Starting phenix.real_space_refine on Fri Sep 19 11:30:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2j_47454/09_2025/9e2j_47454.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2j_47454/09_2025/9e2j_47454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2j_47454/09_2025/9e2j_47454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2j_47454/09_2025/9e2j_47454.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2j_47454/09_2025/9e2j_47454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2j_47454/09_2025/9e2j_47454.cif" } resolution = 3.59 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 155 5.16 5 C 16217 2.51 5 N 4396 2.21 5 O 4792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 155 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25560 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4891 Classifications: {'peptide': 605} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 3 Chain: "B" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4448 Classifications: {'peptide': 553} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 529} Chain breaks: 9 Chain: "C" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4705 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 24, 'TRANS': 559} Chain breaks: 6 Chain: "D" Number of atoms: 4814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4814 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 24, 'TRANS': 571} Chain breaks: 6 Chain: "E" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4387 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 23, 'TRANS': 522} Chain breaks: 9 Chain: "F" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2315 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 12, 'TRANS': 277} Chain breaks: 1 Time building chain proxies: 6.33, per 1000 atoms: 0.25 Number of scatterers: 25560 At special positions: 0 Unit cell: (137.16, 130.68, 172.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 155 16.00 O 4792 8.00 N 4396 7.00 C 16217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5966 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 4 sheets defined 77.5% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 59 through 75 removed outlier: 3.605A pdb=" N GLU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 removed outlier: 4.410A pdb=" N VAL A 96 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 123 removed outlier: 3.785A pdb=" N LEU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 169 removed outlier: 3.720A pdb=" N LEU A 162 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 removed outlier: 3.629A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.698A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 228 through 265 Proline residue: A 237 - end of helix Proline residue: A 241 - end of helix removed outlier: 3.720A pdb=" N GLY A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 285 through 315 removed outlier: 4.120A pdb=" N GLU A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.912A pdb=" N THR A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.860A pdb=" N ASN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.579A pdb=" N HIS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.663A pdb=" N ILE A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 removed outlier: 4.070A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 488 removed outlier: 3.693A pdb=" N LYS A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.963A pdb=" N ILE A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 502' Processing helix chain 'A' and resid 503 through 525 removed outlier: 3.561A pdb=" N ASN A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 555 removed outlier: 4.020A pdb=" N MET A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.558A pdb=" N ASP A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 4.241A pdb=" N PHE A 575 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 617 removed outlier: 3.609A pdb=" N PHE A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 647 Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.775A pdb=" N SER A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.731A pdb=" N THR A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 710 removed outlier: 3.791A pdb=" N ALA A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 690 " --> pdb=" O TYR A 686 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 695 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.674A pdb=" N ARG A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.502A pdb=" N GLU B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 102 through 124 removed outlier: 4.057A pdb=" N ALA B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 169 removed outlier: 3.743A pdb=" N LYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 162 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 188 removed outlier: 3.879A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 4.071A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 224 Processing helix chain 'B' and resid 228 through 235 removed outlier: 3.528A pdb=" N ILE B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.730A pdb=" N TYR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.803A pdb=" N GLU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B 263 " --> pdb=" O TRP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 313 removed outlier: 4.144A pdb=" N GLN B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 319 removed outlier: 4.121A pdb=" N GLU B 318 " --> pdb=" O GLY B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 347 through 350 removed outlier: 3.626A pdb=" N LEU B 350 " --> pdb=" O HIS B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 431 through 439 removed outlier: 4.499A pdb=" N ALA B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 459 removed outlier: 3.708A pdb=" N ASN B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 488 removed outlier: 3.765A pdb=" N ASN B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 467 " --> pdb=" O HIS B 463 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 503 through 522 removed outlier: 3.570A pdb=" N ASN B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 554 removed outlier: 3.515A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.611A pdb=" N ASP B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 Processing helix chain 'B' and resid 587 through 591 removed outlier: 3.544A pdb=" N GLN B 590 " --> pdb=" O PRO B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 619 removed outlier: 3.576A pdb=" N ASP B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 removed outlier: 3.508A pdb=" N HIS B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 643 " --> pdb=" O PRO B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 660 removed outlier: 3.527A pdb=" N GLN B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 679 Processing helix chain 'B' and resid 682 through 710 removed outlier: 4.102A pdb=" N GLU B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 690 " --> pdb=" O TYR B 686 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 695 " --> pdb=" O MET B 691 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 709 " --> pdb=" O LEU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 723 removed outlier: 3.629A pdb=" N LEU B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 721 " --> pdb=" O ARG B 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 77 removed outlier: 3.725A pdb=" N GLY C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 102 through 124 removed outlier: 4.283A pdb=" N VAL C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 169 removed outlier: 3.793A pdb=" N ILE C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C 162 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 188 removed outlier: 3.790A pdb=" N VAL C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.021A pdb=" N TYR C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 228 through 263 Proline residue: C 237 - end of helix Proline residue: C 241 - end of helix removed outlier: 3.976A pdb=" N GLY C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 256 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.556A pdb=" N LEU C 277 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU C 282 " --> pdb=" O PHE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 removed outlier: 3.920A pdb=" N GLN C 299 " --> pdb=" O GLU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 331 through 341 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 350 through 361 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 446 through 459 removed outlier: 3.927A pdb=" N ILE C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP C 452 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 487 removed outlier: 3.690A pdb=" N GLN C 467 " --> pdb=" O HIS C 463 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 525 removed outlier: 3.534A pdb=" N ILE C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 538 Processing helix chain 'C' and resid 538 through 554 removed outlier: 3.859A pdb=" N PHE C 547 " --> pdb=" O ILE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 567 Processing helix chain 'C' and resid 571 through 586 removed outlier: 3.999A pdb=" N PHE C 575 " --> pdb=" O THR C 571 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN C 584 " --> pdb=" O ARG C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 616 removed outlier: 3.541A pdb=" N LEU C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 614 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 647 Processing helix chain 'C' and resid 652 through 657 Processing helix chain 'C' and resid 657 through 664 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 683 through 709 removed outlier: 3.655A pdb=" N GLU C 688 " --> pdb=" O ILE C 684 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 699 " --> pdb=" O MET C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 724 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 59 through 76 removed outlier: 3.835A pdb=" N ARG D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 106 through 124 Processing helix chain 'D' and resid 145 through 156 removed outlier: 3.654A pdb=" N ILE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 4.520A pdb=" N LEU D 162 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 189 removed outlier: 4.181A pdb=" N VAL D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 210 removed outlier: 4.296A pdb=" N TYR D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP D 204 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 208 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 224 Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 235 through 265 removed outlier: 3.601A pdb=" N LYS D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Proline residue: D 241 - end of helix removed outlier: 3.711A pdb=" N ALA D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 282 Processing helix chain 'D' and resid 285 through 314 removed outlier: 3.812A pdb=" N TYR D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 341 removed outlier: 3.732A pdb=" N GLN D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Proline residue: D 334 - end of helix removed outlier: 3.659A pdb=" N TRP D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 350 through 364 removed outlier: 4.174A pdb=" N HIS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 441 removed outlier: 4.473A pdb=" N ALA D 435 " --> pdb=" O LEU D 431 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 441 " --> pdb=" O TYR D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 456 removed outlier: 3.752A pdb=" N ILE D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 456 " --> pdb=" O ASP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 486 removed outlier: 3.762A pdb=" N VAL D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 467 " --> pdb=" O HIS D 463 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE D 471 " --> pdb=" O GLN D 467 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 482 " --> pdb=" O ALA D 478 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 removed outlier: 3.551A pdb=" N ILE D 501 " --> pdb=" O SER D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 522 Processing helix chain 'D' and resid 523 through 526 removed outlier: 3.806A pdb=" N ASP D 526 " --> pdb=" O ARG D 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 526' Processing helix chain 'D' and resid 527 through 538 removed outlier: 4.441A pdb=" N MET D 531 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP D 532 " --> pdb=" O PRO D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 554 removed outlier: 4.018A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 553 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 4.066A pdb=" N ARG D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 569 " --> pdb=" O ASP D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 586 removed outlier: 3.720A pdb=" N ARG D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 586 " --> pdb=" O MET D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 615 removed outlier: 3.585A pdb=" N SER D 599 " --> pdb=" O THR D 595 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU D 606 " --> pdb=" O ASP D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 643 Processing helix chain 'D' and resid 652 through 657 Processing helix chain 'D' and resid 659 through 664 Processing helix chain 'D' and resid 667 through 682 removed outlier: 3.613A pdb=" N GLN D 680 " --> pdb=" O SER D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 710 removed outlier: 3.674A pdb=" N GLU D 688 " --> pdb=" O ILE D 684 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 690 " --> pdb=" O TYR D 686 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 692 " --> pdb=" O GLU D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.700A pdb=" N ARG D 717 " --> pdb=" O ASN D 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.828A pdb=" N LEU E 33 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.813A pdb=" N LEU E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 98 removed outlier: 3.505A pdb=" N VAL E 96 " --> pdb=" O HIS E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 124 removed outlier: 3.574A pdb=" N LEU E 106 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 166 removed outlier: 3.770A pdb=" N GLU E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 189 Processing helix chain 'E' and resid 211 through 224 Processing helix chain 'E' and resid 228 through 234 Processing helix chain 'E' and resid 246 through 254 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 286 through 309 removed outlier: 3.540A pdb=" N LYS E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E 292 " --> pdb=" O GLN E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 331 Processing helix chain 'E' and resid 331 through 342 removed outlier: 4.145A pdb=" N GLY E 335 " --> pdb=" O TYR E 331 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E 336 " --> pdb=" O GLN E 332 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA E 338 " --> pdb=" O PRO E 334 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 358 removed outlier: 4.243A pdb=" N GLU E 353 " --> pdb=" O TRP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 440 Processing helix chain 'E' and resid 446 through 457 removed outlier: 3.654A pdb=" N ILE E 451 " --> pdb=" O ARG E 447 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP E 452 " --> pdb=" O GLU E 448 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TRP E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 488 removed outlier: 3.710A pdb=" N ALA E 472 " --> pdb=" O LEU E 468 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU E 486 " --> pdb=" O LEU E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 521 removed outlier: 3.619A pdb=" N MET E 519 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 521 " --> pdb=" O ASP E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 534 removed outlier: 4.226A pdb=" N MET E 531 " --> pdb=" O ASP E 527 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP E 532 " --> pdb=" O PRO E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 554 removed outlier: 3.655A pdb=" N ILE E 543 " --> pdb=" O ARG E 539 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR E 552 " --> pdb=" O ASP E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.889A pdb=" N ARG E 568 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 569 " --> pdb=" O ASP E 565 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E 571 " --> pdb=" O ILE E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 581 removed outlier: 4.029A pdb=" N PHE E 575 " --> pdb=" O THR E 571 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 578 " --> pdb=" O LEU E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 591 Processing helix chain 'E' and resid 594 through 619 removed outlier: 4.234A pdb=" N LEU E 600 " --> pdb=" O GLN E 596 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY E 605 " --> pdb=" O SER E 601 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 607 " --> pdb=" O VAL E 603 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP E 612 " --> pdb=" O PHE E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 637 through 647 removed outlier: 3.724A pdb=" N HIS E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 643 " --> pdb=" O PRO E 639 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 644 " --> pdb=" O LEU E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 659 Processing helix chain 'E' and resid 667 through 679 removed outlier: 3.626A pdb=" N THR E 673 " --> pdb=" O PRO E 669 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 710 Processing helix chain 'E' and resid 713 through 724 removed outlier: 3.740A pdb=" N LEU E 719 " --> pdb=" O VAL E 715 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS E 721 " --> pdb=" O ARG E 717 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 724 " --> pdb=" O ILE E 720 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 439 removed outlier: 4.469A pdb=" N ALA F 435 " --> pdb=" O LEU F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 454 Processing helix chain 'F' and resid 462 through 486 removed outlier: 4.154A pdb=" N ASN F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN F 467 " --> pdb=" O HIS F 463 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 468 " --> pdb=" O ARG F 464 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 482 " --> pdb=" O ALA F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 524 removed outlier: 4.600A pdb=" N ASN F 512 " --> pdb=" O ILE F 508 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET F 519 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F 520 " --> pdb=" O ILE F 516 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 527 No H-bonds generated for 'chain 'F' and resid 525 through 527' Processing helix chain 'F' and resid 528 through 555 removed outlier: 4.309A pdb=" N ASP F 532 " --> pdb=" O PRO F 528 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR F 534 " --> pdb=" O CYS F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 573 through 585 removed outlier: 3.578A pdb=" N LEU F 578 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR F 579 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE F 585 " --> pdb=" O MET F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 617 removed outlier: 4.081A pdb=" N LEU F 617 " --> pdb=" O ASP F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 647 Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.504A pdb=" N ARG F 654 " --> pdb=" O ASN F 650 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG F 661 " --> pdb=" O LEU F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 681 removed outlier: 3.546A pdb=" N THR F 673 " --> pdb=" O PRO F 669 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 675 " --> pdb=" O LYS F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 710 removed outlier: 3.719A pdb=" N ALA F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS F 690 " --> pdb=" O TYR F 686 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET F 695 " --> pdb=" O MET F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 4.525A pdb=" N LEU A 53 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA3, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'E' and resid 491 through 492 1510 hydrogen bonds defined for protein. 4482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8101 1.34 - 1.46: 3746 1.46 - 1.57: 13973 1.57 - 1.69: 0 1.69 - 1.81: 253 Bond restraints: 26073 Sorted by residual: bond pdb=" C VAL C 333 " pdb=" N PRO C 334 " ideal model delta sigma weight residual 1.335 1.375 -0.041 1.28e-02 6.10e+03 1.02e+01 bond pdb=" N ILE E 225 " pdb=" CA ILE E 225 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.20e-02 6.94e+03 8.23e+00 bond pdb=" N ARG D 291 " pdb=" CA ARG D 291 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.23e-02 6.61e+03 7.55e+00 bond pdb=" N MET E 223 " pdb=" CA MET E 223 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.37e-02 5.33e+03 6.77e+00 bond pdb=" N VAL B 668 " pdb=" CA VAL B 668 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.74e+00 ... (remaining 26068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 34130 2.12 - 4.24: 943 4.24 - 6.37: 138 6.37 - 8.49: 19 8.49 - 10.61: 7 Bond angle restraints: 35237 Sorted by residual: angle pdb=" N LYS D 327 " pdb=" CA LYS D 327 " pdb=" C LYS D 327 " ideal model delta sigma weight residual 111.82 101.21 10.61 1.16e+00 7.43e-01 8.37e+01 angle pdb=" N VAL E 583 " pdb=" CA VAL E 583 " pdb=" C VAL E 583 " ideal model delta sigma weight residual 111.90 107.26 4.64 8.10e-01 1.52e+00 3.28e+01 angle pdb=" N TRP D 457 " pdb=" CA TRP D 457 " pdb=" C TRP D 457 " ideal model delta sigma weight residual 114.16 105.73 8.43 1.48e+00 4.57e-01 3.25e+01 angle pdb=" N ILE E 585 " pdb=" CA ILE E 585 " pdb=" C ILE E 585 " ideal model delta sigma weight residual 113.43 107.46 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" N GLU D 536 " pdb=" CA GLU D 536 " pdb=" C GLU D 536 " ideal model delta sigma weight residual 114.75 107.98 6.77 1.26e+00 6.30e-01 2.88e+01 ... (remaining 35232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12761 17.96 - 35.92: 2138 35.92 - 53.88: 644 53.88 - 71.83: 152 71.83 - 89.79: 44 Dihedral angle restraints: 15739 sinusoidal: 6533 harmonic: 9206 Sorted by residual: dihedral pdb=" CA THR B 297 " pdb=" C THR B 297 " pdb=" N LYS B 298 " pdb=" CA LYS B 298 " ideal model delta harmonic sigma weight residual 180.00 152.88 27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLN D 156 " pdb=" C GLN D 156 " pdb=" N ILE D 157 " pdb=" CA ILE D 157 " ideal model delta harmonic sigma weight residual -180.00 -153.03 -26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA CYS E 101 " pdb=" C CYS E 101 " pdb=" N LYS E 102 " pdb=" CA LYS E 102 " ideal model delta harmonic sigma weight residual 180.00 154.65 25.35 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 15736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2648 0.039 - 0.078: 998 0.078 - 0.117: 211 0.117 - 0.156: 20 0.156 - 0.195: 5 Chirality restraints: 3882 Sorted by residual: chirality pdb=" CA ILE E 225 " pdb=" N ILE E 225 " pdb=" C ILE E 225 " pdb=" CB ILE E 225 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA LYS D 327 " pdb=" N LYS D 327 " pdb=" C LYS D 327 " pdb=" CB LYS D 327 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CA GLU A 236 " pdb=" N GLU A 236 " pdb=" C GLU A 236 " pdb=" CB GLU A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 3879 not shown) Planarity restraints: 4545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 73 " 0.016 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP D 73 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 73 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP D 73 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 73 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 73 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 73 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 73 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 73 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP D 73 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 172 " -0.254 9.50e-02 1.11e+02 1.14e-01 7.97e+00 pdb=" NE ARG B 172 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 172 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 172 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 172 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 324 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.48e+00 pdb=" C THR D 324 " -0.047 2.00e-02 2.50e+03 pdb=" O THR D 324 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR D 325 " 0.016 2.00e-02 2.50e+03 ... (remaining 4542 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 828 2.69 - 3.24: 27780 3.24 - 3.79: 42990 3.79 - 4.35: 58291 4.35 - 4.90: 86848 Nonbonded interactions: 216737 Sorted by model distance: nonbonded pdb=" OH TYR C 304 " pdb=" OE1 GLN C 329 " model vdw 2.136 3.040 nonbonded pdb=" O GLY C 503 " pdb=" OG1 THR C 507 " model vdw 2.156 3.040 nonbonded pdb=" O ILE C 641 " pdb=" OG1 THR C 645 " model vdw 2.163 3.040 nonbonded pdb=" O GLY A 46 " pdb=" NZ LYS A 298 " model vdw 2.169 3.120 nonbonded pdb=" O VAL A 293 " pdb=" OG1 THR A 297 " model vdw 2.174 3.040 ... (remaining 216732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 35 or resid 42 through 50 or resid 56 or resid \ 62 through 83 or resid 90 through 123 or resid 144 or resid 147 through 188 or r \ esid 209 through 239 or resid 245 through 265 or resid 271 through 274 or resid \ 290 through 309 or resid 321 through 358 or resid 427 through 618 or resid 631 t \ hrough 724)) selection = (chain 'B' and (resid 28 through 50 or resid 56 through 188 or resid 209 through \ 239 or resid 245 through 265 or resid 271 through 274 or resid 290 through 309 \ or resid 321 through 618 or resid 631 through 724)) selection = (chain 'C' and (resid 28 through 56 or resid 62 through 83 or resid 90 through 1 \ 24 or resid 147 through 188 or resid 209 through 239 or resid 245 through 265 or \ resid 271 through 274 or resid 290 through 309 or resid 321 through 358 or resi \ d 427 through 724)) selection = (chain 'D' and (resid 28 through 35 or resid 42 through 50 or resid 56 or resid \ 62 through 83 or resid 90 through 123 or resid 144 or resid 147 through 188 or r \ esid 209 through 239 or resid 245 through 265 or resid 271 through 274 or resid \ 290 through 309 or resid 321 through 358 or resid 427 through 618 or resid 631 t \ hrough 724)) selection = (chain 'E' and (resid 28 through 35 or resid 42 through 50 or resid 56 or resid \ 62 through 83 or resid 90 through 188 or resid 209 through 274 or resid 290 thro \ ugh 309 or resid 321 through 358 or resid 427 through 618 or resid 631 through 7 \ 24)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.730 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.004 0.049 26073 Z= 0.219 Angle : 0.843 10.610 35237 Z= 0.519 Chirality : 0.041 0.195 3882 Planarity : 0.006 0.114 4545 Dihedral : 20.101 89.792 9773 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.27 % Favored : 91.92 % Rotamer: Outliers : 6.74 % Allowed : 33.08 % Favored : 60.18 % 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 aren not related in a simple way. whole: -2.51 (0.14), residues: 3094 helix: -1.20 (0.11), residues: 2093 sheet: -6.50 (0.13), residues: 10 loop : -2.36 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 679 TYR 0.040 0.002 TYR D 550 PHE 0.035 0.002 PHE D 113 TRP 0.054 0.002 TRP D 73 HIS 0.009 0.001 HIS E 642 Details of bonding type rmsd covalent geometry : bond 0.00427 (26073) covalent geometry : angle 0.84313 (35237) hydrogen bonds : bond 0.33895 ( 1510) hydrogen bonds : angle 9.02514 ( 4482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 654 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.5336 (m-10) REVERT: A 55 ARG cc_start: 0.8075 (tpm170) cc_final: 0.7809 (tpm170) REVERT: A 68 ARG cc_start: 0.8408 (mtm110) cc_final: 0.7996 (mtp180) REVERT: A 72 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: A 73 TRP cc_start: 0.6971 (t-100) cc_final: 0.6683 (t-100) REVERT: A 74 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7585 (mm-30) REVERT: A 158 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7263 (mm-40) REVERT: A 218 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8580 (mt) REVERT: A 345 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6097 (mmt-90) REVERT: A 436 GLU cc_start: 0.7107 (tt0) cc_final: 0.6874 (tm-30) REVERT: A 466 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7583 (m-40) REVERT: A 560 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6376 (tt0) REVERT: A 575 PHE cc_start: 0.8452 (m-80) cc_final: 0.7993 (m-80) REVERT: A 671 LYS cc_start: 0.7794 (mmtm) cc_final: 0.7501 (mmmm) REVERT: A 672 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6767 (mm-30) REVERT: A 690 LYS cc_start: 0.8199 (tppp) cc_final: 0.7758 (tptm) REVERT: A 693 GLU cc_start: 0.6836 (tt0) cc_final: 0.6538 (mt-10) REVERT: B 73 TRP cc_start: 0.7783 (t-100) cc_final: 0.7223 (t-100) REVERT: B 117 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7749 (t80) REVERT: B 217 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6774 (mpp) REVERT: B 432 LEU cc_start: 0.8529 (mt) cc_final: 0.8219 (mp) REVERT: B 520 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6634 (mm-30) REVERT: B 550 TYR cc_start: 0.7753 (t80) cc_final: 0.7317 (t80) REVERT: B 717 ARG cc_start: 0.7493 (ttt-90) cc_final: 0.7290 (ttt-90) REVERT: C 31 SER cc_start: 0.7349 (OUTLIER) cc_final: 0.6775 (t) REVERT: C 64 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6594 (tm-30) REVERT: C 92 HIS cc_start: 0.6533 (OUTLIER) cc_final: 0.6314 (t70) REVERT: C 109 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8478 (tp) REVERT: C 157 ILE cc_start: 0.8834 (tp) cc_final: 0.8554 (tp) REVERT: C 158 GLN cc_start: 0.8358 (tp40) cc_final: 0.7716 (tp-100) REVERT: C 182 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7269 (tm-30) REVERT: C 183 MET cc_start: 0.8003 (tmm) cc_final: 0.7367 (tmm) REVERT: C 219 MET cc_start: 0.8553 (ttp) cc_final: 0.8293 (ttp) REVERT: C 238 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7161 (mp) REVERT: C 271 MET cc_start: 0.3854 (ttt) cc_final: 0.3335 (ttp) REVERT: C 358 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8645 (mt) REVERT: C 447 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7349 (mtm-85) REVERT: C 483 ASP cc_start: 0.6750 (m-30) cc_final: 0.6533 (t0) REVERT: C 536 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6281 (tp30) REVERT: C 548 ASP cc_start: 0.7604 (t70) cc_final: 0.7196 (t0) REVERT: C 568 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6790 (ttm-80) REVERT: C 602 ASP cc_start: 0.6892 (t0) cc_final: 0.6504 (t0) REVERT: C 672 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7265 (mm-30) REVERT: C 697 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7240 (mtmm) REVERT: C 719 LEU cc_start: 0.8321 (mp) cc_final: 0.8082 (mp) REVERT: C 722 ARG cc_start: 0.7581 (ttm170) cc_final: 0.7220 (ttm170) REVERT: D 68 ARG cc_start: 0.7219 (ptp90) cc_final: 0.6280 (ptp90) REVERT: D 74 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6905 (mm-30) REVERT: D 118 LEU cc_start: 0.7985 (mt) cc_final: 0.7591 (mt) REVERT: D 183 MET cc_start: 0.8188 (ttm) cc_final: 0.7746 (ttm) REVERT: D 206 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7627 (mmt90) REVERT: D 217 MET cc_start: 0.7771 (tpp) cc_final: 0.7232 (tpp) REVERT: D 219 MET cc_start: 0.7638 (tpp) cc_final: 0.6942 (tpp) REVERT: D 229 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6660 (pp30) REVERT: D 231 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7315 (pp20) REVERT: D 271 MET cc_start: 0.5340 (mtt) cc_final: 0.5091 (mtt) REVERT: D 350 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7687 (mt) REVERT: D 542 PHE cc_start: 0.7988 (m-10) cc_final: 0.7633 (m-80) REVERT: D 671 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7425 (mtmt) REVERT: E 113 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6055 (m-10) REVERT: E 155 LYS cc_start: 0.7756 (mtpt) cc_final: 0.7533 (mtpt) REVERT: E 161 MET cc_start: 0.7366 (ppp) cc_final: 0.6659 (ppp) REVERT: E 162 LEU cc_start: 0.8512 (mt) cc_final: 0.7991 (mt) REVERT: E 164 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7583 (mm-30) REVERT: E 165 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7881 (mt) REVERT: E 181 LYS cc_start: 0.8797 (mttt) cc_final: 0.8361 (mttt) REVERT: E 221 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6233 (p90) REVERT: E 229 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: E 260 GLU cc_start: 0.8380 (pt0) cc_final: 0.8175 (tp30) REVERT: E 271 MET cc_start: 0.6057 (ptt) cc_final: 0.5597 (ppp) REVERT: E 539 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7503 (mmm160) REVERT: E 548 ASP cc_start: 0.8128 (t0) cc_final: 0.7667 (t0) REVERT: E 613 ASP cc_start: 0.7360 (m-30) cc_final: 0.7078 (t0) REVERT: E 615 LYS cc_start: 0.7660 (mtpt) cc_final: 0.7352 (mtpt) REVERT: E 632 ASP cc_start: 0.7132 (m-30) cc_final: 0.6897 (m-30) REVERT: E 671 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7345 (mtmm) REVERT: E 672 GLU cc_start: 0.7043 (tp30) cc_final: 0.6728 (tp30) REVERT: F 429 GLU cc_start: 0.6488 (tm-30) cc_final: 0.6100 (tm-30) REVERT: F 483 ASP cc_start: 0.7025 (m-30) cc_final: 0.6756 (m-30) REVERT: F 490 PRO cc_start: 0.8538 (Cg_endo) cc_final: 0.8284 (Cg_exo) REVERT: F 568 ARG cc_start: 0.6981 (ttm-80) cc_final: 0.6587 (ttm-80) REVERT: F 608 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: F 613 ASP cc_start: 0.6938 (m-30) cc_final: 0.6662 (m-30) REVERT: F 614 TYR cc_start: 0.7207 (t80) cc_final: 0.6782 (t80) REVERT: F 671 LYS cc_start: 0.8203 (tttt) cc_final: 0.7901 (tttt) REVERT: F 672 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: F 695 MET cc_start: 0.7602 (mmt) cc_final: 0.7232 (mmm) REVERT: F 696 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: F 706 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7079 (mm-30) outliers start: 189 outliers final: 127 residues processed: 794 average time/residue: 0.2197 time to fit residues: 256.2438 Evaluate side-chains 791 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 638 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 466 ASN Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain C residue 509 ASN Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 530 CYS Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 696 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.5980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 178 ASN B 584 GLN B 647 GLN C 263 GLN C 303 GLN C 336 ASN ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 299 GLN D 336 ASN D 642 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 329 GLN ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 GLN E 596 GLN F 463 HIS F 476 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.176890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135817 restraints weight = 45168.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139289 restraints weight = 19371.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140235 restraints weight = 9421.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140970 restraints weight = 8494.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141126 restraints weight = 6971.061| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26073 Z= 0.207 Angle : 0.741 11.844 35237 Z= 0.397 Chirality : 0.042 0.193 3882 Planarity : 0.006 0.057 4545 Dihedral : 11.034 84.980 3792 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.66 % Favored : 92.66 % Rotamer: Outliers : 9.20 % Allowed : 27.59 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.15), residues: 3094 helix: -0.51 (0.11), residues: 2265 sheet: -6.57 (0.18), residues: 10 loop : -2.61 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 679 TYR 0.038 0.002 TYR D 550 PHE 0.038 0.002 PHE C 311 TRP 0.027 0.002 TRP D 73 HIS 0.010 0.001 HIS E 642 Details of bonding type rmsd covalent geometry : bond 0.00418 (26073) covalent geometry : angle 0.74050 (35237) hydrogen bonds : bond 0.08402 ( 1510) hydrogen bonds : angle 6.06205 ( 4482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 258 poor density : 677 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7746 (mt) REVERT: A 158 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7432 (mm-40) REVERT: A 183 MET cc_start: 0.8101 (tmm) cc_final: 0.7668 (ptm) REVERT: A 194 ARG cc_start: 0.2148 (OUTLIER) cc_final: -0.0152 (mmm160) REVERT: A 218 LEU cc_start: 0.8736 (mt) cc_final: 0.8423 (mt) REVERT: A 267 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8122 (p0) REVERT: A 436 GLU cc_start: 0.7287 (tt0) cc_final: 0.6895 (tm-30) REVERT: A 470 SER cc_start: 0.8157 (m) cc_final: 0.7880 (t) REVERT: A 560 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6486 (tt0) REVERT: A 581 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7469 (mtp) REVERT: A 582 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7407 (tpp) REVERT: A 583 VAL cc_start: 0.8435 (t) cc_final: 0.8109 (p) REVERT: A 591 LYS cc_start: 0.6080 (OUTLIER) cc_final: 0.5861 (mptp) REVERT: A 614 TYR cc_start: 0.7122 (t80) cc_final: 0.6845 (t80) REVERT: A 617 LEU cc_start: 0.8210 (mt) cc_final: 0.8000 (mm) REVERT: A 647 GLN cc_start: 0.7331 (mt0) cc_final: 0.6959 (mt0) REVERT: A 650 ASN cc_start: 0.7004 (t0) cc_final: 0.6688 (t0) REVERT: A 671 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7638 (mmmm) REVERT: A 690 LYS cc_start: 0.7955 (tppp) cc_final: 0.7687 (tptp) REVERT: A 717 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7420 (ttm-80) REVERT: B 69 CYS cc_start: 0.6637 (t) cc_final: 0.6382 (m) REVERT: B 73 TRP cc_start: 0.7733 (t-100) cc_final: 0.7212 (t-100) REVERT: B 117 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7248 (t80) REVERT: B 119 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: B 217 MET cc_start: 0.7310 (mpp) cc_final: 0.6774 (mpp) REVERT: B 298 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8630 (tppt) REVERT: B 477 ASN cc_start: 0.7924 (m-40) cc_final: 0.7648 (m-40) REVERT: B 495 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.6714 (mmm-85) REVERT: B 519 MET cc_start: 0.7442 (mmm) cc_final: 0.7211 (tmm) REVERT: B 550 TYR cc_start: 0.7678 (t80) cc_final: 0.7433 (t80) REVERT: B 574 LEU cc_start: 0.8352 (tp) cc_final: 0.8087 (mt) REVERT: B 589 GLN cc_start: 0.5331 (OUTLIER) cc_final: 0.4507 (tm-30) REVERT: B 608 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7301 (t80) REVERT: B 717 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7419 (mtp85) REVERT: B 718 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8088 (tt) REVERT: C 64 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: C 155 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7715 (mmtm) REVERT: C 157 ILE cc_start: 0.8721 (tp) cc_final: 0.8393 (tp) REVERT: C 158 GLN cc_start: 0.8241 (tp40) cc_final: 0.7386 (tp40) REVERT: C 161 MET cc_start: 0.7447 (mtm) cc_final: 0.6968 (mtm) REVERT: C 182 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7208 (tm-30) REVERT: C 183 MET cc_start: 0.7982 (tmm) cc_final: 0.7362 (tmm) REVERT: C 199 LEU cc_start: 0.1072 (OUTLIER) cc_final: 0.0729 (mt) REVERT: C 219 MET cc_start: 0.8405 (ttp) cc_final: 0.8135 (ttp) REVERT: C 238 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6792 (mp) REVERT: C 279 MET cc_start: 0.7688 (mmm) cc_final: 0.7464 (mmm) REVERT: C 479 SER cc_start: 0.7625 (m) cc_final: 0.7234 (p) REVERT: C 483 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6321 (t0) REVERT: C 520 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6560 (tm-30) REVERT: C 536 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6571 (tp30) REVERT: C 548 ASP cc_start: 0.7663 (t70) cc_final: 0.7177 (t0) REVERT: C 556 GLU cc_start: 0.7278 (tt0) cc_final: 0.7071 (tt0) REVERT: C 566 MET cc_start: 0.7654 (tmm) cc_final: 0.7344 (tmm) REVERT: C 568 ARG cc_start: 0.7410 (ttm110) cc_final: 0.6900 (ttm-80) REVERT: C 602 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6539 (t0) REVERT: C 672 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6887 (mm-30) REVERT: C 695 MET cc_start: 0.7648 (tpt) cc_final: 0.7397 (mmm) REVERT: C 697 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7249 (mtmm) REVERT: C 722 ARG cc_start: 0.7476 (ttm170) cc_final: 0.7070 (ttm170) REVERT: D 68 ARG cc_start: 0.7431 (ptp90) cc_final: 0.6609 (ptp90) REVERT: D 70 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6870 (mpt90) REVERT: D 74 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6953 (mm-30) REVERT: D 113 PHE cc_start: 0.7366 (m-80) cc_final: 0.7010 (m-80) REVERT: D 118 LEU cc_start: 0.8023 (mt) cc_final: 0.7749 (mt) REVERT: D 155 LYS cc_start: 0.8153 (mttm) cc_final: 0.7951 (mttm) REVERT: D 160 LYS cc_start: 0.7118 (tptm) cc_final: 0.6885 (tptm) REVERT: D 161 MET cc_start: 0.7575 (mtt) cc_final: 0.7143 (mtt) REVERT: D 206 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7431 (mmt90) REVERT: D 217 MET cc_start: 0.7651 (tpp) cc_final: 0.7178 (tpp) REVERT: D 219 MET cc_start: 0.7199 (tpp) cc_final: 0.6939 (tpt) REVERT: D 231 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7540 (pp20) REVERT: D 300 TYR cc_start: 0.7196 (t80) cc_final: 0.6653 (t80) REVERT: D 301 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7633 (pt0) REVERT: D 308 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7671 (mm) REVERT: D 350 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7093 (mt) REVERT: D 479 SER cc_start: 0.8163 (m) cc_final: 0.7878 (p) REVERT: D 486 GLU cc_start: 0.6451 (tm-30) cc_final: 0.6229 (tm-30) REVERT: D 561 GLU cc_start: 0.7055 (pm20) cc_final: 0.6592 (pm20) REVERT: D 565 ASP cc_start: 0.7055 (m-30) cc_final: 0.6711 (m-30) REVERT: D 635 LYS cc_start: 0.7200 (mmmt) cc_final: 0.6968 (mmmt) REVERT: D 671 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7639 (mtpp) REVERT: E 69 CYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7007 (p) REVERT: E 155 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7567 (mtpt) REVERT: E 161 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6448 (ppp) REVERT: E 162 LEU cc_start: 0.8329 (mt) cc_final: 0.7588 (mt) REVERT: E 164 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7552 (mm-30) REVERT: E 183 MET cc_start: 0.8210 (mmt) cc_final: 0.7990 (mmm) REVERT: E 221 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6326 (p90) REVERT: E 229 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6369 (tm-30) REVERT: E 271 MET cc_start: 0.6110 (ptt) cc_final: 0.5550 (ppp) REVERT: E 495 ARG cc_start: 0.6688 (mtp85) cc_final: 0.6011 (mtp85) REVERT: E 516 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7425 (tp) REVERT: E 539 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.7063 (tpp80) REVERT: E 548 ASP cc_start: 0.8049 (t70) cc_final: 0.7783 (t0) REVERT: E 583 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7474 (p) REVERT: E 611 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7184 (ttp80) REVERT: E 613 ASP cc_start: 0.7533 (m-30) cc_final: 0.7186 (t0) REVERT: E 615 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7314 (mtpt) REVERT: E 635 LYS cc_start: 0.7081 (mmmt) cc_final: 0.6586 (mmmt) REVERT: E 671 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7404 (mtmm) REVERT: E 690 LYS cc_start: 0.8181 (tptp) cc_final: 0.7963 (tptt) REVERT: E 691 MET cc_start: 0.7942 (mmm) cc_final: 0.7499 (tmm) REVERT: F 429 GLU cc_start: 0.6466 (tm-30) cc_final: 0.5909 (tm-30) REVERT: F 483 ASP cc_start: 0.7013 (m-30) cc_final: 0.6701 (m-30) REVERT: F 489 SER cc_start: 0.8491 (t) cc_final: 0.8165 (m) REVERT: F 490 PRO cc_start: 0.8501 (Cg_endo) cc_final: 0.8281 (Cg_exo) REVERT: F 548 ASP cc_start: 0.8017 (t70) cc_final: 0.7696 (t0) REVERT: F 551 TRP cc_start: 0.8354 (m-10) cc_final: 0.8123 (m-10) REVERT: F 568 ARG cc_start: 0.7011 (ttm-80) cc_final: 0.6538 (ttm-80) REVERT: F 606 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6777 (mt-10) REVERT: F 608 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: F 609 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7278 (tp-100) REVERT: F 671 LYS cc_start: 0.8119 (tttt) cc_final: 0.7722 (tttt) REVERT: F 680 GLN cc_start: 0.7054 (mp10) cc_final: 0.6601 (mp10) REVERT: F 690 LYS cc_start: 0.7886 (tptp) cc_final: 0.7635 (tptp) REVERT: F 695 MET cc_start: 0.7527 (mmt) cc_final: 0.7166 (mmm) REVERT: F 696 GLU cc_start: 0.7062 (mp0) cc_final: 0.6100 (mp0) REVERT: F 700 ASP cc_start: 0.6979 (m-30) cc_final: 0.6746 (m-30) REVERT: F 706 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7025 (mm-30) REVERT: F 722 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7022 (ttp80) REVERT: F 723 LEU cc_start: 0.8633 (tp) cc_final: 0.8420 (tp) REVERT: F 724 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7712 (mmtp) outliers start: 258 outliers final: 137 residues processed: 868 average time/residue: 0.2139 time to fit residues: 274.1569 Evaluate side-chains 831 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 661 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 TRP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 589 GLN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain C residue 509 ASN Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 601 SER Chi-restraints excluded: chain E residue 634 CYS Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 580 ARG Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 673 THR Chi-restraints excluded: chain F residue 708 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 123 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 247 optimal weight: 8.9990 chunk 165 optimal weight: 0.0370 chunk 179 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 154 optimal weight: 0.5980 chunk 297 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN C 307 ASN C 347 HIS ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN C 509 ASN C 554 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 299 GLN D 307 ASN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 GLN F 463 HIS F 584 GLN F 652 GLN F 677 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.178382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137154 restraints weight = 45392.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140933 restraints weight = 19404.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.142013 restraints weight = 9364.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142722 restraints weight = 8349.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142766 restraints weight = 6830.095| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26073 Z= 0.164 Angle : 0.670 12.167 35237 Z= 0.350 Chirality : 0.040 0.215 3882 Planarity : 0.005 0.053 4545 Dihedral : 9.442 61.008 3666 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.01 % Favored : 93.34 % Rotamer: Outliers : 7.27 % Allowed : 29.70 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.15), residues: 3094 helix: -0.10 (0.11), residues: 2287 sheet: -6.54 (0.21), residues: 10 loop : -2.52 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 661 TYR 0.028 0.002 TYR D 550 PHE 0.033 0.002 PHE C 311 TRP 0.027 0.001 TRP D 89 HIS 0.007 0.001 HIS E 642 Details of bonding type rmsd covalent geometry : bond 0.00339 (26073) covalent geometry : angle 0.66961 (35237) hydrogen bonds : bond 0.06299 ( 1510) hydrogen bonds : angle 5.47228 ( 4482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 650 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7307 (mm-40) REVERT: A 194 ARG cc_start: 0.1796 (OUTLIER) cc_final: -0.0513 (mmm160) REVERT: A 218 LEU cc_start: 0.8729 (mt) cc_final: 0.8505 (mt) REVERT: A 232 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 240 LYS cc_start: 0.8298 (UNCLASSIFIED) cc_final: 0.8093 (tptt) REVERT: A 243 TYR cc_start: 0.6622 (m-10) cc_final: 0.6151 (m-80) REVERT: A 267 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7980 (p0) REVERT: A 436 GLU cc_start: 0.7249 (tt0) cc_final: 0.6874 (tm-30) REVERT: A 470 SER cc_start: 0.8083 (m) cc_final: 0.7836 (t) REVERT: A 560 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6324 (tt0) REVERT: A 575 PHE cc_start: 0.8305 (m-80) cc_final: 0.8016 (m-80) REVERT: A 582 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7396 (tpp) REVERT: A 583 VAL cc_start: 0.8390 (t) cc_final: 0.8138 (p) REVERT: A 591 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5820 (mttp) REVERT: A 608 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7320 (t80) REVERT: A 614 TYR cc_start: 0.7169 (t80) cc_final: 0.6875 (t80) REVERT: A 671 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7626 (mmmm) REVERT: A 690 LYS cc_start: 0.7866 (tppp) cc_final: 0.7611 (tptp) REVERT: A 694 LEU cc_start: 0.7689 (mp) cc_final: 0.7487 (mm) REVERT: A 717 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7347 (ttm-80) REVERT: B 69 CYS cc_start: 0.6686 (t) cc_final: 0.6472 (m) REVERT: B 73 TRP cc_start: 0.7772 (t-100) cc_final: 0.7383 (t-100) REVERT: B 117 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7189 (t80) REVERT: B 119 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: B 217 MET cc_start: 0.7294 (mpp) cc_final: 0.6708 (mpp) REVERT: B 454 LEU cc_start: 0.7843 (mt) cc_final: 0.7632 (mm) REVERT: B 477 ASN cc_start: 0.7933 (m-40) cc_final: 0.7656 (m-40) REVERT: B 505 GLU cc_start: 0.6884 (mp0) cc_final: 0.6603 (mt-10) REVERT: B 539 ARG cc_start: 0.6936 (ttt-90) cc_final: 0.6673 (ttt90) REVERT: B 550 TYR cc_start: 0.7712 (t80) cc_final: 0.7493 (t80) REVERT: B 574 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8064 (mt) REVERT: B 589 GLN cc_start: 0.5287 (OUTLIER) cc_final: 0.4492 (tm-30) REVERT: B 608 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7074 (t80) REVERT: B 661 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7685 (mtt-85) REVERT: B 680 GLN cc_start: 0.6759 (tm-30) cc_final: 0.6221 (tm-30) REVERT: B 697 LYS cc_start: 0.8119 (tttp) cc_final: 0.7878 (tttp) REVERT: B 713 ASN cc_start: 0.8236 (t0) cc_final: 0.8019 (t0) REVERT: B 717 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7419 (mtp85) REVERT: B 721 HIS cc_start: 0.8322 (t70) cc_final: 0.8061 (t70) REVERT: C 81 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5630 (tm-30) REVERT: C 157 ILE cc_start: 0.8698 (tp) cc_final: 0.8352 (tp) REVERT: C 158 GLN cc_start: 0.8096 (tp40) cc_final: 0.7208 (mm-40) REVERT: C 161 MET cc_start: 0.7191 (mtm) cc_final: 0.6584 (mtm) REVERT: C 183 MET cc_start: 0.7906 (tmm) cc_final: 0.7496 (tmm) REVERT: C 199 LEU cc_start: 0.0830 (OUTLIER) cc_final: 0.0407 (mt) REVERT: C 219 MET cc_start: 0.8246 (ttp) cc_final: 0.8002 (ttp) REVERT: C 271 MET cc_start: 0.3358 (ttt) cc_final: 0.2210 (ptm) REVERT: C 279 MET cc_start: 0.7762 (mmm) cc_final: 0.7561 (mmm) REVERT: C 353 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8149 (pm20) REVERT: C 359 HIS cc_start: 0.8273 (t70) cc_final: 0.7984 (t-90) REVERT: C 452 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.7013 (m-30) REVERT: C 479 SER cc_start: 0.7665 (m) cc_final: 0.7266 (p) REVERT: C 483 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6290 (t0) REVERT: C 520 GLU cc_start: 0.6765 (tm-30) cc_final: 0.6504 (tm-30) REVERT: C 521 LYS cc_start: 0.7590 (mttp) cc_final: 0.7212 (mttp) REVERT: C 536 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6657 (tp30) REVERT: C 548 ASP cc_start: 0.7667 (t70) cc_final: 0.7322 (t0) REVERT: C 556 GLU cc_start: 0.7313 (tt0) cc_final: 0.7088 (tt0) REVERT: C 560 GLU cc_start: 0.7179 (tp30) cc_final: 0.6884 (mm-30) REVERT: C 568 ARG cc_start: 0.7416 (ttm110) cc_final: 0.6964 (ttm-80) REVERT: C 602 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6534 (t0) REVERT: C 672 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6861 (mm-30) REVERT: C 722 ARG cc_start: 0.7425 (ttm170) cc_final: 0.7012 (ttm170) REVERT: D 68 ARG cc_start: 0.7451 (ptp90) cc_final: 0.6954 (ptp90) REVERT: D 70 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6782 (mpt90) REVERT: D 74 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6891 (mm-30) REVERT: D 109 ILE cc_start: 0.8237 (mt) cc_final: 0.8004 (pt) REVERT: D 113 PHE cc_start: 0.7406 (m-80) cc_final: 0.7130 (m-80) REVERT: D 160 LYS cc_start: 0.7347 (tptm) cc_final: 0.7143 (tptm) REVERT: D 161 MET cc_start: 0.7568 (mtt) cc_final: 0.7336 (mtt) REVERT: D 219 MET cc_start: 0.7196 (tpp) cc_final: 0.6791 (tpt) REVERT: D 223 MET cc_start: 0.5719 (OUTLIER) cc_final: 0.5176 (mpt) REVERT: D 231 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: D 261 GLU cc_start: 0.8822 (tp30) cc_final: 0.8581 (tp30) REVERT: D 300 TYR cc_start: 0.7193 (t80) cc_final: 0.6616 (t80) REVERT: D 301 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: D 305 LEU cc_start: 0.8174 (mp) cc_final: 0.7902 (mp) REVERT: D 437 TYR cc_start: 0.7904 (t80) cc_final: 0.7656 (t80) REVERT: D 479 SER cc_start: 0.8236 (m) cc_final: 0.7949 (p) REVERT: D 556 GLU cc_start: 0.6926 (pm20) cc_final: 0.6533 (pm20) REVERT: D 561 GLU cc_start: 0.7069 (pm20) cc_final: 0.6515 (pm20) REVERT: D 565 ASP cc_start: 0.7043 (m-30) cc_final: 0.6699 (m-30) REVERT: D 606 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6959 (tp30) REVERT: D 635 LYS cc_start: 0.7154 (mmmt) cc_final: 0.6916 (mmmt) REVERT: D 638 TYR cc_start: 0.8206 (t80) cc_final: 0.7730 (t80) REVERT: D 671 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7499 (mtpp) REVERT: D 686 TYR cc_start: 0.7766 (t80) cc_final: 0.7202 (t80) REVERT: D 695 MET cc_start: 0.6865 (tpt) cc_final: 0.6530 (tpt) REVERT: D 706 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6859 (tm-30) REVERT: E 69 CYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7009 (p) REVERT: E 155 LYS cc_start: 0.7897 (mtpt) cc_final: 0.7642 (mtpt) REVERT: E 161 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6512 (ppp) REVERT: E 162 LEU cc_start: 0.8379 (mt) cc_final: 0.7697 (mt) REVERT: E 164 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7650 (mm-30) REVERT: E 174 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: E 181 LYS cc_start: 0.8743 (mttt) cc_final: 0.8267 (mttt) REVERT: E 229 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6464 (tm-30) REVERT: E 271 MET cc_start: 0.6269 (ptt) cc_final: 0.5666 (ppp) REVERT: E 469 LYS cc_start: 0.8107 (mttp) cc_final: 0.7639 (mttp) REVERT: E 484 ASP cc_start: 0.7312 (m-30) cc_final: 0.7100 (m-30) REVERT: E 491 LEU cc_start: 0.7498 (mt) cc_final: 0.7293 (mp) REVERT: E 493 ARG cc_start: 0.6344 (tpp80) cc_final: 0.6067 (tpp80) REVERT: E 495 ARG cc_start: 0.6615 (mtp85) cc_final: 0.6371 (mmm-85) REVERT: E 505 GLU cc_start: 0.7242 (mp0) cc_final: 0.6923 (mp0) REVERT: E 520 GLU cc_start: 0.7219 (tp30) cc_final: 0.7005 (tp30) REVERT: E 548 ASP cc_start: 0.8006 (t70) cc_final: 0.7803 (t0) REVERT: E 615 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7368 (mtpt) REVERT: E 635 LYS cc_start: 0.6844 (mmmt) cc_final: 0.6356 (mmmt) REVERT: F 429 GLU cc_start: 0.6441 (tm-30) cc_final: 0.5885 (tm-30) REVERT: F 443 SER cc_start: 0.8295 (t) cc_final: 0.8018 (p) REVERT: F 483 ASP cc_start: 0.7014 (m-30) cc_final: 0.6695 (m-30) REVERT: F 484 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6321 (t0) REVERT: F 489 SER cc_start: 0.8479 (t) cc_final: 0.7947 (p) REVERT: F 490 PRO cc_start: 0.8623 (Cg_endo) cc_final: 0.8398 (Cg_exo) REVERT: F 545 GLN cc_start: 0.7483 (tp40) cc_final: 0.7278 (tt0) REVERT: F 548 ASP cc_start: 0.8057 (t70) cc_final: 0.7666 (t0) REVERT: F 568 ARG cc_start: 0.7004 (ttm-80) cc_final: 0.6509 (ttm-80) REVERT: F 604 LEU cc_start: 0.7968 (tp) cc_final: 0.7731 (mt) REVERT: F 606 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6675 (mt-10) REVERT: F 608 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: F 609 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7377 (tp-100) REVERT: F 613 ASP cc_start: 0.6787 (m-30) cc_final: 0.6495 (m-30) REVERT: F 614 TYR cc_start: 0.7632 (t80) cc_final: 0.7212 (t80) REVERT: F 671 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7712 (mtmt) REVERT: F 680 GLN cc_start: 0.7081 (mp10) cc_final: 0.6602 (mp10) REVERT: F 695 MET cc_start: 0.7520 (mmt) cc_final: 0.7080 (mmm) REVERT: F 696 GLU cc_start: 0.7060 (mp0) cc_final: 0.6211 (mp0) REVERT: F 700 ASP cc_start: 0.6972 (m-30) cc_final: 0.6724 (m-30) REVERT: F 706 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6956 (mm-30) REVERT: F 722 ARG cc_start: 0.7348 (ttp80) cc_final: 0.7010 (ttp80) REVERT: F 723 LEU cc_start: 0.8641 (tp) cc_final: 0.8429 (tp) REVERT: F 724 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7678 (mmtp) outliers start: 204 outliers final: 109 residues processed: 793 average time/residue: 0.2148 time to fit residues: 251.2441 Evaluate side-chains 773 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 634 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 TRP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 589 GLN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain C residue 509 ASN Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 634 CYS Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 296 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 153 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 286 optimal weight: 0.0870 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 658 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 GLN F 463 HIS F 569 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.177604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136199 restraints weight = 45104.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138951 restraints weight = 22035.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141181 restraints weight = 10545.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.141897 restraints weight = 8135.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142037 restraints weight = 7051.521| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26073 Z= 0.175 Angle : 0.653 10.683 35237 Z= 0.338 Chirality : 0.041 0.186 3882 Planarity : 0.005 0.057 4545 Dihedral : 8.312 59.986 3596 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.01 % Favored : 93.37 % Rotamer: Outliers : 8.20 % Allowed : 28.66 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 3094 helix: 0.14 (0.11), residues: 2279 sheet: -6.46 (0.25), residues: 10 loop : -2.39 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 105 TYR 0.036 0.002 TYR D 550 PHE 0.037 0.002 PHE A 113 TRP 0.024 0.001 TRP B 180 HIS 0.010 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00374 (26073) covalent geometry : angle 0.65278 (35237) hydrogen bonds : bond 0.05679 ( 1510) hydrogen bonds : angle 5.15817 ( 4482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 641 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.2546 (OUTLIER) cc_final: 0.1462 (ptm-80) REVERT: A 64 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6640 (pp20) REVERT: A 158 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7355 (mm-40) REVERT: A 194 ARG cc_start: 0.1661 (OUTLIER) cc_final: -0.0284 (tmm160) REVERT: A 218 LEU cc_start: 0.8858 (mt) cc_final: 0.8609 (mt) REVERT: A 243 TYR cc_start: 0.6546 (m-10) cc_final: 0.6114 (m-80) REVERT: A 267 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8072 (p0) REVERT: A 346 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.5412 (p90) REVERT: A 436 GLU cc_start: 0.7242 (tt0) cc_final: 0.6841 (tm-30) REVERT: A 470 SER cc_start: 0.8066 (m) cc_final: 0.7797 (t) REVERT: A 570 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7846 (ttpp) REVERT: A 575 PHE cc_start: 0.8343 (m-80) cc_final: 0.8070 (m-80) REVERT: A 582 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7436 (tpp) REVERT: A 583 VAL cc_start: 0.8380 (t) cc_final: 0.8120 (p) REVERT: A 591 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5721 (mttp) REVERT: A 608 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7351 (t80) REVERT: A 614 TYR cc_start: 0.7168 (t80) cc_final: 0.6895 (t80) REVERT: A 633 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.5263 (tm-30) REVERT: A 671 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7627 (mmmm) REVERT: A 690 LYS cc_start: 0.7895 (tppp) cc_final: 0.7689 (tptm) REVERT: A 717 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7287 (ttm-80) REVERT: A 722 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7270 (tpp80) REVERT: B 69 CYS cc_start: 0.6784 (t) cc_final: 0.6428 (m) REVERT: B 73 TRP cc_start: 0.7807 (t-100) cc_final: 0.7430 (t-100) REVERT: B 117 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7155 (t80) REVERT: B 119 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: B 217 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6793 (mpp) REVERT: B 432 LEU cc_start: 0.8393 (mt) cc_final: 0.8120 (mp) REVERT: B 477 ASN cc_start: 0.7956 (m-40) cc_final: 0.7747 (m-40) REVERT: B 589 GLN cc_start: 0.5209 (OUTLIER) cc_final: 0.4353 (tm-30) REVERT: B 608 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7023 (t80) REVERT: B 672 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7451 (mm-30) REVERT: B 680 GLN cc_start: 0.6772 (tm-30) cc_final: 0.6256 (tm-30) REVERT: B 713 ASN cc_start: 0.8172 (t0) cc_final: 0.7882 (t0) REVERT: B 717 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7502 (mtp85) REVERT: B 721 HIS cc_start: 0.8356 (t70) cc_final: 0.8112 (t70) REVERT: C 155 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7555 (mmtm) REVERT: C 157 ILE cc_start: 0.8610 (tp) cc_final: 0.8286 (tp) REVERT: C 158 GLN cc_start: 0.8039 (tp40) cc_final: 0.7392 (mm-40) REVERT: C 161 MET cc_start: 0.7015 (mtm) cc_final: 0.6498 (mtm) REVERT: C 182 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7214 (tm-30) REVERT: C 183 MET cc_start: 0.7932 (tmm) cc_final: 0.7310 (tmm) REVERT: C 199 LEU cc_start: 0.0455 (OUTLIER) cc_final: -0.0052 (mt) REVERT: C 238 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6621 (mp) REVERT: C 353 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: C 479 SER cc_start: 0.7719 (m) cc_final: 0.7332 (p) REVERT: C 536 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6691 (tp30) REVERT: C 556 GLU cc_start: 0.7356 (tt0) cc_final: 0.7129 (tt0) REVERT: C 560 GLU cc_start: 0.7240 (tp30) cc_final: 0.6994 (tt0) REVERT: C 568 ARG cc_start: 0.7566 (ttm110) cc_final: 0.6984 (ttm-80) REVERT: C 602 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6567 (t0) REVERT: C 672 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6871 (mm-30) REVERT: C 679 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.7028 (ttm110) REVERT: C 695 MET cc_start: 0.7368 (mmm) cc_final: 0.7079 (tpp) REVERT: C 722 ARG cc_start: 0.7443 (ttm170) cc_final: 0.6993 (ttm170) REVERT: D 68 ARG cc_start: 0.7720 (ptp90) cc_final: 0.6715 (ptp90) REVERT: D 70 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6623 (mpt90) REVERT: D 74 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6920 (mm-30) REVERT: D 109 ILE cc_start: 0.8405 (mt) cc_final: 0.8054 (pt) REVERT: D 113 PHE cc_start: 0.7445 (m-80) cc_final: 0.7201 (m-80) REVERT: D 160 LYS cc_start: 0.7597 (tptm) cc_final: 0.7342 (tptm) REVERT: D 217 MET cc_start: 0.8090 (mtp) cc_final: 0.7790 (mtp) REVERT: D 219 MET cc_start: 0.7217 (tpp) cc_final: 0.6717 (tpt) REVERT: D 223 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5198 (mpt) REVERT: D 231 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7697 (pp20) REVERT: D 261 GLU cc_start: 0.8870 (tp30) cc_final: 0.8535 (tp30) REVERT: D 300 TYR cc_start: 0.7247 (t80) cc_final: 0.6701 (t80) REVERT: D 436 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6805 (mm-30) REVERT: D 444 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.5603 (mtmt) REVERT: D 479 SER cc_start: 0.8264 (m) cc_final: 0.7986 (p) REVERT: D 541 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8177 (tt) REVERT: D 556 GLU cc_start: 0.6815 (pm20) cc_final: 0.6375 (pm20) REVERT: D 561 GLU cc_start: 0.7090 (pm20) cc_final: 0.6559 (pm20) REVERT: D 565 ASP cc_start: 0.7062 (m-30) cc_final: 0.6752 (m-30) REVERT: D 606 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7118 (tp30) REVERT: D 671 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7465 (mtpp) REVERT: D 672 GLU cc_start: 0.6957 (tp30) cc_final: 0.6746 (tp30) REVERT: D 686 TYR cc_start: 0.7830 (t80) cc_final: 0.7217 (t80) REVERT: D 695 MET cc_start: 0.6913 (tpt) cc_final: 0.6614 (tpt) REVERT: D 706 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6897 (tm-30) REVERT: E 69 CYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7061 (p) REVERT: E 155 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7622 (mtpt) REVERT: E 161 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6600 (ppp) REVERT: E 162 LEU cc_start: 0.8349 (mt) cc_final: 0.7641 (mt) REVERT: E 164 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7690 (mm-30) REVERT: E 174 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7578 (pp20) REVERT: E 181 LYS cc_start: 0.8753 (mttt) cc_final: 0.8284 (mttt) REVERT: E 229 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6390 (tm-30) REVERT: E 271 MET cc_start: 0.6394 (ptt) cc_final: 0.5815 (ppp) REVERT: E 440 SER cc_start: 0.8447 (m) cc_final: 0.7904 (p) REVERT: E 484 ASP cc_start: 0.7273 (m-30) cc_final: 0.6957 (m-30) REVERT: E 495 ARG cc_start: 0.6625 (mtp85) cc_final: 0.5997 (mtp85) REVERT: E 517 ASP cc_start: 0.6580 (t70) cc_final: 0.6125 (t0) REVERT: E 519 MET cc_start: 0.6927 (ttp) cc_final: 0.6590 (mtm) REVERT: E 548 ASP cc_start: 0.8035 (t70) cc_final: 0.7786 (t0) REVERT: E 611 ARG cc_start: 0.7629 (ttp80) cc_final: 0.7321 (ttp80) REVERT: E 612 ASP cc_start: 0.7595 (t0) cc_final: 0.7280 (t0) REVERT: E 615 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7579 (mtpt) REVERT: E 635 LYS cc_start: 0.6900 (mmmt) cc_final: 0.6479 (mmmt) REVERT: F 429 GLU cc_start: 0.6474 (tm-30) cc_final: 0.5948 (tm-30) REVERT: F 443 SER cc_start: 0.8284 (t) cc_final: 0.8009 (p) REVERT: F 483 ASP cc_start: 0.7001 (m-30) cc_final: 0.6700 (m-30) REVERT: F 484 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6294 (t0) REVERT: F 489 SER cc_start: 0.8449 (t) cc_final: 0.7830 (p) REVERT: F 490 PRO cc_start: 0.8608 (Cg_endo) cc_final: 0.8348 (Cg_exo) REVERT: F 545 GLN cc_start: 0.7537 (tp40) cc_final: 0.7324 (tt0) REVERT: F 548 ASP cc_start: 0.8056 (t70) cc_final: 0.7660 (t0) REVERT: F 551 TRP cc_start: 0.8352 (m-10) cc_final: 0.8115 (m-10) REVERT: F 604 LEU cc_start: 0.7963 (tp) cc_final: 0.7710 (mt) REVERT: F 608 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: F 614 TYR cc_start: 0.7690 (t80) cc_final: 0.7179 (t80) REVERT: F 671 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7603 (tttt) REVERT: F 679 ARG cc_start: 0.7593 (mtt90) cc_final: 0.7272 (mtt90) REVERT: F 680 GLN cc_start: 0.7118 (mp10) cc_final: 0.6604 (mp10) REVERT: F 695 MET cc_start: 0.7505 (mmt) cc_final: 0.7061 (mmm) REVERT: F 696 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: F 700 ASP cc_start: 0.7007 (m-30) cc_final: 0.6725 (m-30) REVERT: F 706 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6955 (mm-30) REVERT: F 724 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7722 (mmtp) outliers start: 230 outliers final: 138 residues processed: 795 average time/residue: 0.2098 time to fit residues: 246.2557 Evaluate side-chains 809 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 636 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 589 GLN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 680 GLN Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 634 CYS Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 579 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 615 LYS Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 696 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 136 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 229 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 GLN A 650 ASN ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN C 263 GLN C 294 GLN C 302 GLN ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 299 GLN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 647 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 250 ASN E 347 HIS ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 GLN F 463 HIS ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.175374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133695 restraints weight = 45449.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136301 restraints weight = 22593.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138143 restraints weight = 11011.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139362 restraints weight = 8552.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139359 restraints weight = 6950.593| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26073 Z= 0.196 Angle : 0.667 13.697 35237 Z= 0.342 Chirality : 0.042 0.189 3882 Planarity : 0.005 0.053 4545 Dihedral : 7.823 59.691 3575 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.21 % Favored : 93.18 % Rotamer: Outliers : 8.31 % Allowed : 29.13 % Favored : 62.57 % 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 aren not related in a simple way. whole: -0.68 (0.15), residues: 3094 helix: 0.26 (0.11), residues: 2282 sheet: -6.51 (0.24), residues: 10 loop : -2.29 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 568 TYR 0.036 0.002 TYR D 550 PHE 0.036 0.002 PHE A 113 TRP 0.034 0.002 TRP B 89 HIS 0.012 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00427 (26073) covalent geometry : angle 0.66654 (35237) hydrogen bonds : bond 0.05584 ( 1510) hydrogen bonds : angle 5.01054 ( 4482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 639 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.2707 (OUTLIER) cc_final: 0.1983 (ptm-80) REVERT: A 64 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6650 (pp20) REVERT: A 158 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: A 194 ARG cc_start: 0.1787 (OUTLIER) cc_final: -0.0287 (tmm160) REVERT: A 217 MET cc_start: 0.7791 (mmt) cc_final: 0.7520 (mmm) REVERT: A 218 LEU cc_start: 0.8872 (mt) cc_final: 0.8615 (mt) REVERT: A 232 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8062 (tm-30) REVERT: A 243 TYR cc_start: 0.6683 (m-10) cc_final: 0.6203 (m-80) REVERT: A 290 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8364 (ptpt) REVERT: A 346 TYR cc_start: 0.5577 (OUTLIER) cc_final: 0.5376 (p90) REVERT: A 436 GLU cc_start: 0.7254 (tt0) cc_final: 0.6896 (tm-30) REVERT: A 470 SER cc_start: 0.8066 (m) cc_final: 0.7788 (t) REVERT: A 473 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7184 (mm110) REVERT: A 570 LYS cc_start: 0.8137 (ttpp) cc_final: 0.7822 (ttpp) REVERT: A 575 PHE cc_start: 0.8353 (m-80) cc_final: 0.8088 (m-80) REVERT: A 582 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7467 (tpp) REVERT: A 583 VAL cc_start: 0.8389 (t) cc_final: 0.8129 (p) REVERT: A 591 LYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5736 (mttp) REVERT: A 608 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7459 (t80) REVERT: A 614 TYR cc_start: 0.7217 (t80) cc_final: 0.6943 (t80) REVERT: A 633 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5277 (tm-30) REVERT: A 638 TYR cc_start: 0.7818 (t80) cc_final: 0.7437 (t80) REVERT: A 654 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8141 (mmt180) REVERT: A 671 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7647 (mmmm) REVERT: A 690 LYS cc_start: 0.7890 (tppp) cc_final: 0.7676 (tptp) REVERT: A 695 MET cc_start: 0.7362 (tpp) cc_final: 0.7155 (mmm) REVERT: A 717 ARG cc_start: 0.7694 (tpp80) cc_final: 0.7303 (ttm-80) REVERT: A 722 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7173 (tpp80) REVERT: B 69 CYS cc_start: 0.6764 (t) cc_final: 0.6493 (m) REVERT: B 73 TRP cc_start: 0.7807 (t-100) cc_final: 0.7443 (t-100) REVERT: B 113 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: B 114 GLU cc_start: 0.7959 (tt0) cc_final: 0.7674 (tm-30) REVERT: B 117 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7262 (t80) REVERT: B 119 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7053 (m-80) REVERT: B 217 MET cc_start: 0.7309 (mpp) cc_final: 0.6665 (mpp) REVERT: B 324 THR cc_start: 0.3073 (OUTLIER) cc_final: 0.2791 (t) REVERT: B 477 ASN cc_start: 0.7941 (m-40) cc_final: 0.7722 (m-40) REVERT: B 539 ARG cc_start: 0.6995 (ttt-90) cc_final: 0.6708 (ttt90) REVERT: B 589 GLN cc_start: 0.5142 (OUTLIER) cc_final: 0.4719 (tm-30) REVERT: B 608 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7020 (t80) REVERT: B 672 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7476 (mm-30) REVERT: B 680 GLN cc_start: 0.6801 (tm-30) cc_final: 0.6242 (tm-30) REVERT: B 697 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7958 (ttmm) REVERT: B 713 ASN cc_start: 0.8186 (t0) cc_final: 0.7891 (t0) REVERT: B 717 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7539 (mtp85) REVERT: C 81 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.5666 (tm-30) REVERT: C 157 ILE cc_start: 0.8633 (tp) cc_final: 0.8348 (tp) REVERT: C 158 GLN cc_start: 0.7994 (tp40) cc_final: 0.7331 (mm-40) REVERT: C 161 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6586 (mtm) REVERT: C 183 MET cc_start: 0.7966 (tmm) cc_final: 0.7564 (tmm) REVERT: C 199 LEU cc_start: 0.0562 (OUTLIER) cc_final: 0.0152 (mt) REVERT: C 219 MET cc_start: 0.8328 (ttp) cc_final: 0.8079 (ttp) REVERT: C 238 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6683 (mp) REVERT: C 353 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: C 479 SER cc_start: 0.7586 (m) cc_final: 0.7263 (p) REVERT: C 536 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6741 (tp30) REVERT: C 548 ASP cc_start: 0.7659 (t70) cc_final: 0.7284 (t0) REVERT: C 568 ARG cc_start: 0.7628 (ttm110) cc_final: 0.6830 (ttm-80) REVERT: C 602 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6565 (t0) REVERT: C 672 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6934 (mm-30) REVERT: C 679 ARG cc_start: 0.7229 (ttm-80) cc_final: 0.7020 (ttm110) REVERT: C 695 MET cc_start: 0.7379 (mmm) cc_final: 0.7088 (tpp) REVERT: C 722 ARG cc_start: 0.7407 (ttm170) cc_final: 0.7006 (ttt180) REVERT: D 68 ARG cc_start: 0.7732 (ptp90) cc_final: 0.7360 (ttp-110) REVERT: D 70 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6645 (mpt90) REVERT: D 74 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7085 (mm-30) REVERT: D 109 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.7887 (mp) REVERT: D 113 PHE cc_start: 0.7634 (m-80) cc_final: 0.7263 (m-80) REVERT: D 175 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7837 (t) REVERT: D 217 MET cc_start: 0.8240 (mtp) cc_final: 0.7902 (mtp) REVERT: D 219 MET cc_start: 0.7323 (tpp) cc_final: 0.6878 (tpt) REVERT: D 223 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5189 (mpt) REVERT: D 287 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: D 300 TYR cc_start: 0.7351 (t80) cc_final: 0.6817 (t80) REVERT: D 326 LEU cc_start: 0.8472 (pt) cc_final: 0.8153 (mp) REVERT: D 436 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6774 (mm-30) REVERT: D 444 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5690 (mtmt) REVERT: D 479 SER cc_start: 0.8204 (m) cc_final: 0.7713 (p) REVERT: D 519 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5566 (mmt) REVERT: D 541 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8204 (tt) REVERT: D 556 GLU cc_start: 0.6929 (pm20) cc_final: 0.6406 (pm20) REVERT: D 561 GLU cc_start: 0.7127 (pm20) cc_final: 0.6803 (pm20) REVERT: D 606 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7054 (tp30) REVERT: D 671 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7357 (mtpp) REVERT: D 672 GLU cc_start: 0.7037 (tp30) cc_final: 0.6576 (tp30) REVERT: D 686 TYR cc_start: 0.7835 (t80) cc_final: 0.7186 (t80) REVERT: D 695 MET cc_start: 0.6875 (tpt) cc_final: 0.6566 (tpt) REVERT: D 706 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6926 (tm-30) REVERT: E 69 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7132 (p) REVERT: E 155 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7682 (mtpt) REVERT: E 161 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6743 (ppp) REVERT: E 164 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7707 (mm-30) REVERT: E 181 LYS cc_start: 0.8772 (mttt) cc_final: 0.8334 (mttt) REVERT: E 229 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: E 484 ASP cc_start: 0.7230 (m-30) cc_final: 0.6892 (m-30) REVERT: E 517 ASP cc_start: 0.6555 (t70) cc_final: 0.6182 (t0) REVERT: E 519 MET cc_start: 0.6999 (ttp) cc_final: 0.6546 (mtm) REVERT: E 548 ASP cc_start: 0.8021 (t70) cc_final: 0.7764 (t0) REVERT: E 611 ARG cc_start: 0.7582 (ttp80) cc_final: 0.7353 (ttp-170) REVERT: E 612 ASP cc_start: 0.7599 (t0) cc_final: 0.7230 (t0) REVERT: E 615 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7617 (mtpt) REVERT: E 635 LYS cc_start: 0.6887 (mmmt) cc_final: 0.6458 (mmmt) REVERT: E 666 LEU cc_start: 0.6795 (tt) cc_final: 0.6403 (tt) REVERT: E 671 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7832 (mtmm) REVERT: F 429 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6032 (tm-30) REVERT: F 432 LEU cc_start: 0.8024 (mm) cc_final: 0.7759 (mm) REVERT: F 469 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7504 (ttpp) REVERT: F 483 ASP cc_start: 0.6875 (m-30) cc_final: 0.6613 (m-30) REVERT: F 484 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.6341 (t0) REVERT: F 489 SER cc_start: 0.8429 (t) cc_final: 0.7695 (p) REVERT: F 490 PRO cc_start: 0.8591 (Cg_endo) cc_final: 0.8354 (Cg_exo) REVERT: F 548 ASP cc_start: 0.8014 (t70) cc_final: 0.7540 (t0) REVERT: F 556 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6423 (mm-30) REVERT: F 608 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: F 614 TYR cc_start: 0.7709 (t80) cc_final: 0.7216 (t80) REVERT: F 671 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7518 (tttt) REVERT: F 679 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7297 (mtt90) REVERT: F 680 GLN cc_start: 0.7133 (mp10) cc_final: 0.6601 (mp10) REVERT: F 695 MET cc_start: 0.7510 (mmt) cc_final: 0.7071 (mmm) REVERT: F 696 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: F 700 ASP cc_start: 0.7014 (m-30) cc_final: 0.6746 (m-30) REVERT: F 724 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7874 (mmtp) outliers start: 233 outliers final: 141 residues processed: 795 average time/residue: 0.2145 time to fit residues: 251.7206 Evaluate side-chains 814 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 631 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 589 GLN Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 680 GLN Chi-restraints excluded: chain D residue 700 ASP Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 634 CYS Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 516 ILE Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 579 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain F residue 696 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 14 optimal weight: 0.4980 chunk 261 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 278 optimal weight: 0.5980 chunk 143 optimal weight: 0.3980 chunk 133 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN B 545 GLN B 609 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS F 499 HIS F 569 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.176624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134883 restraints weight = 45460.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138239 restraints weight = 19874.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139567 restraints weight = 9889.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.140670 restraints weight = 8423.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140954 restraints weight = 7146.773| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26073 Z= 0.155 Angle : 0.645 15.895 35237 Z= 0.328 Chirality : 0.040 0.184 3882 Planarity : 0.005 0.076 4545 Dihedral : 7.453 59.552 3563 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.88 % Favored : 93.54 % Rotamer: Outliers : 7.45 % Allowed : 29.52 % Favored : 63.03 % 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 aren not related in a simple way. whole: -0.35 (0.15), residues: 3094 helix: 0.53 (0.11), residues: 2276 sheet: -6.24 (0.33), residues: 10 loop : -2.22 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 149 TYR 0.029 0.002 TYR B 686 PHE 0.038 0.001 PHE A 113 TRP 0.020 0.001 TRP D 73 HIS 0.012 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00337 (26073) covalent geometry : angle 0.64511 (35237) hydrogen bonds : bond 0.04997 ( 1510) hydrogen bonds : angle 4.79086 ( 4482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 645 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6600 (pp20) REVERT: A 110 CYS cc_start: 0.8308 (m) cc_final: 0.8059 (m) REVERT: A 158 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7319 (mm-40) REVERT: A 194 ARG cc_start: 0.1500 (OUTLIER) cc_final: -0.0391 (tmm160) REVERT: A 218 LEU cc_start: 0.8838 (mt) cc_final: 0.8599 (mt) REVERT: A 232 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 236 GLU cc_start: 0.7748 (pp20) cc_final: 0.6993 (pp20) REVERT: A 243 TYR cc_start: 0.6561 (m-10) cc_final: 0.6080 (m-80) REVERT: A 346 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.5107 (p90) REVERT: A 436 GLU cc_start: 0.7240 (tt0) cc_final: 0.6854 (tm-30) REVERT: A 470 SER cc_start: 0.8021 (m) cc_final: 0.7753 (t) REVERT: A 538 MET cc_start: 0.7368 (mmm) cc_final: 0.7036 (mmp) REVERT: A 570 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7778 (ttpp) REVERT: A 575 PHE cc_start: 0.8316 (m-80) cc_final: 0.8058 (m-80) REVERT: A 582 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7443 (tpp) REVERT: A 583 VAL cc_start: 0.8405 (t) cc_final: 0.8124 (p) REVERT: A 608 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7453 (t80) REVERT: A 614 TYR cc_start: 0.7192 (t80) cc_final: 0.6930 (t80) REVERT: A 633 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.5218 (tm-30) REVERT: A 654 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8156 (mmt180) REVERT: A 671 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7592 (mmmm) REVERT: A 690 LYS cc_start: 0.7876 (tppp) cc_final: 0.7569 (tptp) REVERT: A 695 MET cc_start: 0.7214 (tpp) cc_final: 0.6988 (mmm) REVERT: A 717 ARG cc_start: 0.7632 (tpp80) cc_final: 0.7215 (ttm-80) REVERT: A 722 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7142 (tpp80) REVERT: B 69 CYS cc_start: 0.6745 (t) cc_final: 0.6437 (m) REVERT: B 73 TRP cc_start: 0.7802 (t-100) cc_final: 0.7461 (t-100) REVERT: B 113 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7740 (m-10) REVERT: B 114 GLU cc_start: 0.8014 (tt0) cc_final: 0.7803 (tm-30) REVERT: B 117 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 119 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: B 217 MET cc_start: 0.7294 (mpp) cc_final: 0.6685 (mpp) REVERT: B 477 ASN cc_start: 0.7944 (m-40) cc_final: 0.7736 (m-40) REVERT: B 589 GLN cc_start: 0.5070 (OUTLIER) cc_final: 0.4649 (tm-30) REVERT: B 593 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6960 (pp) REVERT: B 607 PHE cc_start: 0.7900 (t80) cc_final: 0.7464 (t80) REVERT: B 608 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7034 (t80) REVERT: B 672 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 680 GLN cc_start: 0.6755 (tm-30) cc_final: 0.6221 (tm-30) REVERT: B 697 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7908 (ttmm) REVERT: B 713 ASN cc_start: 0.8094 (t0) cc_final: 0.7876 (t0) REVERT: B 717 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: C 69 CYS cc_start: 0.8372 (m) cc_final: 0.7878 (m) REVERT: C 81 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5619 (tm-30) REVERT: C 102 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5516 (mtpt) REVERT: C 155 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7607 (mmtm) REVERT: C 157 ILE cc_start: 0.8636 (tp) cc_final: 0.8359 (tp) REVERT: C 158 GLN cc_start: 0.7935 (tp40) cc_final: 0.7299 (mm-40) REVERT: C 161 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6511 (mtm) REVERT: C 183 MET cc_start: 0.7936 (tmm) cc_final: 0.7545 (tmm) REVERT: C 199 LEU cc_start: 0.0660 (OUTLIER) cc_final: 0.0202 (mt) REVERT: C 219 MET cc_start: 0.8263 (ttp) cc_final: 0.7993 (ttp) REVERT: C 255 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6328 (t80) REVERT: C 479 SER cc_start: 0.7611 (m) cc_final: 0.7296 (p) REVERT: C 536 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6696 (tp30) REVERT: C 560 GLU cc_start: 0.7154 (tp30) cc_final: 0.6883 (tp30) REVERT: C 568 ARG cc_start: 0.7580 (ttm110) cc_final: 0.6785 (ttm-80) REVERT: C 602 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6637 (t0) REVERT: C 672 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6817 (mm-30) REVERT: C 695 MET cc_start: 0.7302 (mmm) cc_final: 0.7055 (tpp) REVERT: C 722 ARG cc_start: 0.7378 (ttm170) cc_final: 0.6963 (ttt180) REVERT: D 68 ARG cc_start: 0.7687 (ptp90) cc_final: 0.6736 (ptp90) REVERT: D 70 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6528 (mpt90) REVERT: D 74 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6975 (mm-30) REVERT: D 109 ILE cc_start: 0.8482 (mt) cc_final: 0.7872 (mp) REVERT: D 113 PHE cc_start: 0.7534 (m-80) cc_final: 0.7190 (m-80) REVERT: D 175 VAL cc_start: 0.7990 (OUTLIER) cc_final: 0.7723 (t) REVERT: D 217 MET cc_start: 0.8220 (mtp) cc_final: 0.7804 (mtp) REVERT: D 219 MET cc_start: 0.7251 (tpp) cc_final: 0.6774 (tpt) REVERT: D 223 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5032 (mpt) REVERT: D 234 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7108 (tpt-90) REVERT: D 261 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8473 (mm-30) REVERT: D 287 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6258 (pm20) REVERT: D 300 TYR cc_start: 0.7282 (t80) cc_final: 0.6774 (t80) REVERT: D 436 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6732 (mm-30) REVERT: D 444 LYS cc_start: 0.6528 (OUTLIER) cc_final: 0.5430 (mtmt) REVERT: D 473 GLN cc_start: 0.6771 (tp40) cc_final: 0.6419 (tp40) REVERT: D 479 SER cc_start: 0.8232 (m) cc_final: 0.7932 (p) REVERT: D 541 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8023 (tt) REVERT: D 561 GLU cc_start: 0.7186 (pm20) cc_final: 0.6597 (pm20) REVERT: D 565 ASP cc_start: 0.7137 (m-30) cc_final: 0.6786 (m-30) REVERT: D 606 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7078 (tp30) REVERT: D 672 GLU cc_start: 0.6967 (tp30) cc_final: 0.6479 (tp30) REVERT: D 686 TYR cc_start: 0.7872 (t80) cc_final: 0.7203 (t80) REVERT: D 695 MET cc_start: 0.6821 (tpt) cc_final: 0.6516 (tpt) REVERT: D 706 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6978 (tm-30) REVERT: E 57 HIS cc_start: 0.7047 (m-70) cc_final: 0.6656 (m170) REVERT: E 69 CYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7096 (p) REVERT: E 155 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7681 (mtpt) REVERT: E 181 LYS cc_start: 0.8784 (mttt) cc_final: 0.8338 (mttt) REVERT: E 219 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6111 (ppp) REVERT: E 223 MET cc_start: 0.8272 (mmt) cc_final: 0.8023 (mmp) REVERT: E 271 MET cc_start: 0.6326 (ptt) cc_final: 0.5810 (ppp) REVERT: E 484 ASP cc_start: 0.7200 (m-30) cc_final: 0.6859 (m-30) REVERT: E 517 ASP cc_start: 0.6539 (t70) cc_final: 0.6188 (t0) REVERT: E 548 ASP cc_start: 0.8001 (t70) cc_final: 0.7783 (t0) REVERT: E 606 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6896 (mm-30) REVERT: E 611 ARG cc_start: 0.7597 (ttp80) cc_final: 0.7309 (ttp-170) REVERT: E 612 ASP cc_start: 0.7594 (t0) cc_final: 0.7239 (t0) REVERT: E 615 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7588 (mtpt) REVERT: E 635 LYS cc_start: 0.6872 (mmmt) cc_final: 0.6433 (mmmt) REVERT: E 671 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7720 (mtmm) REVERT: E 699 THR cc_start: 0.7718 (m) cc_final: 0.7380 (p) REVERT: F 429 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6133 (tm-30) REVERT: F 432 LEU cc_start: 0.8091 (mm) cc_final: 0.7788 (mm) REVERT: F 469 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7438 (ttpp) REVERT: F 483 ASP cc_start: 0.6923 (m-30) cc_final: 0.6654 (m-30) REVERT: F 489 SER cc_start: 0.8451 (t) cc_final: 0.8195 (m) REVERT: F 490 PRO cc_start: 0.8535 (Cg_endo) cc_final: 0.8308 (Cg_exo) REVERT: F 548 ASP cc_start: 0.8082 (t70) cc_final: 0.7552 (t0) REVERT: F 556 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6379 (mm-30) REVERT: F 604 LEU cc_start: 0.7958 (tp) cc_final: 0.7740 (mt) REVERT: F 608 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: F 609 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7537 (tp-100) REVERT: F 614 TYR cc_start: 0.7741 (t80) cc_final: 0.7297 (t80) REVERT: F 671 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7479 (tttt) REVERT: F 679 ARG cc_start: 0.7560 (mtt90) cc_final: 0.7243 (mtt90) REVERT: F 680 GLN cc_start: 0.7118 (mp10) cc_final: 0.6589 (mp10) REVERT: F 695 MET cc_start: 0.7546 (mmt) cc_final: 0.7108 (mmm) REVERT: F 696 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: F 700 ASP cc_start: 0.7094 (m-30) cc_final: 0.6810 (m-30) REVERT: F 724 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7881 (mmtp) outliers start: 209 outliers final: 138 residues processed: 781 average time/residue: 0.2149 time to fit residues: 248.5723 Evaluate side-chains 807 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 633 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 589 GLN Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 680 GLN Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 342 ARG Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 516 ILE Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 579 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain F residue 696 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 94 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 171 optimal weight: 0.6980 chunk 276 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN A 650 ASN ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 ASN D 616 ASN D 647 GLN D 721 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 GLN E 488 HIS ** E 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN F 463 HIS F 499 HIS F 569 GLN F 609 GLN F 647 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.176300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134719 restraints weight = 45552.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137958 restraints weight = 20073.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139404 restraints weight = 9998.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140209 restraints weight = 8672.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140498 restraints weight = 7163.353| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26073 Z= 0.165 Angle : 0.657 15.007 35237 Z= 0.334 Chirality : 0.040 0.176 3882 Planarity : 0.005 0.094 4545 Dihedral : 6.955 59.114 3548 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.91 % Favored : 93.54 % Rotamer: Outliers : 7.45 % Allowed : 29.52 % Favored : 63.03 % 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 aren not related in a simple way. whole: -0.20 (0.16), residues: 3094 helix: 0.61 (0.11), residues: 2282 sheet: -6.11 (0.39), residues: 10 loop : -2.13 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 149 TYR 0.030 0.002 TYR D 325 PHE 0.037 0.002 PHE A 113 TRP 0.029 0.001 TRP D 73 HIS 0.012 0.001 HIS D 721 Details of bonding type rmsd covalent geometry : bond 0.00361 (26073) covalent geometry : angle 0.65731 (35237) hydrogen bonds : bond 0.04972 ( 1510) hydrogen bonds : angle 4.68106 ( 4482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 640 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6595 (pp20) REVERT: A 110 CYS cc_start: 0.8382 (m) cc_final: 0.8113 (m) REVERT: A 158 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7415 (mm-40) REVERT: A 218 LEU cc_start: 0.8765 (mt) cc_final: 0.8517 (mt) REVERT: A 232 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 243 TYR cc_start: 0.6441 (m-10) cc_final: 0.6108 (m-80) REVERT: A 279 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4725 (mmm) REVERT: A 346 TYR cc_start: 0.5491 (OUTLIER) cc_final: 0.5116 (p90) REVERT: A 436 GLU cc_start: 0.7251 (tt0) cc_final: 0.6915 (tm-30) REVERT: A 470 SER cc_start: 0.8009 (m) cc_final: 0.7755 (t) REVERT: A 473 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7203 (mm110) REVERT: A 538 MET cc_start: 0.7369 (mmm) cc_final: 0.7117 (mmp) REVERT: A 570 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7775 (ttpp) REVERT: A 575 PHE cc_start: 0.8343 (m-80) cc_final: 0.8071 (m-80) REVERT: A 582 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7455 (tpp) REVERT: A 583 VAL cc_start: 0.8444 (t) cc_final: 0.8162 (p) REVERT: A 608 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7444 (t80) REVERT: A 614 TYR cc_start: 0.7241 (t80) cc_final: 0.6978 (t80) REVERT: A 633 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5229 (tm-30) REVERT: A 654 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8204 (mmt180) REVERT: A 671 LYS cc_start: 0.7839 (mmtm) cc_final: 0.7583 (mmmm) REVERT: A 695 MET cc_start: 0.7202 (tpp) cc_final: 0.6990 (mmm) REVERT: A 717 ARG cc_start: 0.7601 (tpp80) cc_final: 0.7189 (ttm-80) REVERT: A 722 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7118 (tpp80) REVERT: B 54 ARG cc_start: 0.4774 (OUTLIER) cc_final: 0.4522 (mtp180) REVERT: B 69 CYS cc_start: 0.6695 (t) cc_final: 0.6329 (m) REVERT: B 73 TRP cc_start: 0.7773 (t-100) cc_final: 0.7453 (t-100) REVERT: B 113 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7734 (m-10) REVERT: B 160 LYS cc_start: 0.7279 (tttp) cc_final: 0.7018 (tttp) REVERT: B 206 ARG cc_start: 0.6676 (mtp-110) cc_final: 0.6324 (mtp-110) REVERT: B 217 MET cc_start: 0.7285 (mpp) cc_final: 0.6680 (mpp) REVERT: B 477 ASN cc_start: 0.7941 (m-40) cc_final: 0.7736 (m-40) REVERT: B 505 GLU cc_start: 0.7017 (mp0) cc_final: 0.6798 (mp0) REVERT: B 539 ARG cc_start: 0.6957 (ttt-90) cc_final: 0.6649 (ttt90) REVERT: B 589 GLN cc_start: 0.4994 (OUTLIER) cc_final: 0.4584 (tm-30) REVERT: B 593 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6942 (pp) REVERT: B 607 PHE cc_start: 0.7875 (t80) cc_final: 0.7459 (t80) REVERT: B 608 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6960 (t80) REVERT: B 672 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7437 (mm-30) REVERT: B 680 GLN cc_start: 0.6735 (tm-30) cc_final: 0.6187 (tm-30) REVERT: B 713 ASN cc_start: 0.8097 (t0) cc_final: 0.7860 (t0) REVERT: C 69 CYS cc_start: 0.8394 (m) cc_final: 0.7908 (m) REVERT: C 81 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5543 (tm-30) REVERT: C 102 LYS cc_start: 0.5878 (OUTLIER) cc_final: 0.5587 (mtpt) REVERT: C 155 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7600 (mmtm) REVERT: C 157 ILE cc_start: 0.8628 (tp) cc_final: 0.8368 (tp) REVERT: C 158 GLN cc_start: 0.7926 (tp40) cc_final: 0.7393 (mm-40) REVERT: C 161 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6602 (mtm) REVERT: C 183 MET cc_start: 0.7922 (tmm) cc_final: 0.7541 (tmm) REVERT: C 199 LEU cc_start: 0.0576 (OUTLIER) cc_final: 0.0127 (mt) REVERT: C 219 MET cc_start: 0.8258 (ttp) cc_final: 0.7924 (ttp) REVERT: C 223 MET cc_start: 0.7194 (pmt) cc_final: 0.6727 (pmt) REVERT: C 255 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6301 (t80) REVERT: C 479 SER cc_start: 0.7588 (m) cc_final: 0.7298 (p) REVERT: C 483 ASP cc_start: 0.6852 (t0) cc_final: 0.6628 (t0) REVERT: C 519 MET cc_start: 0.7352 (mtp) cc_final: 0.7083 (mtm) REVERT: C 536 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6713 (tp30) REVERT: C 548 ASP cc_start: 0.7667 (t70) cc_final: 0.7248 (t0) REVERT: C 560 GLU cc_start: 0.7142 (tp30) cc_final: 0.6929 (tp30) REVERT: C 568 ARG cc_start: 0.7561 (ttm110) cc_final: 0.6782 (ttm-80) REVERT: C 602 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6652 (t0) REVERT: C 672 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6835 (mm-30) REVERT: C 695 MET cc_start: 0.7284 (mmm) cc_final: 0.7045 (tpp) REVERT: C 722 ARG cc_start: 0.7383 (ttm170) cc_final: 0.6979 (ttt180) REVERT: D 68 ARG cc_start: 0.7664 (ptp90) cc_final: 0.7071 (ttp80) REVERT: D 70 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6469 (mpt90) REVERT: D 74 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7018 (mm-30) REVERT: D 109 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.7880 (mp) REVERT: D 113 PHE cc_start: 0.7530 (m-80) cc_final: 0.7171 (m-80) REVERT: D 217 MET cc_start: 0.8095 (mtp) cc_final: 0.7874 (mtp) REVERT: D 219 MET cc_start: 0.7231 (tpp) cc_final: 0.6736 (tpt) REVERT: D 223 MET cc_start: 0.5891 (OUTLIER) cc_final: 0.4939 (mpt) REVERT: D 234 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7205 (tpt-90) REVERT: D 261 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8417 (mm-30) REVERT: D 287 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: D 300 TYR cc_start: 0.7295 (t80) cc_final: 0.6829 (t80) REVERT: D 436 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6733 (mm-30) REVERT: D 444 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5523 (mtmt) REVERT: D 473 GLN cc_start: 0.6775 (tp40) cc_final: 0.6427 (tp40) REVERT: D 479 SER cc_start: 0.8243 (m) cc_final: 0.7949 (p) REVERT: D 541 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8160 (tt) REVERT: D 554 ASN cc_start: 0.8329 (t0) cc_final: 0.8106 (m110) REVERT: D 560 GLU cc_start: 0.7558 (tp30) cc_final: 0.7168 (tp30) REVERT: D 561 GLU cc_start: 0.7256 (pm20) cc_final: 0.6703 (pm20) REVERT: D 565 ASP cc_start: 0.7214 (m-30) cc_final: 0.6838 (m-30) REVERT: D 606 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7104 (tp30) REVERT: D 686 TYR cc_start: 0.7872 (t80) cc_final: 0.7204 (t80) REVERT: D 706 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6968 (tm-30) REVERT: E 69 CYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7093 (p) REVERT: E 155 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7693 (mtpt) REVERT: E 181 LYS cc_start: 0.8781 (mttt) cc_final: 0.8310 (mttt) REVERT: E 219 MET cc_start: 0.6769 (ptp) cc_final: 0.6102 (ppp) REVERT: E 223 MET cc_start: 0.8265 (mmt) cc_final: 0.8036 (mmp) REVERT: E 271 MET cc_start: 0.6343 (ptt) cc_final: 0.5800 (ppp) REVERT: E 481 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7263 (mtp) REVERT: E 484 ASP cc_start: 0.7187 (m-30) cc_final: 0.6851 (m-30) REVERT: E 517 ASP cc_start: 0.6562 (t70) cc_final: 0.6126 (t0) REVERT: E 606 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6850 (mm-30) REVERT: E 611 ARG cc_start: 0.7580 (ttp80) cc_final: 0.7345 (ttp-170) REVERT: E 612 ASP cc_start: 0.7652 (t0) cc_final: 0.7301 (t0) REVERT: E 615 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7599 (mtpt) REVERT: E 635 LYS cc_start: 0.6847 (mmmt) cc_final: 0.6387 (mmmt) REVERT: E 666 LEU cc_start: 0.7332 (pt) cc_final: 0.6532 (pt) REVERT: E 667 ASP cc_start: 0.7495 (m-30) cc_final: 0.6902 (p0) REVERT: E 671 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7709 (mtmm) REVERT: E 699 THR cc_start: 0.7660 (m) cc_final: 0.7340 (p) REVERT: F 429 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6067 (tm-30) REVERT: F 432 LEU cc_start: 0.8137 (mm) cc_final: 0.7823 (mm) REVERT: F 469 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7443 (ttpp) REVERT: F 483 ASP cc_start: 0.6916 (m-30) cc_final: 0.6490 (m-30) REVERT: F 484 ASP cc_start: 0.6602 (OUTLIER) cc_final: 0.6287 (t0) REVERT: F 489 SER cc_start: 0.8447 (t) cc_final: 0.7828 (p) REVERT: F 545 GLN cc_start: 0.7699 (tp40) cc_final: 0.7494 (tp-100) REVERT: F 548 ASP cc_start: 0.7996 (t70) cc_final: 0.7543 (t0) REVERT: F 604 LEU cc_start: 0.7949 (tp) cc_final: 0.7734 (mt) REVERT: F 608 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: F 614 TYR cc_start: 0.7722 (t80) cc_final: 0.7338 (t80) REVERT: F 671 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7454 (tttt) REVERT: F 679 ARG cc_start: 0.7582 (mtt90) cc_final: 0.7278 (mtt90) REVERT: F 680 GLN cc_start: 0.7124 (mp10) cc_final: 0.6591 (mp10) REVERT: F 695 MET cc_start: 0.7555 (mmt) cc_final: 0.7129 (mmm) REVERT: F 696 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6149 (mp0) REVERT: F 700 ASP cc_start: 0.7072 (m-30) cc_final: 0.6781 (m-30) REVERT: F 724 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7867 (mmtp) outliers start: 209 outliers final: 140 residues processed: 771 average time/residue: 0.2103 time to fit residues: 239.3311 Evaluate side-chains 803 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 629 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 589 GLN Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 680 GLN Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 481 MET Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 590 GLN Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 516 ILE Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 579 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain F residue 696 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 172 optimal weight: 0.0050 chunk 227 optimal weight: 0.6980 chunk 230 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 0.0070 chunk 40 optimal weight: 0.5980 chunk 314 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN A 650 ASN ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 721 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 GLN ** E 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN F 463 HIS F 499 HIS ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN F 647 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.177269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136144 restraints weight = 45202.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139115 restraints weight = 19694.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140561 restraints weight = 10034.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.141217 restraints weight = 8495.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141692 restraints weight = 7042.038| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26073 Z= 0.143 Angle : 0.650 15.152 35237 Z= 0.331 Chirality : 0.040 0.200 3882 Planarity : 0.005 0.138 4545 Dihedral : 6.676 59.209 3539 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.43 % Favored : 94.02 % Rotamer: Outliers : 6.70 % Allowed : 30.23 % Favored : 63.07 % 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 aren not related in a simple way. whole: -0.01 (0.16), residues: 3094 helix: 0.76 (0.11), residues: 2286 sheet: -6.03 (0.42), residues: 10 loop : -2.10 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 292 TYR 0.031 0.002 TYR B 550 PHE 0.041 0.001 PHE A 113 TRP 0.041 0.002 TRP A 89 HIS 0.018 0.001 HIS E 430 Details of bonding type rmsd covalent geometry : bond 0.00311 (26073) covalent geometry : angle 0.64950 (35237) hydrogen bonds : bond 0.04581 ( 1510) hydrogen bonds : angle 4.55540 ( 4482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 642 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6626 (pp20) REVERT: A 110 CYS cc_start: 0.8404 (m) cc_final: 0.8116 (m) REVERT: A 114 GLU cc_start: 0.7920 (tp30) cc_final: 0.7423 (tp30) REVERT: A 158 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7334 (mm-40) REVERT: A 194 ARG cc_start: 0.1521 (OUTLIER) cc_final: -0.0429 (tmm160) REVERT: A 218 LEU cc_start: 0.8758 (mt) cc_final: 0.8524 (mt) REVERT: A 232 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 279 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4685 (mmm) REVERT: A 346 TYR cc_start: 0.5502 (OUTLIER) cc_final: 0.5170 (p90) REVERT: A 360 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7113 (tp40) REVERT: A 436 GLU cc_start: 0.7227 (tt0) cc_final: 0.6843 (tm-30) REVERT: A 538 MET cc_start: 0.7350 (mmm) cc_final: 0.7115 (mmp) REVERT: A 570 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7629 (mtpp) REVERT: A 575 PHE cc_start: 0.8310 (m-80) cc_final: 0.8041 (m-80) REVERT: A 582 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7390 (tpp) REVERT: A 583 VAL cc_start: 0.8398 (t) cc_final: 0.8078 (p) REVERT: A 608 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7443 (t80) REVERT: A 614 TYR cc_start: 0.7202 (t80) cc_final: 0.6940 (t80) REVERT: A 633 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.5245 (tm-30) REVERT: A 654 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8183 (mmt180) REVERT: A 671 LYS cc_start: 0.7827 (mmtm) cc_final: 0.7525 (mmmm) REVERT: A 686 TYR cc_start: 0.7879 (t80) cc_final: 0.7616 (t80) REVERT: A 717 ARG cc_start: 0.7548 (tpp80) cc_final: 0.7150 (ttm-80) REVERT: A 722 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7064 (tpp80) REVERT: B 54 ARG cc_start: 0.4675 (OUTLIER) cc_final: 0.4447 (mtp180) REVERT: B 73 TRP cc_start: 0.7750 (t-100) cc_final: 0.7443 (t-100) REVERT: B 113 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7737 (m-10) REVERT: B 160 LYS cc_start: 0.7261 (tttp) cc_final: 0.6992 (tttp) REVERT: B 206 ARG cc_start: 0.6499 (mtp-110) cc_final: 0.6186 (mtp-110) REVERT: B 448 GLU cc_start: 0.7093 (mp0) cc_final: 0.6774 (mp0) REVERT: B 477 ASN cc_start: 0.7966 (m-40) cc_final: 0.7763 (m-40) REVERT: B 570 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8106 (ttpp) REVERT: B 589 GLN cc_start: 0.5009 (OUTLIER) cc_final: 0.4566 (tm-30) REVERT: B 593 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6856 (pp) REVERT: B 607 PHE cc_start: 0.7895 (t80) cc_final: 0.7474 (t80) REVERT: B 608 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.6951 (t80) REVERT: B 672 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7416 (mm-30) REVERT: B 680 GLN cc_start: 0.6739 (tm-30) cc_final: 0.6214 (tm-30) REVERT: B 717 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7362 (ttm-80) REVERT: C 69 CYS cc_start: 0.8395 (m) cc_final: 0.7897 (m) REVERT: C 81 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5532 (tm-30) REVERT: C 102 LYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5611 (mtpt) REVERT: C 155 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7590 (mmtm) REVERT: C 157 ILE cc_start: 0.8643 (tp) cc_final: 0.8369 (tp) REVERT: C 158 GLN cc_start: 0.7922 (tp40) cc_final: 0.7448 (tp40) REVERT: C 183 MET cc_start: 0.7939 (tmm) cc_final: 0.7564 (tmm) REVERT: C 219 MET cc_start: 0.8176 (ttp) cc_final: 0.7850 (ttp) REVERT: C 223 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6681 (pmt) REVERT: C 255 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6498 (t80) REVERT: C 271 MET cc_start: 0.2300 (ttt) cc_final: 0.1050 (ptm) REVERT: C 479 SER cc_start: 0.7566 (m) cc_final: 0.7326 (p) REVERT: C 502 PHE cc_start: 0.7819 (m-80) cc_final: 0.7241 (m-80) REVERT: C 519 MET cc_start: 0.7326 (mtp) cc_final: 0.7049 (mtm) REVERT: C 536 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6694 (tp30) REVERT: C 556 GLU cc_start: 0.7338 (tt0) cc_final: 0.7084 (tt0) REVERT: C 568 ARG cc_start: 0.7532 (ttm110) cc_final: 0.6757 (ttm-80) REVERT: C 596 GLN cc_start: 0.7119 (mt0) cc_final: 0.6821 (mt0) REVERT: C 602 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6588 (t0) REVERT: C 695 MET cc_start: 0.7159 (mmm) cc_final: 0.6949 (tpp) REVERT: C 722 ARG cc_start: 0.7359 (ttm170) cc_final: 0.7065 (ttt180) REVERT: D 68 ARG cc_start: 0.7626 (ptp90) cc_final: 0.7063 (ttp80) REVERT: D 70 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6417 (mpt90) REVERT: D 74 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7001 (mm-30) REVERT: D 109 ILE cc_start: 0.8402 (mt) cc_final: 0.7791 (mp) REVERT: D 113 PHE cc_start: 0.7535 (m-80) cc_final: 0.7156 (m-80) REVERT: D 217 MET cc_start: 0.8187 (mtp) cc_final: 0.7919 (mtp) REVERT: D 219 MET cc_start: 0.7105 (tpp) cc_final: 0.6604 (tpt) REVERT: D 223 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.4943 (mpt) REVERT: D 234 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7151 (tpt-90) REVERT: D 261 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8382 (mm-30) REVERT: D 287 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6058 (pm20) REVERT: D 300 TYR cc_start: 0.7235 (t80) cc_final: 0.6664 (t80) REVERT: D 349 TRP cc_start: 0.6005 (OUTLIER) cc_final: 0.5751 (p90) REVERT: D 436 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6710 (mm-30) REVERT: D 444 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5225 (mtmt) REVERT: D 473 GLN cc_start: 0.6710 (tp40) cc_final: 0.6395 (tp40) REVERT: D 479 SER cc_start: 0.8237 (m) cc_final: 0.7892 (p) REVERT: D 541 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8038 (tt) REVERT: D 554 ASN cc_start: 0.8332 (t0) cc_final: 0.8064 (m110) REVERT: D 560 GLU cc_start: 0.7474 (tp30) cc_final: 0.7107 (tp30) REVERT: D 561 GLU cc_start: 0.7095 (pm20) cc_final: 0.6510 (pm20) REVERT: D 564 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7920 (mt) REVERT: D 565 ASP cc_start: 0.7113 (m-30) cc_final: 0.6780 (m-30) REVERT: D 606 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6515 (tp30) REVERT: D 650 ASN cc_start: 0.7667 (t0) cc_final: 0.7280 (t0) REVERT: D 686 TYR cc_start: 0.7822 (t80) cc_final: 0.7174 (t80) REVERT: D 706 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6989 (tm-30) REVERT: E 69 CYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7087 (p) REVERT: E 155 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7760 (mtpt) REVERT: E 181 LYS cc_start: 0.8794 (mttt) cc_final: 0.8281 (mttt) REVERT: E 219 MET cc_start: 0.6673 (ptp) cc_final: 0.6072 (ppp) REVERT: E 220 ARG cc_start: 0.7873 (ttt180) cc_final: 0.7608 (ttt180) REVERT: E 223 MET cc_start: 0.8250 (mmt) cc_final: 0.8050 (mmp) REVERT: E 271 MET cc_start: 0.6344 (ptt) cc_final: 0.5838 (ppp) REVERT: E 440 SER cc_start: 0.8361 (m) cc_final: 0.7821 (p) REVERT: E 484 ASP cc_start: 0.7183 (m-30) cc_final: 0.6837 (m-30) REVERT: E 505 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6999 (mm-30) REVERT: E 516 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7238 (tp) REVERT: E 517 ASP cc_start: 0.6533 (t70) cc_final: 0.6095 (t0) REVERT: E 548 ASP cc_start: 0.8281 (t0) cc_final: 0.7728 (t0) REVERT: E 606 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6812 (mm-30) REVERT: E 611 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7406 (ttp-170) REVERT: E 612 ASP cc_start: 0.7659 (t0) cc_final: 0.7322 (t0) REVERT: E 615 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7630 (mtpt) REVERT: E 635 LYS cc_start: 0.6938 (mmmt) cc_final: 0.6725 (mmmt) REVERT: E 666 LEU cc_start: 0.7335 (pt) cc_final: 0.6457 (pt) REVERT: E 667 ASP cc_start: 0.7663 (m-30) cc_final: 0.7172 (p0) REVERT: E 671 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7713 (mtmm) REVERT: E 699 THR cc_start: 0.7595 (m) cc_final: 0.7287 (p) REVERT: F 429 GLU cc_start: 0.6640 (tm-30) cc_final: 0.6080 (tm-30) REVERT: F 432 LEU cc_start: 0.8079 (mm) cc_final: 0.7824 (mm) REVERT: F 489 SER cc_start: 0.8475 (t) cc_final: 0.7922 (p) REVERT: F 548 ASP cc_start: 0.8016 (t70) cc_final: 0.7497 (t0) REVERT: F 551 TRP cc_start: 0.8344 (m-10) cc_final: 0.8084 (m-10) REVERT: F 554 ASN cc_start: 0.7972 (m110) cc_final: 0.7708 (m-40) REVERT: F 604 LEU cc_start: 0.7932 (tp) cc_final: 0.7730 (mt) REVERT: F 608 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: F 614 TYR cc_start: 0.7742 (t80) cc_final: 0.7296 (t80) REVERT: F 671 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7440 (tttt) REVERT: F 679 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7258 (mtt90) REVERT: F 680 GLN cc_start: 0.7099 (mp10) cc_final: 0.6575 (mp10) REVERT: F 695 MET cc_start: 0.7557 (mmt) cc_final: 0.7117 (mmm) REVERT: F 696 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: F 700 ASP cc_start: 0.7069 (m-30) cc_final: 0.6783 (m-30) REVERT: F 724 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7858 (mmtp) outliers start: 188 outliers final: 127 residues processed: 758 average time/residue: 0.2070 time to fit residues: 231.4823 Evaluate side-chains 792 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 631 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 589 GLN Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 680 GLN Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 342 ARG Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 590 GLN Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 579 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 696 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 119 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN A 650 ASN ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 HIS B 650 ASN ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 198 ASN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 GLN ** E 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN F 463 HIS F 499 HIS F 554 ASN F 569 GLN F 609 GLN F 647 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.176777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136234 restraints weight = 45198.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138247 restraints weight = 20702.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.140106 restraints weight = 11474.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140624 restraints weight = 9042.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140850 restraints weight = 7695.184| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26073 Z= 0.162 Angle : 0.667 12.631 35237 Z= 0.339 Chirality : 0.041 0.209 3882 Planarity : 0.005 0.050 4545 Dihedral : 6.576 58.950 3537 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.59 % Favored : 93.92 % Rotamer: Outliers : 6.63 % Allowed : 30.55 % Favored : 62.82 % 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 aren not related in a simple way. whole: 0.06 (0.16), residues: 3094 helix: 0.81 (0.11), residues: 2293 sheet: -6.01 (0.44), residues: 10 loop : -2.10 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 679 TYR 0.026 0.002 TYR B 686 PHE 0.042 0.002 PHE A 113 TRP 0.054 0.002 TRP A 89 HIS 0.014 0.001 HIS D 721 Details of bonding type rmsd covalent geometry : bond 0.00358 (26073) covalent geometry : angle 0.66670 (35237) hydrogen bonds : bond 0.04665 ( 1510) hydrogen bonds : angle 4.54992 ( 4482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 641 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6652 (pp20) REVERT: A 110 CYS cc_start: 0.8444 (m) cc_final: 0.8148 (m) REVERT: A 114 GLU cc_start: 0.7974 (tp30) cc_final: 0.7453 (tp30) REVERT: A 158 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7422 (mm-40) REVERT: A 165 LEU cc_start: 0.8300 (tt) cc_final: 0.8078 (tp) REVERT: A 194 ARG cc_start: 0.1781 (OUTLIER) cc_final: -0.0317 (mmm160) REVERT: A 218 LEU cc_start: 0.8713 (mt) cc_final: 0.8471 (mt) REVERT: A 232 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 346 TYR cc_start: 0.5601 (OUTLIER) cc_final: 0.5241 (p90) REVERT: A 360 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7201 (tp40) REVERT: A 436 GLU cc_start: 0.7219 (tt0) cc_final: 0.6862 (tm-30) REVERT: A 470 SER cc_start: 0.8005 (m) cc_final: 0.7746 (t) REVERT: A 538 MET cc_start: 0.7354 (mmm) cc_final: 0.7128 (mmp) REVERT: A 570 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7646 (mtpp) REVERT: A 575 PHE cc_start: 0.8321 (m-80) cc_final: 0.8062 (m-80) REVERT: A 582 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7412 (tpp) REVERT: A 583 VAL cc_start: 0.8405 (t) cc_final: 0.8090 (p) REVERT: A 608 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7440 (t80) REVERT: A 614 TYR cc_start: 0.7217 (t80) cc_final: 0.6967 (t80) REVERT: A 633 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5311 (tm-30) REVERT: A 654 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8219 (mmt180) REVERT: A 671 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7593 (mmmm) REVERT: A 717 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7126 (tpp80) REVERT: A 722 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7083 (tpp80) REVERT: B 54 ARG cc_start: 0.4654 (OUTLIER) cc_final: 0.4426 (mtp180) REVERT: B 73 TRP cc_start: 0.7700 (t-100) cc_final: 0.7469 (t-100) REVERT: B 448 GLU cc_start: 0.7091 (mp0) cc_final: 0.6773 (mp0) REVERT: B 477 ASN cc_start: 0.7950 (m-40) cc_final: 0.7701 (m-40) REVERT: B 505 GLU cc_start: 0.6997 (mp0) cc_final: 0.6770 (mp0) REVERT: B 593 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6870 (pp) REVERT: B 607 PHE cc_start: 0.7914 (t80) cc_final: 0.7503 (t80) REVERT: B 608 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 672 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 680 GLN cc_start: 0.6701 (tm-30) cc_final: 0.6144 (tm-30) REVERT: B 717 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7579 (mtp85) REVERT: C 69 CYS cc_start: 0.8391 (m) cc_final: 0.7894 (m) REVERT: C 81 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5570 (tm-30) REVERT: C 102 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5729 (mtpt) REVERT: C 155 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7637 (mmtm) REVERT: C 157 ILE cc_start: 0.8702 (tp) cc_final: 0.8411 (tp) REVERT: C 158 GLN cc_start: 0.8102 (tp40) cc_final: 0.7367 (tp40) REVERT: C 161 MET cc_start: 0.7073 (mtm) cc_final: 0.6613 (mtm) REVERT: C 183 MET cc_start: 0.7980 (tmm) cc_final: 0.7611 (tmm) REVERT: C 219 MET cc_start: 0.8201 (ttp) cc_final: 0.7881 (ttp) REVERT: C 223 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6715 (pmt) REVERT: C 255 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6494 (t80) REVERT: C 271 MET cc_start: 0.2416 (ttt) cc_final: 0.1133 (ptm) REVERT: C 479 SER cc_start: 0.7606 (m) cc_final: 0.7324 (p) REVERT: C 502 PHE cc_start: 0.7857 (m-80) cc_final: 0.7267 (m-80) REVERT: C 519 MET cc_start: 0.7357 (mtp) cc_final: 0.7069 (mtm) REVERT: C 536 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6713 (tp30) REVERT: C 548 ASP cc_start: 0.7646 (t70) cc_final: 0.7249 (t0) REVERT: C 568 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7064 (ttm-80) REVERT: C 596 GLN cc_start: 0.7158 (mt0) cc_final: 0.6846 (mt0) REVERT: C 602 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6615 (t0) REVERT: C 722 ARG cc_start: 0.7377 (ttm170) cc_final: 0.7076 (ttt180) REVERT: D 68 ARG cc_start: 0.7567 (ptp90) cc_final: 0.7048 (ttp80) REVERT: D 70 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6468 (mpt90) REVERT: D 74 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7033 (mm-30) REVERT: D 109 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7699 (mp) REVERT: D 113 PHE cc_start: 0.7545 (m-80) cc_final: 0.7180 (m-80) REVERT: D 217 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: D 219 MET cc_start: 0.7130 (tpp) cc_final: 0.6611 (tpt) REVERT: D 223 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.4923 (mpt) REVERT: D 234 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7188 (tpt-90) REVERT: D 261 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8467 (mm-30) REVERT: D 287 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6054 (pm20) REVERT: D 300 TYR cc_start: 0.7274 (t80) cc_final: 0.6734 (t80) REVERT: D 301 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: D 349 TRP cc_start: 0.6009 (OUTLIER) cc_final: 0.5742 (p90) REVERT: D 436 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6733 (mm-30) REVERT: D 444 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5418 (mtmt) REVERT: D 473 GLN cc_start: 0.6742 (tp40) cc_final: 0.6425 (tp40) REVERT: D 479 SER cc_start: 0.8210 (m) cc_final: 0.7874 (p) REVERT: D 493 ARG cc_start: 0.7173 (mtp85) cc_final: 0.6910 (ttm-80) REVERT: D 537 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6977 (mm-30) REVERT: D 541 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8067 (tt) REVERT: D 554 ASN cc_start: 0.8331 (t0) cc_final: 0.8110 (m-40) REVERT: D 560 GLU cc_start: 0.7487 (tp30) cc_final: 0.7142 (tp30) REVERT: D 561 GLU cc_start: 0.7165 (pm20) cc_final: 0.6567 (pm20) REVERT: D 564 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8048 (mt) REVERT: D 565 ASP cc_start: 0.7168 (m-30) cc_final: 0.6831 (m-30) REVERT: D 606 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6572 (tp30) REVERT: D 650 ASN cc_start: 0.7702 (t0) cc_final: 0.7163 (t0) REVERT: D 672 GLU cc_start: 0.6984 (tp30) cc_final: 0.6734 (tp30) REVERT: D 686 TYR cc_start: 0.7866 (t80) cc_final: 0.7227 (t80) REVERT: D 706 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6990 (tm-30) REVERT: E 69 CYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7131 (p) REVERT: E 155 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7758 (mtpt) REVERT: E 181 LYS cc_start: 0.8804 (mttt) cc_final: 0.8297 (mttt) REVERT: E 219 MET cc_start: 0.6643 (ptp) cc_final: 0.6060 (ppp) REVERT: E 220 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7629 (ttt180) REVERT: E 440 SER cc_start: 0.8359 (m) cc_final: 0.7815 (p) REVERT: E 484 ASP cc_start: 0.7190 (m-30) cc_final: 0.6832 (m-30) REVERT: E 505 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6968 (mm-30) REVERT: E 516 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7216 (tp) REVERT: E 517 ASP cc_start: 0.6534 (t70) cc_final: 0.6098 (t0) REVERT: E 548 ASP cc_start: 0.8266 (t0) cc_final: 0.7909 (t0) REVERT: E 606 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6808 (mm-30) REVERT: E 611 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7470 (ttp-170) REVERT: E 612 ASP cc_start: 0.7687 (t0) cc_final: 0.7357 (t0) REVERT: E 615 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7616 (mtpt) REVERT: E 635 LYS cc_start: 0.6953 (mmmt) cc_final: 0.6655 (mmmt) REVERT: E 666 LEU cc_start: 0.7255 (pt) cc_final: 0.6373 (pt) REVERT: E 667 ASP cc_start: 0.7728 (m-30) cc_final: 0.7175 (p0) REVERT: E 671 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7771 (mtmm) REVERT: E 699 THR cc_start: 0.7595 (m) cc_final: 0.7323 (p) REVERT: F 429 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6117 (tm-30) REVERT: F 432 LEU cc_start: 0.8092 (mm) cc_final: 0.7843 (mm) REVERT: F 469 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7469 (ttpp) REVERT: F 483 ASP cc_start: 0.6465 (m-30) cc_final: 0.6252 (m-30) REVERT: F 489 SER cc_start: 0.8482 (t) cc_final: 0.8112 (p) REVERT: F 548 ASP cc_start: 0.7915 (t70) cc_final: 0.7401 (t0) REVERT: F 604 LEU cc_start: 0.7967 (tp) cc_final: 0.7740 (mt) REVERT: F 608 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: F 614 TYR cc_start: 0.7764 (t80) cc_final: 0.7233 (t80) REVERT: F 671 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7416 (tttt) REVERT: F 679 ARG cc_start: 0.7571 (mtt90) cc_final: 0.7258 (mtt90) REVERT: F 680 GLN cc_start: 0.7119 (mp10) cc_final: 0.6573 (mp10) REVERT: F 695 MET cc_start: 0.7544 (mmt) cc_final: 0.7117 (mmm) REVERT: F 696 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: F 700 ASP cc_start: 0.7060 (m-30) cc_final: 0.6783 (m-30) REVERT: F 724 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7869 (mmtp) outliers start: 186 outliers final: 133 residues processed: 760 average time/residue: 0.2165 time to fit residues: 242.5812 Evaluate side-chains 801 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 633 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 680 GLN Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 342 ARG Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 590 GLN Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 499 HIS Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 579 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain F residue 696 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 246 optimal weight: 0.9980 chunk 253 optimal weight: 9.9990 chunk 166 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN A 650 ASN ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN E 650 ASN E 677 HIS F 463 HIS ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.176394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135506 restraints weight = 45411.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137836 restraints weight = 20791.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139629 restraints weight = 11316.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140098 restraints weight = 8642.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140411 restraints weight = 7457.922| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26073 Z= 0.191 Angle : 0.700 14.502 35237 Z= 0.355 Chirality : 0.042 0.276 3882 Planarity : 0.005 0.051 4545 Dihedral : 6.513 58.758 3533 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.69 % Favored : 93.83 % Rotamer: Outliers : 6.27 % Allowed : 30.87 % Favored : 62.85 % 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 aren not related in a simple way. whole: 0.02 (0.16), residues: 3094 helix: 0.78 (0.11), residues: 2292 sheet: -5.93 (0.46), residues: 10 loop : -2.10 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 679 TYR 0.049 0.002 TYR D 550 PHE 0.044 0.002 PHE A 113 TRP 0.057 0.002 TRP A 89 HIS 0.018 0.002 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00424 (26073) covalent geometry : angle 0.70047 (35237) hydrogen bonds : bond 0.04913 ( 1510) hydrogen bonds : angle 4.58184 ( 4482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 646 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8460 (m) cc_final: 0.8093 (m) REVERT: A 114 GLU cc_start: 0.7992 (tp30) cc_final: 0.7468 (tp30) REVERT: A 158 GLN cc_start: 0.7702 (tp40) cc_final: 0.7431 (mm-40) REVERT: A 165 LEU cc_start: 0.8313 (tt) cc_final: 0.8077 (tp) REVERT: A 194 ARG cc_start: 0.1710 (OUTLIER) cc_final: -0.0460 (mmm160) REVERT: A 218 LEU cc_start: 0.8721 (mt) cc_final: 0.8475 (mt) REVERT: A 233 LYS cc_start: 0.8482 (mttp) cc_final: 0.8189 (mttp) REVERT: A 279 MET cc_start: 0.5235 (mmt) cc_final: 0.4847 (mmm) REVERT: A 346 TYR cc_start: 0.5651 (OUTLIER) cc_final: 0.5283 (p90) REVERT: A 360 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7040 (tp40) REVERT: A 436 GLU cc_start: 0.7231 (tt0) cc_final: 0.6854 (tm-30) REVERT: A 470 SER cc_start: 0.8026 (m) cc_final: 0.7782 (t) REVERT: A 538 MET cc_start: 0.7363 (mmm) cc_final: 0.7140 (mmp) REVERT: A 575 PHE cc_start: 0.8342 (m-80) cc_final: 0.8085 (m-80) REVERT: A 582 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7434 (tpp) REVERT: A 583 VAL cc_start: 0.8427 (t) cc_final: 0.8114 (p) REVERT: A 608 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7434 (t80) REVERT: A 614 TYR cc_start: 0.7269 (t80) cc_final: 0.6985 (t80) REVERT: A 633 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5299 (tm-30) REVERT: A 671 LYS cc_start: 0.7812 (mmtm) cc_final: 0.7538 (mmmm) REVERT: A 686 TYR cc_start: 0.7954 (t80) cc_final: 0.7670 (t80) REVERT: A 708 GLU cc_start: 0.7792 (tp30) cc_final: 0.7563 (tp30) REVERT: A 717 ARG cc_start: 0.7604 (tpp80) cc_final: 0.7148 (tpp80) REVERT: A 722 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7125 (tpp80) REVERT: B 73 TRP cc_start: 0.7701 (t-100) cc_final: 0.7487 (t-100) REVERT: B 217 MET cc_start: 0.7322 (mpp) cc_final: 0.6819 (mpp) REVERT: B 448 GLU cc_start: 0.7094 (mp0) cc_final: 0.6761 (mp0) REVERT: B 477 ASN cc_start: 0.7905 (m-40) cc_final: 0.7688 (m-40) REVERT: B 505 GLU cc_start: 0.7017 (mp0) cc_final: 0.6815 (mp0) REVERT: B 593 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6946 (pp) REVERT: B 607 PHE cc_start: 0.7915 (t80) cc_final: 0.7561 (t80) REVERT: B 608 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.6973 (t80) REVERT: B 672 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 680 GLN cc_start: 0.6776 (tm-30) cc_final: 0.6223 (tm-30) REVERT: B 717 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7603 (mtp85) REVERT: C 69 CYS cc_start: 0.8404 (m) cc_final: 0.7900 (m) REVERT: C 102 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5846 (mtpt) REVERT: C 155 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7694 (mmtm) REVERT: C 157 ILE cc_start: 0.8722 (tp) cc_final: 0.8433 (tp) REVERT: C 158 GLN cc_start: 0.8097 (tp40) cc_final: 0.7361 (tp40) REVERT: C 161 MET cc_start: 0.7186 (mtm) cc_final: 0.6773 (mtm) REVERT: C 182 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7276 (tm-30) REVERT: C 183 MET cc_start: 0.8012 (tmm) cc_final: 0.7463 (tmm) REVERT: C 219 MET cc_start: 0.8199 (ttp) cc_final: 0.7883 (ttp) REVERT: C 223 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6746 (pmt) REVERT: C 271 MET cc_start: 0.2402 (ttt) cc_final: 0.1097 (ptm) REVERT: C 479 SER cc_start: 0.7700 (m) cc_final: 0.7411 (p) REVERT: C 519 MET cc_start: 0.7369 (mtp) cc_final: 0.7091 (mtm) REVERT: C 536 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6734 (tp30) REVERT: C 548 ASP cc_start: 0.7696 (t70) cc_final: 0.7242 (t0) REVERT: C 568 ARG cc_start: 0.7557 (ttm110) cc_final: 0.6753 (ttm-80) REVERT: C 596 GLN cc_start: 0.7176 (mt0) cc_final: 0.6863 (mt0) REVERT: C 602 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6623 (t0) REVERT: C 722 ARG cc_start: 0.7403 (ttm170) cc_final: 0.7100 (ttt180) REVERT: D 68 ARG cc_start: 0.7574 (ptp90) cc_final: 0.7053 (ttp80) REVERT: D 70 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6439 (mpt90) REVERT: D 74 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7149 (mm-30) REVERT: D 109 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7788 (mp) REVERT: D 113 PHE cc_start: 0.7537 (m-80) cc_final: 0.7186 (m-80) REVERT: D 219 MET cc_start: 0.7101 (tpp) cc_final: 0.6860 (tpt) REVERT: D 223 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.5417 (mpt) REVERT: D 234 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7252 (tpt-90) REVERT: D 261 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8483 (mm-30) REVERT: D 287 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6028 (pm20) REVERT: D 300 TYR cc_start: 0.7345 (t80) cc_final: 0.6752 (t80) REVERT: D 349 TRP cc_start: 0.5945 (OUTLIER) cc_final: 0.5692 (p90) REVERT: D 436 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6732 (mm-30) REVERT: D 444 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.5462 (mtmt) REVERT: D 473 GLN cc_start: 0.6751 (tp40) cc_final: 0.6419 (tp40) REVERT: D 479 SER cc_start: 0.8221 (m) cc_final: 0.7923 (p) REVERT: D 493 ARG cc_start: 0.7172 (mtp85) cc_final: 0.6921 (ttm-80) REVERT: D 537 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6980 (mm-30) REVERT: D 560 GLU cc_start: 0.7535 (tp30) cc_final: 0.7255 (tp30) REVERT: D 561 GLU cc_start: 0.7193 (pm20) cc_final: 0.6613 (pm20) REVERT: D 564 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8160 (mt) REVERT: D 565 ASP cc_start: 0.7108 (m-30) cc_final: 0.6763 (m-30) REVERT: D 606 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6886 (tp30) REVERT: D 638 TYR cc_start: 0.8356 (t80) cc_final: 0.7507 (t80) REVERT: D 650 ASN cc_start: 0.7651 (t0) cc_final: 0.7074 (t0) REVERT: D 672 GLU cc_start: 0.7023 (tp30) cc_final: 0.6794 (tp30) REVERT: D 706 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6991 (tm-30) REVERT: E 69 CYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7154 (p) REVERT: E 155 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7762 (mtpt) REVERT: E 181 LYS cc_start: 0.8782 (mttt) cc_final: 0.8293 (mttt) REVERT: E 220 ARG cc_start: 0.7866 (ttt180) cc_final: 0.7611 (ttt180) REVERT: E 271 MET cc_start: 0.6152 (ptt) cc_final: 0.5644 (ppp) REVERT: E 440 SER cc_start: 0.8367 (m) cc_final: 0.7813 (p) REVERT: E 484 ASP cc_start: 0.7176 (m-30) cc_final: 0.6811 (m-30) REVERT: E 505 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6955 (mm-30) REVERT: E 516 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7174 (tp) REVERT: E 517 ASP cc_start: 0.6564 (t70) cc_final: 0.5973 (t0) REVERT: E 522 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8170 (m) REVERT: E 548 ASP cc_start: 0.8159 (t0) cc_final: 0.7603 (t0) REVERT: E 606 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6819 (mm-30) REVERT: E 611 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7437 (ttp-170) REVERT: E 612 ASP cc_start: 0.7695 (t0) cc_final: 0.7370 (t0) REVERT: E 615 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7654 (mtpt) REVERT: E 635 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6738 (mmmt) REVERT: E 666 LEU cc_start: 0.7253 (pt) cc_final: 0.6381 (pt) REVERT: E 667 ASP cc_start: 0.7758 (m-30) cc_final: 0.7171 (p0) REVERT: E 671 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7775 (mtmm) REVERT: E 699 THR cc_start: 0.7542 (m) cc_final: 0.7228 (p) REVERT: E 700 ASP cc_start: 0.7694 (p0) cc_final: 0.7461 (p0) REVERT: F 429 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6141 (tm-30) REVERT: F 432 LEU cc_start: 0.8133 (mm) cc_final: 0.7846 (mm) REVERT: F 469 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7466 (ttpp) REVERT: F 483 ASP cc_start: 0.6521 (m-30) cc_final: 0.6305 (m-30) REVERT: F 489 SER cc_start: 0.8438 (t) cc_final: 0.8001 (p) REVERT: F 548 ASP cc_start: 0.7875 (t70) cc_final: 0.7400 (t0) REVERT: F 556 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6375 (mm-30) REVERT: F 604 LEU cc_start: 0.7961 (tp) cc_final: 0.7730 (mt) REVERT: F 608 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: F 614 TYR cc_start: 0.7768 (t80) cc_final: 0.7240 (t80) REVERT: F 671 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7502 (tttt) REVERT: F 679 ARG cc_start: 0.7607 (mtt90) cc_final: 0.7274 (mtt90) REVERT: F 680 GLN cc_start: 0.7156 (mp10) cc_final: 0.6585 (mp10) REVERT: F 690 LYS cc_start: 0.7958 (tptp) cc_final: 0.7532 (tptp) REVERT: F 695 MET cc_start: 0.7554 (mmt) cc_final: 0.7169 (mmm) REVERT: F 696 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: F 700 ASP cc_start: 0.7077 (m-30) cc_final: 0.6803 (m-30) REVERT: F 724 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7860 (mmtp) outliers start: 176 outliers final: 136 residues processed: 750 average time/residue: 0.2138 time to fit residues: 236.5832 Evaluate side-chains 796 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 632 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 677 HIS Chi-restraints excluded: chain D residue 680 GLN Chi-restraints excluded: chain D residue 701 SER Chi-restraints excluded: chain D residue 720 ILE Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 342 ARG Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 481 MET Chi-restraints excluded: chain E residue 487 ASP Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 516 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 590 GLN Chi-restraints excluded: chain E residue 608 PHE Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 677 HIS Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 516 ILE Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 579 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 608 PHE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 672 GLU Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain F residue 696 GLU Chi-restraints excluded: chain F residue 724 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 186 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 206 optimal weight: 0.3980 chunk 292 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 211 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 268 optimal weight: 0.0070 chunk 163 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN A 642 HIS A 650 ASN ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 GLN ** E 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN ** E 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS F 467 GLN F 499 HIS F 554 ASN F 647 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.177907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137488 restraints weight = 44982.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139816 restraints weight = 20663.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141223 restraints weight = 11412.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141875 restraints weight = 8764.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142819 restraints weight = 7687.773| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26073 Z= 0.143 Angle : 0.686 14.939 35237 Z= 0.344 Chirality : 0.040 0.223 3882 Planarity : 0.005 0.049 4545 Dihedral : 6.381 58.721 3529 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.14 % Favored : 94.38 % Rotamer: Outliers : 6.02 % Allowed : 31.30 % Favored : 62.67 % 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 aren not related in a simple way. whole: 0.19 (0.16), residues: 3094 helix: 0.92 (0.11), residues: 2291 sheet: -5.90 (0.45), residues: 10 loop : -2.09 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 679 TYR 0.042 0.002 TYR D 550 PHE 0.045 0.001 PHE A 113 TRP 0.048 0.002 TRP A 89 HIS 0.015 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00317 (26073) covalent geometry : angle 0.68552 (35237) hydrogen bonds : bond 0.04445 ( 1510) hydrogen bonds : angle 4.45621 ( 4482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5695.09 seconds wall clock time: 98 minutes 54.18 seconds (5934.18 seconds total)