cc_start: 0.7454 (p90) cc_final: 0.7101 (p90) REVERT: A 430 GLU cc_start: 0.7832 (pm20) cc_final: 0.7537 (mp0) REVERT: A 548 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7167 (ttp) REVERT: B 8 LEU cc_start: 0.8465 (mt) cc_final: 0.8232 (mt) REVERT: B 391 LYS cc_start: 0.8559 (tttt) cc_final: 0.8074 (tttm) REVERT: B 571 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7477 (tpp-160) REVERT: B 667 ILE cc_start: 0.8537 (mt) cc_final: 0.8236 (mp) REVERT: B 716 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7425 (tt0) REVERT: B 750 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6388 (tp) REVERT: C 102 ASN cc_start: 0.7096 (p0) cc_final: 0.6889 (p0) REVERT: C 122 VAL cc_start: 0.7529 (p) cc_final: 0.7082 (t) REVERT: C 187 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7925 (ptpt) REVERT: C 197 LYS cc_start: 0.6659 (pmtt) cc_final: 0.5825 (pttt) REVERT: D 110 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6877 (pp) REVERT: D 119 ILE cc_start: -0.0149 (OUTLIER) cc_final: -0.0837 (tt) REVERT: D 166 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5208 (tp) REVERT: D 193 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8043 (mp) REVERT: D 220 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6985 (mm-30) REVERT: D 222 MET cc_start: 0.7804 (mtt) cc_final: 0.7270 (mtm) REVERT: D 243 ARG cc_start: 0.7136 (ttp-110) cc_final: 0.6863 (ttp80) REVERT: D 264 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5454 (tp) REVERT: D 308 GLN cc_start: 0.2237 (OUTLIER) cc_final: 0.2033 (mp10) REVERT: D 339 GLU cc_start: 0.2828 (OUTLIER) cc_final: 0.0800 (tm-30) REVERT: D 360 THR cc_start: 0.2681 (OUTLIER) cc_final: 0.2459 (t) REVERT: D 379 LEU cc_start: 0.0217 (OUTLIER) cc_final: -0.0081 (tp) REVERT: D 416 ARG cc_start: 0.4117 (OUTLIER) cc_final: 0.3235 (mmm160) REVERT: D 455 GLU cc_start: 0.3737 (OUTLIER) cc_final: 0.1053 (pt0) REVERT: D 479 PHE cc_start: -0.2096 (OUTLIER) cc_final: -0.3959 (m-80) outliers start: 111 outliers final: 53 residues processed: 443 average time/residue: 0.6607 time to fit residues: 322.8514 Evaluate side-chains 440 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 368 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 209 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN A 359 ASN A 519 ASN B 276 ASN B 603 ASN B 642 ASN C 110 HIS C 236 GLN D 125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.182022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144520 restraints weight = 25236.380| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.50 r_work: 0.3631 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18262 Z= 0.167 Angle : 0.659 18.359 24787 Z= 0.345 Chirality : 0.043 0.217 2728 Planarity : 0.005 0.065 3066 Dihedral : 14.398 179.967 2986 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 5.60 % Allowed : 21.40 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2106 helix: -0.08 (0.17), residues: 965 sheet: -0.60 (0.36), residues: 200 loop : -2.75 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 116 TYR 0.016 0.002 TYR A 131 PHE 0.021 0.002 PHE A 46 TRP 0.028 0.002 TRP D 139 HIS 0.007 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (18262) covalent geometry : angle 0.65894 / 0.34 (24787) hydrogen bonds : bond 0.05394 / 3.53 ( 740) hydrogen bonds : angle 4.67838 / 3.27 ( 2069) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 375 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.3928 (OUTLIER) cc_final: 0.3502 (mm-30) REVERT: A 47 MET cc_start: 0.6055 (tpt) cc_final: 0.5481 (tpt) REVERT: A 97 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6580 (p) REVERT: A 133 GLU cc_start: 0.4052 (OUTLIER) cc_final: 0.3576 (mp0) REVERT: A 217 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6835 (mt0) REVERT: A 321 TYR cc_start: 0.7296 (p90) cc_final: 0.6951 (p90) REVERT: A 430 GLU cc_start: 0.7406 (pm20) cc_final: 0.7162 (mp0) REVERT: A 548 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6951 (ttp) REVERT: B 8 LEU cc_start: 0.8367 (mt) cc_final: 0.8119 (mt) REVERT: B 391 LYS cc_start: 0.8316 (tttt) cc_final: 0.7869 (tttm) REVERT: B 571 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7361 (tpp-160) REVERT: B 667 ILE cc_start: 0.8445 (mt) cc_final: 0.8123 (mp) REVERT: B 695 LEU cc_start: 0.8249 (mp) cc_final: 0.8021 (mp) REVERT: B 750 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.6263 (tp) REVERT: C 122 VAL cc_start: 0.7277 (p) cc_final: 0.7016 (t) REVERT: C 197 LYS cc_start: 0.6498 (pmtt) cc_final: 0.6075 (pmtt) REVERT: D 110 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6833 (pp) REVERT: D 119 ILE cc_start: -0.0192 (OUTLIER) cc_final: -0.0872 (tt) REVERT: D 166 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5274 (tp) REVERT: D 175 ARG cc_start: 0.5851 (pmt-80) cc_final: 0.5601 (pmt-80) REVERT: D 193 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7908 (mp) REVERT: D 196 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6412 (mmt) REVERT: D 220 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6811 (mm-30) REVERT: D 222 MET cc_start: 0.7614 (mtt) cc_final: 0.6997 (mtm) REVERT: D 243 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6727 (ttp80) REVERT: D 339 GLU cc_start: 0.2320 (OUTLIER) cc_final: 0.0587 (tm-30) REVERT: D 360 THR cc_start: 0.2697 (OUTLIER) cc_final: 0.2490 (t) REVERT: D 379 LEU cc_start: -0.0229 (OUTLIER) cc_final: -0.0546 (tp) REVERT: D 416 ARG cc_start: 0.3998 (OUTLIER) cc_final: 0.3149 (mmm160) REVERT: D 455 GLU cc_start: 0.2597 (OUTLIER) cc_final: 0.1047 (pt0) REVERT: D 479 PHE cc_start: -0.2270 (OUTLIER) cc_final: -0.4045 (m-80) outliers start: 105 outliers final: 60 residues processed: 440 average time/residue: 0.6575 time to fit residues: 318.7092 Evaluate side-chains 446 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 368 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 106 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 138 optimal weight: 0.0000 chunk 87 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN A 359 ASN A 519 ASN B 276 ASN B 346 ASN B 603 ASN B 642 ASN C 27 HIS C 110 HIS D 125 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.182940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144581 restraints weight = 25086.145| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.05 r_work: 0.3686 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18262 Z= 0.142 Angle : 0.633 18.632 24787 Z= 0.332 Chirality : 0.042 0.211 2728 Planarity : 0.005 0.066 3066 Dihedral : 14.213 179.485 2978 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.59 % Rotamer: Outliers : 5.39 % Allowed : 22.09 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.18), residues: 2106 helix: 0.05 (0.17), residues: 963 sheet: -0.48 (0.37), residues: 200 loop : -2.69 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 213 TYR 0.016 0.001 TYR A 131 PHE 0.019 0.001 PHE A 46 TRP 0.040 0.002 TRP D 139 HIS 0.006 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (18262) covalent geometry : angle 0.63300 / 0.33 (24787) hydrogen bonds : bond 0.04928 / 3.23 ( 740) hydrogen bonds : angle 4.59671 / 3.22 ( 2069) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 371 time to evaluate : 0.605 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 18 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: A 26 GLU cc_start: 0.3900 (OUTLIER) cc_final: 0.3490 (mm-30) REVERT: A 47 MET cc_start: 0.6140 (tpt) cc_final: 0.5570 (tpt) REVERT: A 97 THR cc_start: 0.7119 (OUTLIER) cc_final: 0.6630 (p) REVERT: A 129 ILE cc_start: 0.1427 (OUTLIER) cc_final: 0.0762 (pp) REVERT: A 133 GLU cc_start: 0.4039 (OUTLIER) cc_final: 0.3572 (mp0) REVERT: A 217 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6923 (mt0) REVERT: A 321 TYR cc_start: 0.7449 (p90) cc_final: 0.7068 (p90) REVERT: A 396 ASP cc_start: 0.7622 (m-30) cc_final: 0.7358 (m-30) REVERT: A 430 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 456 THR cc_start: 0.7566 (m) cc_final: 0.7324 (p) REVERT: A 623 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: B 8 LEU cc_start: 0.8356 (mt) cc_final: 0.8104 (mt) REVERT: B 92 MET cc_start: 0.7297 (mmt) cc_final: 0.6289 (mmt) REVERT: B 311 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6733 (mp0) REVERT: B 391 LYS cc_start: 0.8442 (tttt) cc_final: 0.7941 (tttm) REVERT: B 506 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7817 (m) REVERT: B 571 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7575 (tpp-160) REVERT: B 619 ASP cc_start: 0.6411 (p0) cc_final: 0.6103 (p0) REVERT: B 667 ILE cc_start: 0.8459 (mt) cc_final: 0.8129 (mp) REVERT: B 679 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6864 (mm-40) REVERT: B 750 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6307 (tp) REVERT: C 38 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7965 (ptp-170) REVERT: C 122 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6815 (t) REVERT: C 197 LYS cc_start: 0.6583 (pmtt) cc_final: 0.6211 (pmtt) REVERT: D 110 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6821 (pp) REVERT: D 163 MET cc_start: 0.5091 (ttt) cc_final: 0.4663 (tpt) REVERT: D 166 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5179 (tp) REVERT: D 175 ARG cc_start: 0.5972 (pmt-80) cc_final: 0.5643 (pmt-80) REVERT: D 193 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7903 (mp) REVERT: D 220 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6928 (mm-30) REVERT: D 243 ARG cc_start: 0.7004 (ttp-110) cc_final: 0.6750 (ttp80) REVERT: D 339 GLU cc_start: 0.2437 (OUTLIER) cc_final: 0.0684 (tm-30) REVERT: D 360 THR cc_start: 0.2692 (OUTLIER) cc_final: 0.2479 (t) REVERT: D 379 LEU cc_start: -0.0092 (OUTLIER) cc_final: -0.0399 (tp) REVERT: D 416 ARG cc_start: 0.4085 (OUTLIER) cc_final: 0.3168 (mmm160) REVERT: D 479 PHE cc_start: -0.2170 (OUTLIER) cc_final: -0.3964 (m-80) outliers start: 101 outliers final: 57 residues processed: 433 average time/residue: 0.6443 time to fit residues: 307.5011 Evaluate side-chains 444 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 366 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 165 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN A 519 ASN B 276 ASN B 476 ASN B 603 ASN B 642 ASN C 110 HIS ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.181897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144246 restraints weight = 25356.916| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.40 r_work: 0.3641 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18262 Z= 0.180 Angle : 0.662 18.446 24787 Z= 0.345 Chirality : 0.043 0.210 2728 Planarity : 0.005 0.101 3066 Dihedral : 14.070 179.185 2967 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 5.28 % Allowed : 22.95 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.18), residues: 2106 helix: 0.03 (0.17), residues: 961 sheet: -0.48 (0.37), residues: 200 loop : -2.67 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 168 TYR 0.017 0.002 TYR A 540 PHE 0.018 0.002 PHE B 574 TRP 0.022 0.002 TRP D 139 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (18262) covalent geometry : angle 0.66223 / 0.34 (24787) hydrogen bonds : bond 0.05303 / 3.44 ( 740) hydrogen bonds : angle 4.62974 / 3.23 ( 2069) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 370 time to evaluate : 0.624 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 18 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: A 26 GLU cc_start: 0.3965 (OUTLIER) cc_final: 0.3604 (mm-30) REVERT: A 47 MET cc_start: 0.6093 (tpt) cc_final: 0.5567 (tpt) REVERT: A 97 THR cc_start: 0.7172 (OUTLIER) cc_final: 0.6666 (p) REVERT: A 129 ILE cc_start: 0.1627 (OUTLIER) cc_final: 0.0938 (pp) REVERT: A 133 GLU cc_start: 0.4050 (OUTLIER) cc_final: 0.3583 (mp0) REVERT: A 217 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7028 (mt0) REVERT: A 321 TYR cc_start: 0.7458 (p90) cc_final: 0.7088 (p90) REVERT: A 430 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: B 8 LEU cc_start: 0.8437 (mt) cc_final: 0.8185 (mt) REVERT: B 92 MET cc_start: 0.7408 (mmt) cc_final: 0.6321 (mmt) REVERT: B 311 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6748 (mp0) REVERT: B 391 LYS cc_start: 0.8513 (tttt) cc_final: 0.8035 (tttm) REVERT: B 667 ILE cc_start: 0.8528 (mt) cc_final: 0.8219 (mp) REVERT: B 679 GLN cc_start: 0.7276 (mm-40) cc_final: 0.7040 (mm-40) REVERT: B 716 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7455 (tt0) REVERT: B 750 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6400 (tp) REVERT: C 38 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7465 (mtp180) REVERT: C 122 VAL cc_start: 0.7263 (OUTLIER) cc_final: 0.6855 (t) REVERT: C 186 THR cc_start: 0.8245 (m) cc_final: 0.7976 (p) REVERT: C 197 LYS cc_start: 0.6599 (pmtt) cc_final: 0.6237 (pmtt) REVERT: D 105 MET cc_start: 0.3766 (mmm) cc_final: 0.3528 (mmm) REVERT: D 110 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6872 (pp) REVERT: D 119 ILE cc_start: -0.0195 (OUTLIER) cc_final: -0.0979 (tt) REVERT: D 137 MET cc_start: 0.4254 (tmm) cc_final: 0.4026 (tmm) REVERT: D 163 MET cc_start: 0.5077 (ttt) cc_final: 0.4550 (tpt) REVERT: D 166 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5304 (tp) REVERT: D 175 ARG cc_start: 0.5903 (pmt-80) cc_final: 0.5672 (pmt-80) REVERT: D 189 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7310 (mpt) REVERT: D 220 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6993 (mm-30) REVERT: D 243 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6815 (ttp80) REVERT: D 339 GLU cc_start: 0.2704 (OUTLIER) cc_final: 0.0748 (tm-30) REVERT: D 379 LEU cc_start: -0.0144 (OUTLIER) cc_final: -0.0521 (tp) REVERT: D 416 ARG cc_start: 0.4182 (OUTLIER) cc_final: 0.3166 (mmm160) REVERT: D 479 PHE cc_start: -0.1961 (OUTLIER) cc_final: -0.3874 (m-80) outliers start: 99 outliers final: 58 residues processed: 429 average time/residue: 0.6750 time to fit residues: 318.2484 Evaluate side-chains 447 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 371 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 149 optimal weight: 0.0970 chunk 136 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.1980 chunk 148 optimal weight: 0.5980 chunk 117 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 359 ASN A 519 ASN B 276 ASN B 310 ASN B 476 ASN B 603 ASN B 642 ASN C 110 HIS ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.183149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145357 restraints weight = 25366.767| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.04 r_work: 0.3689 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18262 Z= 0.132 Angle : 0.650 18.848 24787 Z= 0.333 Chirality : 0.042 0.205 2728 Planarity : 0.005 0.067 3066 Dihedral : 13.970 178.982 2967 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 4.48 % Allowed : 23.64 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.18), residues: 2106 helix: 0.18 (0.17), residues: 964 sheet: -0.35 (0.38), residues: 195 loop : -2.58 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 213 TYR 0.016 0.001 TYR A 131 PHE 0.019 0.001 PHE A 446 TRP 0.056 0.002 TRP D 139 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (18262) covalent geometry : angle 0.64955 / 0.33 (24787) hydrogen bonds : bond 0.04682 / 3.07 ( 740) hydrogen bonds : angle 4.53310 / 3.17 ( 2069) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 367 time to evaluate : 0.634 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 18 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: A 26 GLU cc_start: 0.3814 (OUTLIER) cc_final: 0.3476 (mm-30) REVERT: A 47 MET cc_start: 0.5948 (tpt) cc_final: 0.5479 (tpt) REVERT: A 97 THR cc_start: 0.7112 (OUTLIER) cc_final: 0.6603 (p) REVERT: A 129 ILE cc_start: 0.1649 (OUTLIER) cc_final: 0.0962 (pp) REVERT: A 133 GLU cc_start: 0.3947 (OUTLIER) cc_final: 0.3500 (mp0) REVERT: A 211 MET cc_start: 0.7623 (tpt) cc_final: 0.7397 (mmt) REVERT: A 217 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.6876 (mt0) REVERT: A 234 ASP cc_start: 0.7258 (m-30) cc_final: 0.7054 (m-30) REVERT: A 263 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7837 (p) REVERT: A 321 TYR cc_start: 0.7403 (p90) cc_final: 0.7075 (p90) REVERT: A 396 ASP cc_start: 0.7632 (m-30) cc_final: 0.7382 (m-30) REVERT: A 430 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 8 LEU cc_start: 0.8419 (mt) cc_final: 0.8164 (mt) REVERT: B 92 MET cc_start: 0.7380 (mmt) cc_final: 0.6316 (mmt) REVERT: B 311 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6537 (mp0) REVERT: B 391 LYS cc_start: 0.8446 (tttt) cc_final: 0.7996 (tttm) REVERT: B 506 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7794 (m) REVERT: B 667 ILE cc_start: 0.8450 (mt) cc_final: 0.8129 (mp) REVERT: B 679 GLN cc_start: 0.7237 (mm-40) cc_final: 0.7036 (mm-40) REVERT: B 750 ILE cc_start: 0.6666 (OUTLIER) cc_final: 0.6358 (tp) REVERT: B 753 LEU cc_start: 0.8133 (mt) cc_final: 0.7931 (tt) REVERT: C 38 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7953 (ptp-170) REVERT: C 122 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6785 (t) REVERT: C 186 THR cc_start: 0.8199 (m) cc_final: 0.7949 (p) REVERT: C 197 LYS cc_start: 0.6554 (pmtt) cc_final: 0.6219 (pmtt) REVERT: D 110 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6807 (pp) REVERT: D 163 MET cc_start: 0.4962 (ttt) cc_final: 0.4493 (tpt) REVERT: D 166 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5463 (tp) REVERT: D 167 MET cc_start: 0.5687 (mtt) cc_final: 0.5457 (mtm) REVERT: D 175 ARG cc_start: 0.5930 (pmt-80) cc_final: 0.5662 (pmt-80) REVERT: D 220 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6924 (mm-30) REVERT: D 243 ARG cc_start: 0.7013 (ttp-110) cc_final: 0.6754 (ttp80) REVERT: D 339 GLU cc_start: 0.2591 (OUTLIER) cc_final: 0.0726 (tm-30) REVERT: D 360 THR cc_start: 0.2318 (OUTLIER) cc_final: 0.2088 (t) REVERT: D 416 ARG cc_start: 0.4113 (OUTLIER) cc_final: 0.3120 (mmm160) outliers start: 84 outliers final: 51 residues processed: 423 average time/residue: 0.6882 time to fit residues: 320.6205 Evaluate side-chains 436 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 368 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 147 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 166 optimal weight: 0.1980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 ASN B 276 ASN B 603 ASN B 642 ASN C 110 HIS D 59 ASN ** D 308 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 = 0.4285 r_free = 0.4285 target = 0.183152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145032 restraints weight = 25316.783| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.29 r_work: 0.3653 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18262 Z= 0.138 Angle : 0.651 18.680 24787 Z= 0.335 Chirality : 0.041 0.202 2728 Planarity : 0.005 0.066 3066 Dihedral : 13.854 178.868 2964 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 4.32 % Allowed : 24.49 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 2106 helix: 0.25 (0.17), residues: 967 sheet: -0.31 (0.38), residues: 196 loop : -2.52 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 168 TYR 0.016 0.001 TYR A 131 PHE 0.015 0.001 PHE A 46 TRP 0.036 0.002 TRP D 139 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (18262) covalent geometry : angle 0.65106 / 0.33 (24787) hydrogen bonds : bond 0.04695 / 3.07 ( 740) hydrogen bonds : angle 4.50145 / 3.14 ( 2069) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 372 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: A 26 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.3535 (mm-30) REVERT: A 47 MET cc_start: 0.5993 (tpt) cc_final: 0.5502 (tpt) REVERT: A 97 THR cc_start: 0.7136 (OUTLIER) cc_final: 0.6600 (p) REVERT: A 129 ILE cc_start: 0.1676 (OUTLIER) cc_final: 0.0969 (pp) REVERT: A 133 GLU cc_start: 0.3932 (OUTLIER) cc_final: 0.3487 (mp0) REVERT: A 217 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6926 (mt0) REVERT: A 234 ASP cc_start: 0.7326 (m-30) cc_final: 0.7114 (m-30) REVERT: A 263 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7865 (p) REVERT: A 321 TYR cc_start: 0.7440 (p90) cc_final: 0.7102 (p90) REVERT: A 430 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: B 8 LEU cc_start: 0.8462 (mt) cc_final: 0.8212 (mt) REVERT: B 92 MET cc_start: 0.7407 (mmt) cc_final: 0.6361 (mmt) REVERT: B 311 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6603 (mp0) REVERT: B 391 LYS cc_start: 0.8505 (tttt) cc_final: 0.8279 (tttm) REVERT: B 506 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7857 (m) REVERT: B 667 ILE cc_start: 0.8480 (mt) cc_final: 0.8161 (mp) REVERT: B 685 ASP cc_start: 0.7987 (m-30) cc_final: 0.7767 (m-30) REVERT: B 750 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6339 (tp) REVERT: C 38 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7977 (ptp-170) REVERT: C 122 VAL cc_start: 0.7164 (OUTLIER) cc_final: 0.6709 (t) REVERT: C 186 THR cc_start: 0.8257 (m) cc_final: 0.7980 (p) REVERT: C 197 LYS cc_start: 0.6587 (pmtt) cc_final: 0.6258 (pmtt) REVERT: C 236 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: D 110 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6817 (pp) REVERT: D 163 MET cc_start: 0.5068 (ttt) cc_final: 0.4560 (tpt) REVERT: D 166 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5068 (tp) REVERT: D 167 MET cc_start: 0.5874 (mtt) cc_final: 0.5614 (mtm) REVERT: D 174 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.6480 (tpp80) REVERT: D 175 ARG cc_start: 0.6009 (pmt-80) cc_final: 0.5740 (pmt-80) REVERT: D 189 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7296 (mpt) REVERT: D 196 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6737 (mmt) REVERT: D 243 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6792 (ttp80) REVERT: D 339 GLU cc_start: 0.2643 (OUTLIER) cc_final: 0.0578 (tm-30) REVERT: D 360 THR cc_start: 0.2323 (OUTLIER) cc_final: 0.2097 (t) REVERT: D 416 ARG cc_start: 0.4189 (OUTLIER) cc_final: 0.3138 (mmm160) outliers start: 81 outliers final: 48 residues processed: 424 average time/residue: 0.6781 time to fit residues: 316.2467 Evaluate side-chains 436 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 368 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 81 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 189 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 134 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 340 GLN A 519 ASN B 276 ASN B 603 ASN B 642 ASN C 110 HIS C 236 GLN D 308 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.182770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144518 restraints weight = 25197.375| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.06 r_work: 0.3674 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18262 Z= 0.154 Angle : 0.682 18.509 24787 Z= 0.349 Chirality : 0.042 0.200 2728 Planarity : 0.005 0.061 3066 Dihedral : 13.767 178.703 2960 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 3.95 % Allowed : 24.81 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.18), residues: 2106 helix: 0.29 (0.17), residues: 965 sheet: -0.32 (0.38), residues: 195 loop : -2.55 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 213 TYR 0.015 0.001 TYR A 131 PHE 0.022 0.001 PHE B 696 TRP 0.061 0.002 TRP D 139 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (18262) covalent geometry : angle 0.68230 / 0.35 (24787) hydrogen bonds : bond 0.04956 / 3.23 ( 740) hydrogen bonds : angle 4.51741 / 3.15 ( 2069) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 366 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: A 26 GLU cc_start: 0.3673 (OUTLIER) cc_final: 0.3373 (mm-30) REVERT: A 47 MET cc_start: 0.5939 (tpt) cc_final: 0.5454 (tpt) REVERT: A 97 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6555 (p) REVERT: A 102 LYS cc_start: 0.4028 (OUTLIER) cc_final: 0.3796 (ptpt) REVERT: A 129 ILE cc_start: 0.1793 (OUTLIER) cc_final: 0.1086 (pp) REVERT: A 133 GLU cc_start: 0.3947 (OUTLIER) cc_final: 0.3502 (mp0) REVERT: A 185 ARG cc_start: 0.7608 (mmp80) cc_final: 0.7289 (mmp80) REVERT: A 211 MET cc_start: 0.7659 (tpt) cc_final: 0.7453 (mmt) REVERT: A 217 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6953 (mt0) REVERT: A 234 ASP cc_start: 0.7300 (m-30) cc_final: 0.7092 (m-30) REVERT: A 321 TYR cc_start: 0.7391 (p90) cc_final: 0.7083 (p90) REVERT: A 430 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: B 8 LEU cc_start: 0.8455 (mt) cc_final: 0.8206 (mt) REVERT: B 92 MET cc_start: 0.7454 (mmt) cc_final: 0.6401 (mmt) REVERT: B 506 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7845 (m) REVERT: B 667 ILE cc_start: 0.8496 (mt) cc_final: 0.8174 (mp) REVERT: B 695 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 750 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6348 (tp) REVERT: C 38 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7944 (ptp-170) REVERT: C 122 VAL cc_start: 0.7089 (OUTLIER) cc_final: 0.6707 (t) REVERT: C 197 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6238 (pmtt) REVERT: D 32 MET cc_start: 0.3721 (ttp) cc_final: 0.2094 (tmm) REVERT: D 110 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6830 (pp) REVERT: D 166 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5166 (tp) REVERT: D 175 ARG cc_start: 0.6110 (pmt-80) cc_final: 0.5904 (pmt-80) REVERT: D 189 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7779 (mpp) REVERT: D 193 LEU cc_start: 0.8270 (mp) cc_final: 0.8004 (mp) REVERT: D 238 MET cc_start: 0.7658 (mmm) cc_final: 0.7113 (tpp) REVERT: D 243 ARG cc_start: 0.7037 (ttp-110) cc_final: 0.6831 (ttp80) REVERT: D 339 GLU cc_start: 0.2517 (OUTLIER) cc_final: 0.0504 (tm-30) REVERT: D 360 THR cc_start: 0.2230 (OUTLIER) cc_final: 0.2002 (t) REVERT: D 416 ARG cc_start: 0.4180 (OUTLIER) cc_final: 0.3111 (mmm160) outliers start: 74 outliers final: 44 residues processed: 413 average time/residue: 0.6943 time to fit residues: 315.9395 Evaluate side-chains 427 residues out of total 1874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 363 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 416 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 479 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 132 optimal weight: 0.0570 chunk 163 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 31 optimal weight: 0.0570 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 340 GLN A 519 ASN B 276 ASN B 603 ASN B 642 ASN C 110 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.184383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147960 restraints weight = 25371.207| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.49 r_work: 0.3683 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18262 Z= 0.124 Angle : 0.653 18.950 24787 Z= 0.333 Chirality : 0.041 0.197 2728 Planarity : 0.005 0.066 3066 Dihedral : 13.679 178.715 2956 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 3.79 % Allowed : 25.29 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.34 (0.18), residues: 2106 helix: 0.40 (0.17), residues: 970 sheet: -0.25 (0.38), residues: 198 loop : -2.51 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 116 TYR 0.016 0.001 TYR A 131 PHE 0.016 0.001 PHE A 46 TRP 0.047 0.002 TRP D 139 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (18262) covalent geometry : angle 0.65282 / 0.33 (24787) hydrogen bonds : bond 0.04343 / 2.86 ( 740) hydrogen bonds : angle 4.43453 / 3.10 ( 2069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8288.07 seconds wall clock time: 141 minutes 30.48 seconds (8490.48 seconds total)