Starting phenix.real_space_refine on Sun Jun 22 03:34:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2j_47454/06_2025/9e2j_47454.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2j_47454/06_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_47454/06_2025/9e2j_47454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2j_47454/06_2025/9e2j_47454.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2j_47454/06_2025/9e2j_47454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2j_47454/06_2025/9e2j_47454.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.00, per 1000 atoms: 0.63 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: 6.92 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.30 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: 7.78 Time building geometry restraints manager: 7.69 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: 3.710 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: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 55.590 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.100 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.060 ------------------------------------------------------------------------------- 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 : 21.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.054 0.002 TRP D 73 HIS 0.009 0.001 HIS E 642 PHE 0.035 0.002 PHE D 113 TYR 0.040 0.002 TYR D 550 ARG 0.014 0.001 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.33895 ( 1510) hydrogen bonds : angle 9.02514 ( 4482) covalent geometry : bond 0.00427 (26073) covalent geometry : angle 0.84313 (35237) *********************** 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 : 2.776 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: 0.4492 time to fit residues: 522.1807 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 : 2.669 ------------------------------------------------------------------------------- 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 265 optimal weight: 0.6980 chunk 238 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 246 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 150 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 286 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.176639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135566 restraints weight = 44985.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139088 restraints weight = 19484.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140089 restraints weight = 9403.782| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26073 Z= 0.217 Angle : 0.745 11.815 35237 Z= 0.399 Chirality : 0.043 0.226 3882 Planarity : 0.006 0.057 4545 Dihedral : 11.040 86.472 3792 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.76 % Favored : 92.53 % Rotamer: Outliers : 9.38 % Allowed : 27.52 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 3094 helix: -0.54 (0.11), residues: 2270 sheet: -6.58 (0.19), residues: 10 loop : -2.60 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 73 HIS 0.010 0.001 HIS E 642 PHE 0.037 0.002 PHE C 311 TYR 0.040 0.002 TYR D 550 ARG 0.009 0.001 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.08261 ( 1510) hydrogen bonds : angle 6.04869 ( 4482) covalent geometry : bond 0.00442 (26073) covalent geometry : angle 0.74450 (35237) *********************** 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 944 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 681 time to evaluate : 2.936 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: A 109 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7719 (mt) REVERT: A 158 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7457 (mm-40) REVERT: A 183 MET cc_start: 0.8086 (tmm) cc_final: 0.7668 (ptm) REVERT: A 194 ARG cc_start: 0.2145 (OUTLIER) cc_final: -0.0170 (mmm160) REVERT: A 218 LEU cc_start: 0.8825 (mt) cc_final: 0.8496 (mt) REVERT: A 267 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8117 (p0) REVERT: A 436 GLU cc_start: 0.7312 (tt0) cc_final: 0.6913 (tm-30) REVERT: A 470 SER cc_start: 0.8176 (m) cc_final: 0.7883 (t) REVERT: A 560 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6500 (tt0) REVERT: A 581 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7473 (mtp) REVERT: A 583 VAL cc_start: 0.8441 (t) cc_final: 0.8062 (p) REVERT: A 614 TYR cc_start: 0.7135 (t80) cc_final: 0.6859 (t80) REVERT: A 617 LEU cc_start: 0.8216 (mt) cc_final: 0.7999 (mm) REVERT: A 671 LYS cc_start: 0.7980 (mmtm) cc_final: 0.7647 (mmmm) REVERT: A 690 LYS cc_start: 0.7957 (tppp) cc_final: 0.7696 (tptp) REVERT: A 717 ARG cc_start: 0.7801 (tpp80) cc_final: 0.7431 (ttm-80) REVERT: B 69 CYS cc_start: 0.6650 (t) cc_final: 0.6393 (m) REVERT: B 73 TRP cc_start: 0.7730 (t-100) cc_final: 0.7216 (t-100) REVERT: B 117 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7263 (t80) REVERT: B 119 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: B 217 MET cc_start: 0.7302 (mpp) cc_final: 0.6771 (mpp) REVERT: B 298 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8666 (tppt) REVERT: B 477 ASN cc_start: 0.7929 (m-40) cc_final: 0.7656 (m-40) REVERT: B 495 ARG cc_start: 0.7409 (mmm-85) cc_final: 0.6708 (mmm-85) REVERT: B 519 MET cc_start: 0.7437 (mmm) cc_final: 0.7218 (tmm) REVERT: B 550 TYR cc_start: 0.7681 (t80) cc_final: 0.7458 (t80) REVERT: B 574 LEU cc_start: 0.8339 (tp) cc_final: 0.8082 (mt) REVERT: B 589 GLN cc_start: 0.5344 (OUTLIER) cc_final: 0.4506 (tm-30) REVERT: B 608 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7304 (t80) REVERT: B 717 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7392 (mtp85) REVERT: B 718 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8100 (tt) REVERT: C 64 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: C 157 ILE cc_start: 0.8723 (tp) cc_final: 0.8405 (tp) REVERT: C 158 GLN cc_start: 0.8248 (tp40) cc_final: 0.7418 (tp40) REVERT: C 161 MET cc_start: 0.7466 (mtm) cc_final: 0.6974 (mtm) REVERT: C 182 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7202 (tm-30) REVERT: C 183 MET cc_start: 0.7973 (tmm) cc_final: 0.7362 (tmm) REVERT: C 199 LEU cc_start: 0.1067 (OUTLIER) cc_final: 0.0724 (mt) REVERT: C 219 MET cc_start: 0.8408 (ttp) cc_final: 0.8147 (ttp) REVERT: C 238 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6832 (mp) REVERT: C 271 MET cc_start: 0.3414 (ttt) cc_final: 0.3038 (ttp) REVERT: C 279 MET cc_start: 0.7691 (mmm) cc_final: 0.7452 (mmm) REVERT: C 319 ASN cc_start: 0.3076 (OUTLIER) cc_final: 0.2596 (m-40) REVERT: C 479 SER cc_start: 0.7628 (m) cc_final: 0.7240 (p) REVERT: C 483 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.6299 (t0) REVERT: C 520 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6576 (tm-30) REVERT: C 536 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6635 (tp30) REVERT: C 548 ASP cc_start: 0.7664 (t70) cc_final: 0.7187 (t0) REVERT: C 556 GLU cc_start: 0.7293 (tt0) cc_final: 0.7081 (tt0) REVERT: C 566 MET cc_start: 0.7663 (tmm) cc_final: 0.7349 (tmm) REVERT: C 568 ARG cc_start: 0.7444 (ttm110) cc_final: 0.6940 (ttm-80) REVERT: C 583 VAL cc_start: 0.8572 (p) cc_final: 0.8364 (t) REVERT: C 602 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6587 (t0) REVERT: C 672 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6931 (mm-30) REVERT: C 695 MET cc_start: 0.7668 (tpt) cc_final: 0.7420 (mmm) REVERT: C 697 LYS cc_start: 0.7639 (mtmm) cc_final: 0.7279 (mtmm) REVERT: C 722 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7045 (ttm170) REVERT: D 68 ARG cc_start: 0.7429 (ptp90) cc_final: 0.6572 (ptp90) REVERT: D 70 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6830 (mpt90) REVERT: D 74 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6964 (mm-30) REVERT: D 113 PHE cc_start: 0.7358 (m-80) cc_final: 0.7004 (m-80) REVERT: D 118 LEU cc_start: 0.8014 (mt) cc_final: 0.7750 (mt) REVERT: D 155 LYS cc_start: 0.8156 (mttm) cc_final: 0.7947 (mttm) REVERT: D 161 MET cc_start: 0.7572 (mtt) cc_final: 0.7124 (mtt) REVERT: D 206 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7387 (mmt90) REVERT: D 217 MET cc_start: 0.7658 (tpp) cc_final: 0.7185 (tpp) REVERT: D 219 MET cc_start: 0.7187 (tpp) cc_final: 0.6930 (tpt) REVERT: D 231 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7543 (pp20) REVERT: D 300 TYR cc_start: 0.7197 (t80) cc_final: 0.6648 (t80) REVERT: D 301 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: D 308 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7693 (mm) REVERT: D 350 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7065 (mt) REVERT: D 429 GLU cc_start: 0.6750 (pm20) cc_final: 0.6542 (pm20) REVERT: D 479 SER cc_start: 0.8155 (m) cc_final: 0.7867 (p) REVERT: D 486 GLU cc_start: 0.6413 (tm-30) cc_final: 0.6207 (tm-30) REVERT: D 561 GLU cc_start: 0.7118 (pm20) cc_final: 0.6648 (pm20) REVERT: D 565 ASP cc_start: 0.7081 (m-30) cc_final: 0.6741 (m-30) REVERT: D 635 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6957 (mmmt) REVERT: D 671 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7637 (mtpp) REVERT: E 69 CYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7011 (p) REVERT: E 155 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7581 (mtpt) REVERT: E 161 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6426 (ppp) REVERT: E 162 LEU cc_start: 0.8351 (mt) cc_final: 0.7581 (mt) REVERT: E 164 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7581 (mm-30) REVERT: E 183 MET cc_start: 0.8175 (mmt) cc_final: 0.7963 (mmm) REVERT: E 221 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6388 (p90) REVERT: E 229 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: E 271 MET cc_start: 0.6077 (ptt) cc_final: 0.5549 (ppp) REVERT: E 495 ARG cc_start: 0.6697 (mtp85) cc_final: 0.5735 (ttm170) REVERT: E 548 ASP cc_start: 0.8023 (t70) cc_final: 0.7760 (t0) REVERT: E 583 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7499 (p) REVERT: E 611 ARG cc_start: 0.7425 (ttp80) cc_final: 0.7164 (ttp80) REVERT: E 613 ASP cc_start: 0.7507 (m-30) cc_final: 0.7149 (t0) REVERT: E 615 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7332 (mtpt) REVERT: E 635 LYS cc_start: 0.7095 (mmmt) cc_final: 0.6598 (mmmt) REVERT: E 690 LYS cc_start: 0.8178 (tptp) cc_final: 0.7972 (tptt) REVERT: E 691 MET cc_start: 0.7940 (mmm) cc_final: 0.7500 (tmm) REVERT: F 429 GLU cc_start: 0.6471 (tm-30) cc_final: 0.5891 (tm-30) REVERT: F 483 ASP cc_start: 0.7049 (m-30) cc_final: 0.6700 (m-30) REVERT: F 489 SER cc_start: 0.8501 (t) cc_final: 0.8153 (m) REVERT: F 490 PRO cc_start: 0.8508 (Cg_endo) cc_final: 0.8285 (Cg_exo) REVERT: F 548 ASP cc_start: 0.7996 (t70) cc_final: 0.7684 (t0) REVERT: F 551 TRP cc_start: 0.8352 (m-10) cc_final: 0.8134 (m-10) REVERT: F 568 ARG cc_start: 0.7057 (ttm-80) cc_final: 0.6572 (ttm-80) REVERT: F 606 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6783 (mt-10) REVERT: F 608 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7021 (m-80) REVERT: F 609 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7283 (tp-100) REVERT: F 671 LYS cc_start: 0.8142 (tttt) cc_final: 0.7728 (tttt) REVERT: F 680 GLN cc_start: 0.7057 (mp10) cc_final: 0.6605 (mp10) REVERT: F 690 LYS cc_start: 0.7901 (tptp) cc_final: 0.7568 (tptp) REVERT: F 695 MET cc_start: 0.7519 (mmt) cc_final: 0.7162 (mmm) REVERT: F 696 GLU cc_start: 0.7090 (mp0) cc_final: 0.6126 (mp0) REVERT: F 700 ASP cc_start: 0.6967 (m-30) cc_final: 0.6733 (m-30) REVERT: F 706 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7043 (mm-30) REVERT: F 722 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7031 (ttp80) REVERT: F 723 LEU cc_start: 0.8644 (tp) cc_final: 0.8428 (tp) REVERT: F 724 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7724 (mmtp) outliers start: 263 outliers final: 138 residues processed: 875 average time/residue: 0.4366 time to fit residues: 561.5013 Evaluate side-chains 831 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 662 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 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 319 ASN 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 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 89 TRP 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 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 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 698 ILE 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 165 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 174 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 289 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN ** 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 ** 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 329 GLN ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 GLN F 463 HIS F 584 GLN F 652 GLN F 659 GLN F 677 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.178482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138975 restraints weight = 45153.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140897 restraints weight = 19698.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141993 restraints weight = 10676.657| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26073 Z= 0.160 Angle : 0.665 11.970 35237 Z= 0.348 Chirality : 0.040 0.225 3882 Planarity : 0.005 0.054 4545 Dihedral : 9.364 61.170 3661 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.04 % Favored : 93.31 % Rotamer: Outliers : 7.38 % Allowed : 29.30 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3094 helix: -0.09 (0.11), residues: 2287 sheet: -6.58 (0.23), residues: 10 loop : -2.54 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 89 HIS 0.006 0.001 HIS E 642 PHE 0.033 0.002 PHE C 311 TYR 0.025 0.002 TYR D 550 ARG 0.009 0.001 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.06266 ( 1510) hydrogen bonds : angle 5.48739 ( 4482) covalent geometry : bond 0.00329 (26073) covalent geometry : angle 0.66481 (35237) *********************** 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 857 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 650 time to evaluate : 3.011 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 158 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7297 (mm-40) REVERT: A 194 ARG cc_start: 0.1923 (OUTLIER) cc_final: -0.0355 (mmm160) REVERT: A 218 LEU cc_start: 0.8720 (mt) cc_final: 0.8488 (mt) REVERT: A 240 LYS cc_start: 0.8333 (mmtp) cc_final: 0.8111 (tptt) REVERT: A 243 TYR cc_start: 0.6640 (m-10) cc_final: 0.6123 (m-80) REVERT: A 267 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8014 (p0) REVERT: A 339 TRP cc_start: 0.6013 (OUTLIER) cc_final: 0.5494 (t60) REVERT: A 436 GLU cc_start: 0.7249 (tt0) cc_final: 0.6900 (tm-30) REVERT: A 470 SER cc_start: 0.8102 (m) cc_final: 0.7836 (t) REVERT: A 538 MET cc_start: 0.7301 (mmm) cc_final: 0.6992 (mmp) REVERT: A 548 ASP cc_start: 0.8024 (t0) cc_final: 0.7719 (t0) REVERT: A 575 PHE cc_start: 0.8323 (m-80) cc_final: 0.8008 (m-80) REVERT: A 583 VAL cc_start: 0.8390 (t) cc_final: 0.8134 (p) REVERT: A 591 LYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5770 (mttp) REVERT: A 614 TYR cc_start: 0.7176 (t80) cc_final: 0.6826 (t80) REVERT: A 671 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7617 (mmmm) REVERT: A 690 LYS cc_start: 0.7853 (tppp) cc_final: 0.7569 (tptp) REVERT: A 717 ARG cc_start: 0.7579 (tpp80) cc_final: 0.7314 (ttm-80) REVERT: B 69 CYS cc_start: 0.6690 (t) cc_final: 0.6455 (m) REVERT: B 73 TRP cc_start: 0.7774 (t-100) cc_final: 0.7374 (t-100) REVERT: B 117 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7206 (t80) REVERT: B 119 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: B 217 MET cc_start: 0.7294 (mpp) cc_final: 0.6708 (mpp) REVERT: B 477 ASN cc_start: 0.7971 (m-40) cc_final: 0.7687 (m-40) REVERT: B 505 GLU cc_start: 0.6860 (mp0) cc_final: 0.6599 (mt-10) REVERT: B 519 MET cc_start: 0.7375 (mmm) cc_final: 0.7166 (tmm) REVERT: B 539 ARG cc_start: 0.6960 (ttt-90) cc_final: 0.6734 (ttt90) REVERT: B 550 TYR cc_start: 0.7725 (t80) cc_final: 0.7507 (t80) REVERT: B 574 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8094 (mt) REVERT: B 589 GLN cc_start: 0.5320 (OUTLIER) cc_final: 0.4527 (tm-30) REVERT: B 608 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7079 (t80) REVERT: B 661 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7670 (mtm-85) REVERT: B 721 HIS cc_start: 0.8283 (t70) cc_final: 0.8027 (t70) REVERT: C 81 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5626 (tm-30) REVERT: C 157 ILE cc_start: 0.8710 (tp) cc_final: 0.8356 (tp) REVERT: C 158 GLN cc_start: 0.8089 (tp40) cc_final: 0.7154 (mm-40) REVERT: C 161 MET cc_start: 0.7202 (mtm) cc_final: 0.6578 (mtm) REVERT: C 183 MET cc_start: 0.7908 (tmm) cc_final: 0.7494 (tmm) REVERT: C 199 LEU cc_start: 0.0555 (OUTLIER) cc_final: 0.0126 (mt) REVERT: C 219 MET cc_start: 0.8288 (ttp) cc_final: 0.8031 (ttp) REVERT: C 479 SER cc_start: 0.7710 (m) cc_final: 0.7319 (p) REVERT: C 483 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6279 (t0) REVERT: C 520 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6484 (tm-30) REVERT: C 521 LYS cc_start: 0.7613 (mttp) cc_final: 0.7231 (mttp) REVERT: C 536 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6680 (tp30) REVERT: C 548 ASP cc_start: 0.7665 (t70) cc_final: 0.7326 (t0) REVERT: C 556 GLU cc_start: 0.7288 (tt0) cc_final: 0.7050 (tt0) REVERT: C 560 GLU cc_start: 0.7223 (tp30) cc_final: 0.6771 (mm-30) REVERT: C 568 ARG cc_start: 0.7449 (ttm110) cc_final: 0.7007 (ttm-80) REVERT: C 602 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6550 (t0) REVERT: C 672 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6779 (mm-30) REVERT: C 722 ARG cc_start: 0.7472 (ttm170) cc_final: 0.7048 (ttm170) REVERT: D 68 ARG cc_start: 0.7425 (ptp90) cc_final: 0.6939 (ptp90) REVERT: D 70 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6782 (mpt90) REVERT: D 74 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6886 (mm-30) REVERT: D 109 ILE cc_start: 0.8293 (mt) cc_final: 0.8051 (pt) REVERT: D 113 PHE cc_start: 0.7402 (m-80) cc_final: 0.7115 (m-80) REVERT: D 161 MET cc_start: 0.7569 (mtt) cc_final: 0.7262 (mtt) REVERT: D 219 MET cc_start: 0.7229 (tpp) cc_final: 0.6731 (tpt) REVERT: D 223 MET cc_start: 0.5796 (OUTLIER) cc_final: 0.5275 (mpt) REVERT: D 231 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: D 261 GLU cc_start: 0.8799 (tp30) cc_final: 0.8579 (tp30) REVERT: D 300 TYR cc_start: 0.7231 (t80) cc_final: 0.6596 (t80) REVERT: D 301 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: D 479 SER cc_start: 0.8253 (m) cc_final: 0.8007 (p) REVERT: D 561 GLU cc_start: 0.7068 (pm20) cc_final: 0.6530 (pm20) REVERT: D 565 ASP cc_start: 0.7004 (m-30) cc_final: 0.6656 (m-30) REVERT: D 606 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6933 (tp30) REVERT: D 635 LYS cc_start: 0.7129 (mmmt) cc_final: 0.6897 (mmmt) REVERT: D 686 TYR cc_start: 0.7734 (t80) cc_final: 0.7155 (t80) REVERT: D 695 MET cc_start: 0.6830 (tpt) cc_final: 0.6514 (tpt) REVERT: E 69 CYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7043 (p) REVERT: E 155 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7616 (mtpt) REVERT: E 161 MET cc_start: 0.7078 (ppp) cc_final: 0.6426 (ppp) REVERT: E 162 LEU cc_start: 0.8388 (mt) cc_final: 0.7742 (mt) REVERT: E 164 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7656 (mm-30) REVERT: E 174 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: E 181 LYS cc_start: 0.8741 (mttt) cc_final: 0.8268 (mttt) REVERT: E 219 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6093 (ptp) REVERT: E 229 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6429 (tm-30) REVERT: E 271 MET cc_start: 0.6269 (ptt) cc_final: 0.5663 (ppp) REVERT: E 469 LYS cc_start: 0.8068 (mttp) cc_final: 0.7608 (mttp) REVERT: E 481 MET cc_start: 0.7383 (mtp) cc_final: 0.7182 (ttm) REVERT: E 484 ASP cc_start: 0.7310 (m-30) cc_final: 0.7091 (m-30) REVERT: E 493 ARG cc_start: 0.6309 (tpp80) cc_final: 0.6060 (tpp80) REVERT: E 505 GLU cc_start: 0.7316 (mp0) cc_final: 0.6967 (mp0) REVERT: E 564 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7649 (mt) REVERT: E 583 VAL cc_start: 0.7803 (OUTLIER) cc_final: 0.7548 (p) REVERT: E 615 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7377 (mtpt) REVERT: E 635 LYS cc_start: 0.6879 (mmmt) cc_final: 0.6381 (mmmt) REVERT: E 638 TYR cc_start: 0.8141 (t80) cc_final: 0.7925 (t80) REVERT: F 443 SER cc_start: 0.8285 (t) cc_final: 0.8009 (p) REVERT: F 483 ASP cc_start: 0.7011 (m-30) cc_final: 0.6717 (m-30) REVERT: F 484 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6316 (t0) REVERT: F 489 SER cc_start: 0.8489 (t) cc_final: 0.7946 (p) REVERT: F 490 PRO cc_start: 0.8618 (Cg_endo) cc_final: 0.8388 (Cg_exo) REVERT: F 548 ASP cc_start: 0.8027 (t70) cc_final: 0.7634 (t0) REVERT: F 568 ARG cc_start: 0.7000 (ttm-80) cc_final: 0.6532 (ttm-80) REVERT: F 604 LEU cc_start: 0.7991 (tp) cc_final: 0.7753 (mt) REVERT: F 606 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6692 (mt-10) REVERT: F 608 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: F 609 GLN cc_start: 0.7741 (tp-100) cc_final: 0.7376 (tp-100) REVERT: F 613 ASP cc_start: 0.6768 (m-30) cc_final: 0.6493 (m-30) REVERT: F 614 TYR cc_start: 0.7603 (t80) cc_final: 0.7167 (t80) REVERT: F 680 GLN cc_start: 0.7070 (mp10) cc_final: 0.6591 (mp10) REVERT: F 695 MET cc_start: 0.7468 (mmt) cc_final: 0.7018 (mmm) REVERT: F 696 GLU cc_start: 0.7020 (mp0) cc_final: 0.6190 (mp0) REVERT: F 700 ASP cc_start: 0.6881 (m-30) cc_final: 0.6641 (m-30) REVERT: F 706 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6935 (mm-30) REVERT: F 722 ARG cc_start: 0.7281 (ttp80) cc_final: 0.6952 (ttp80) REVERT: F 723 LEU cc_start: 0.8610 (tp) cc_final: 0.8398 (tp) REVERT: F 724 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7698 (mmtp) outliers start: 207 outliers final: 109 residues processed: 796 average time/residue: 0.4596 time to fit residues: 537.5532 Evaluate side-chains 779 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 643 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 63 ASN 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 339 TRP 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 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 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 479 SER 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 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 248 LEU 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 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 649 LYS 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 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 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 564 LEU Chi-restraints excluded: chain E residue 583 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 535 LEU 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 616 ASN 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 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 246 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 51 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN C 332 GLN ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS C 721 HIS ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 GLN D 658 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 562 GLN F 463 HIS F 569 GLN F 642 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.175456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135447 restraints weight = 45611.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136505 restraints weight = 22097.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138549 restraints weight = 11978.978| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 26073 Z= 0.264 Angle : 0.713 9.677 35237 Z= 0.372 Chirality : 0.044 0.187 3882 Planarity : 0.006 0.056 4545 Dihedral : 8.535 59.829 3598 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.56 % Favored : 92.82 % Rotamer: Outliers : 8.63 % Allowed : 28.16 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3094 helix: -0.11 (0.11), residues: 2289 sheet: -6.49 (0.24), residues: 10 loop : -2.51 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 73 HIS 0.011 0.002 HIS D 430 PHE 0.035 0.002 PHE A 113 TYR 0.044 0.002 TYR D 550 ARG 0.007 0.001 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.06600 ( 1510) hydrogen bonds : angle 5.41533 ( 4482) covalent geometry : bond 0.00571 (26073) covalent geometry : angle 0.71309 (35237) *********************** 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 898 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 656 time to evaluate : 3.080 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: 0.6736 (OUTLIER) cc_final: 0.6507 (pp20) REVERT: A 158 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7291 (mm-40) REVERT: A 194 ARG cc_start: 0.1613 (OUTLIER) cc_final: -0.0301 (tmm160) REVERT: A 218 LEU cc_start: 0.8804 (mt) cc_final: 0.8564 (mt) REVERT: A 243 TYR cc_start: 0.6537 (m-10) cc_final: 0.6131 (m-80) REVERT: A 267 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8088 (p0) REVERT: A 292 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7340 (ttt90) REVERT: A 436 GLU cc_start: 0.7224 (tt0) cc_final: 0.6921 (tm-30) REVERT: A 470 SER cc_start: 0.8256 (m) cc_final: 0.7927 (t) REVERT: A 548 ASP cc_start: 0.8013 (t0) cc_final: 0.7737 (t0) REVERT: A 570 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7966 (ttpp) REVERT: A 575 PHE cc_start: 0.8409 (m-80) cc_final: 0.7872 (m-80) REVERT: A 583 VAL cc_start: 0.8392 (t) cc_final: 0.8166 (p) REVERT: A 591 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5701 (mttp) REVERT: A 608 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7430 (t80) REVERT: A 614 TYR cc_start: 0.7266 (t80) cc_final: 0.6960 (t80) REVERT: A 633 GLU cc_start: 0.5629 (OUTLIER) cc_final: 0.5239 (tm-30) REVERT: A 638 TYR cc_start: 0.7866 (t80) cc_final: 0.7518 (t80) REVERT: A 671 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7641 (mmmm) REVERT: A 691 MET cc_start: 0.7081 (tpp) cc_final: 0.6787 (ttm) REVERT: A 717 ARG cc_start: 0.7664 (tpp80) cc_final: 0.7253 (ttm-80) REVERT: A 722 ARG cc_start: 0.7566 (tpp80) cc_final: 0.7298 (tpp80) REVERT: B 69 CYS cc_start: 0.6794 (t) cc_final: 0.6391 (m) REVERT: B 73 TRP cc_start: 0.7803 (t-100) cc_final: 0.7451 (t-100) REVERT: B 114 GLU cc_start: 0.7898 (tt0) cc_final: 0.7492 (tt0) REVERT: B 117 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7094 (t80) REVERT: B 119 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: B 217 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6669 (mpp) REVERT: B 432 LEU cc_start: 0.8514 (mt) cc_final: 0.8235 (mp) REVERT: B 495 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.6692 (mmm-85) REVERT: B 589 GLN cc_start: 0.5282 (OUTLIER) cc_final: 0.4507 (tm-30) REVERT: B 680 GLN cc_start: 0.6756 (tm-30) cc_final: 0.6253 (tm-30) REVERT: C 155 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7760 (mmtm) REVERT: C 158 GLN cc_start: 0.8086 (tp40) cc_final: 0.7220 (mm-40) REVERT: C 161 MET cc_start: 0.7063 (mtm) cc_final: 0.6531 (mtm) REVERT: C 182 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7139 (tm-30) REVERT: C 183 MET cc_start: 0.7780 (tmm) cc_final: 0.7150 (tmm) REVERT: C 199 LEU cc_start: 0.0870 (OUTLIER) cc_final: 0.0320 (mt) REVERT: C 238 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6607 (mp) REVERT: C 271 MET cc_start: 0.3802 (ttt) cc_final: 0.2689 (ptm) REVERT: C 279 MET cc_start: 0.7627 (mmm) cc_final: 0.7337 (mmm) REVERT: C 479 SER cc_start: 0.7733 (m) cc_final: 0.7314 (p) REVERT: C 483 ASP cc_start: 0.6618 (m-30) cc_final: 0.6261 (t0) REVERT: C 520 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6602 (tm-30) REVERT: C 536 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6736 (tp30) REVERT: C 560 GLU cc_start: 0.7267 (tp30) cc_final: 0.7054 (tt0) REVERT: C 602 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6486 (t0) REVERT: C 695 MET cc_start: 0.7469 (mmm) cc_final: 0.7226 (tpp) REVERT: C 722 ARG cc_start: 0.7489 (ttm170) cc_final: 0.6809 (ttm170) REVERT: D 68 ARG cc_start: 0.7746 (ptp90) cc_final: 0.6772 (ptp90) REVERT: D 70 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6639 (mpt90) REVERT: D 74 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6979 (mm-30) REVERT: D 109 ILE cc_start: 0.8435 (mt) cc_final: 0.8117 (pt) REVERT: D 113 PHE cc_start: 0.7408 (m-80) cc_final: 0.7184 (m-80) REVERT: D 175 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7856 (t) REVERT: D 217 MET cc_start: 0.8093 (mtp) cc_final: 0.7794 (mtp) REVERT: D 219 MET cc_start: 0.7172 (tpp) cc_final: 0.6747 (tpt) REVERT: D 223 MET cc_start: 0.5812 (OUTLIER) cc_final: 0.5193 (mpt) REVERT: D 226 MET cc_start: 0.7653 (pmm) cc_final: 0.7238 (pmm) REVERT: D 261 GLU cc_start: 0.8804 (tp30) cc_final: 0.8563 (tp30) REVERT: D 300 TYR cc_start: 0.7111 (t80) cc_final: 0.6603 (t80) REVERT: D 326 LEU cc_start: 0.8596 (pt) cc_final: 0.8301 (mp) REVERT: D 479 SER cc_start: 0.8319 (m) cc_final: 0.7596 (t) REVERT: D 541 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8265 (tt) REVERT: D 606 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6913 (tp30) REVERT: D 671 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7422 (mtpp) REVERT: D 672 GLU cc_start: 0.6929 (tp30) cc_final: 0.6589 (tp30) REVERT: D 686 TYR cc_start: 0.7776 (t80) cc_final: 0.7191 (t80) REVERT: E 69 CYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7002 (p) REVERT: E 155 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7678 (mtpt) REVERT: E 161 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6350 (ppp) REVERT: E 162 LEU cc_start: 0.8397 (mt) cc_final: 0.7549 (mt) REVERT: E 174 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7545 (pp20) REVERT: E 181 LYS cc_start: 0.8831 (mttt) cc_final: 0.8371 (mttt) REVERT: E 229 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6410 (tm-30) REVERT: E 271 MET cc_start: 0.6257 (ptt) cc_final: 0.5725 (ppp) REVERT: E 484 ASP cc_start: 0.7284 (m-30) cc_final: 0.7003 (m-30) REVERT: E 493 ARG cc_start: 0.6347 (tpp80) cc_final: 0.6140 (tpp80) REVERT: E 517 ASP cc_start: 0.6495 (t70) cc_final: 0.6129 (t0) REVERT: E 519 MET cc_start: 0.7017 (ttp) cc_final: 0.6742 (mtm) REVERT: E 520 GLU cc_start: 0.7293 (tp30) cc_final: 0.7013 (tp30) REVERT: E 548 ASP cc_start: 0.8244 (t0) cc_final: 0.8036 (t0) REVERT: E 553 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7876 (ttp80) REVERT: E 612 ASP cc_start: 0.7623 (t0) cc_final: 0.7263 (t0) REVERT: E 615 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7399 (mtpt) REVERT: E 635 LYS cc_start: 0.7088 (mmmt) cc_final: 0.6719 (mmmt) REVERT: E 638 TYR cc_start: 0.8222 (t80) cc_final: 0.8013 (t80) REVERT: F 429 GLU cc_start: 0.6457 (tm-30) cc_final: 0.5996 (tm-30) REVERT: F 483 ASP cc_start: 0.6894 (m-30) cc_final: 0.6682 (m-30) REVERT: F 484 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6325 (t0) REVERT: F 489 SER cc_start: 0.8428 (t) cc_final: 0.7674 (p) REVERT: F 490 PRO cc_start: 0.8643 (Cg_endo) cc_final: 0.8397 (Cg_exo) REVERT: F 548 ASP cc_start: 0.8115 (t70) cc_final: 0.7703 (t0) REVERT: F 608 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: F 613 ASP cc_start: 0.6714 (m-30) cc_final: 0.6460 (m-30) REVERT: F 614 TYR cc_start: 0.7625 (t80) cc_final: 0.7238 (t80) REVERT: F 679 ARG cc_start: 0.7525 (mtt90) cc_final: 0.7243 (mtt90) REVERT: F 680 GLN cc_start: 0.7101 (mp10) cc_final: 0.6587 (mp10) REVERT: F 695 MET cc_start: 0.7410 (mmt) cc_final: 0.7032 (mmm) REVERT: F 696 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: F 700 ASP cc_start: 0.6897 (m-30) cc_final: 0.6652 (m-30) REVERT: F 706 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6815 (mm-30) REVERT: F 723 LEU cc_start: 0.8692 (tp) cc_final: 0.8445 (tp) outliers start: 242 outliers final: 152 residues processed: 824 average time/residue: 0.4547 time to fit residues: 550.0111 Evaluate side-chains 820 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 641 time to evaluate : 2.662 ------------------------------------------------------------------------------- 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 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 292 ARG 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 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 581 MET 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 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 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 429 GLU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 475 LEU 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 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 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 426 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 492 ARG 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 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 66 SER 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 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 248 LEU 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 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 523 ARG 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 615 LYS Chi-restraints excluded: chain D residue 618 THR 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 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 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 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 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 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 533 ILE 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 581 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 25 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 295 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 256 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.0050 chunk 233 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 ** 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 545 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** 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 616 ASN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 250 ASN ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.178342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137284 restraints weight = 45256.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139829 restraints weight = 21162.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142093 restraints weight = 10302.439| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3669 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= 0.145 Angle : 0.641 10.331 35237 Z= 0.331 Chirality : 0.040 0.208 3882 Planarity : 0.005 0.053 4545 Dihedral : 7.915 59.888 3582 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.59 % Favored : 93.79 % Rotamer: Outliers : 7.20 % Allowed : 29.80 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3094 helix: 0.35 (0.11), residues: 2280 sheet: -6.40 (0.29), residues: 10 loop : -2.28 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 73 HIS 0.013 0.001 HIS F 499 PHE 0.038 0.002 PHE A 113 TYR 0.032 0.002 TYR D 550 ARG 0.011 0.001 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.05111 ( 1510) hydrogen bonds : angle 4.96710 ( 4482) covalent geometry : bond 0.00308 (26073) covalent geometry : angle 0.64140 (35237) *********************** 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 849 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 647 time to evaluate : 3.125 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 39 ARG cc_start: 0.2525 (OUTLIER) cc_final: 0.2216 (ptm-80) REVERT: A 64 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6552 (pp20) REVERT: A 158 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7312 (mm-40) REVERT: A 169 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6061 (t0) REVERT: A 194 ARG cc_start: 0.1625 (OUTLIER) cc_final: -0.0409 (tmm160) REVERT: A 218 LEU cc_start: 0.8811 (mt) cc_final: 0.8573 (mt) REVERT: A 243 TYR cc_start: 0.6507 (m-10) cc_final: 0.6085 (m-80) REVERT: A 346 TYR cc_start: 0.5554 (OUTLIER) cc_final: 0.5334 (p90) REVERT: A 436 GLU cc_start: 0.7246 (tt0) cc_final: 0.6856 (tm-30) REVERT: A 470 SER cc_start: 0.8062 (m) cc_final: 0.7805 (t) REVERT: A 538 MET cc_start: 0.7399 (mmm) cc_final: 0.7069 (mmp) REVERT: A 570 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7849 (ttpp) REVERT: A 575 PHE cc_start: 0.8283 (m-80) cc_final: 0.7976 (m-80) REVERT: A 582 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7352 (tpp) REVERT: A 583 VAL cc_start: 0.8356 (t) cc_final: 0.8053 (p) REVERT: A 591 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5742 (mttp) REVERT: A 608 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7430 (t80) REVERT: A 614 TYR cc_start: 0.7212 (t80) cc_final: 0.6900 (t80) REVERT: A 633 GLU cc_start: 0.5612 (OUTLIER) cc_final: 0.5236 (tm-30) REVERT: A 671 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7622 (mmmm) REVERT: A 690 LYS cc_start: 0.7654 (tptp) cc_final: 0.7322 (tptm) REVERT: A 691 MET cc_start: 0.7085 (tpp) cc_final: 0.6766 (ttm) REVERT: A 708 GLU cc_start: 0.7707 (tp30) cc_final: 0.7468 (tp30) REVERT: A 717 ARG cc_start: 0.7634 (tpp80) cc_final: 0.7193 (ttm-80) REVERT: A 722 ARG cc_start: 0.7571 (tpp80) cc_final: 0.7156 (tpp80) REVERT: B 69 CYS cc_start: 0.6682 (t) cc_final: 0.6472 (m) REVERT: B 73 TRP cc_start: 0.7784 (t-100) cc_final: 0.7371 (t-100) REVERT: B 113 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7592 (m-10) REVERT: B 114 GLU cc_start: 0.8005 (tt0) cc_final: 0.7700 (tm-30) REVERT: B 117 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7223 (t80) REVERT: B 119 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6999 (m-80) REVERT: B 217 MET cc_start: 0.7262 (mpp) cc_final: 0.6635 (mpp) REVERT: B 333 VAL cc_start: 0.5503 (OUTLIER) cc_final: 0.5281 (t) REVERT: B 432 LEU cc_start: 0.8385 (mt) cc_final: 0.8150 (mp) REVERT: B 539 ARG cc_start: 0.6913 (ttt-90) cc_final: 0.6646 (ttt90) REVERT: B 570 LYS cc_start: 0.8344 (ttpt) cc_final: 0.8088 (ttpp) REVERT: B 589 GLN cc_start: 0.5254 (OUTLIER) cc_final: 0.4382 (tm-30) REVERT: B 593 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7053 (pp) REVERT: B 607 PHE cc_start: 0.7919 (t80) cc_final: 0.7646 (t80) REVERT: B 608 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7021 (t80) REVERT: B 672 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7416 (mm-30) REVERT: B 680 GLN cc_start: 0.6756 (tm-30) cc_final: 0.6223 (tm-30) REVERT: B 721 HIS cc_start: 0.8279 (t70) cc_final: 0.8064 (t70) REVERT: C 81 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5665 (tm-30) REVERT: C 155 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7568 (mmtm) REVERT: C 158 GLN cc_start: 0.7960 (tp40) cc_final: 0.7190 (mm-40) REVERT: C 161 MET cc_start: 0.6863 (mtm) cc_final: 0.6384 (mtm) REVERT: C 180 TRP cc_start: 0.7936 (t60) cc_final: 0.7708 (t60) REVERT: C 183 MET cc_start: 0.7897 (tmm) cc_final: 0.7475 (tmm) REVERT: C 199 LEU cc_start: 0.0594 (OUTLIER) cc_final: 0.0185 (mt) REVERT: C 219 MET cc_start: 0.8256 (ttp) cc_final: 0.7981 (ttp) REVERT: C 279 MET cc_start: 0.7669 (mmm) cc_final: 0.7344 (mmm) REVERT: C 479 SER cc_start: 0.7511 (m) cc_final: 0.7150 (p) REVERT: C 519 MET cc_start: 0.7304 (mtp) cc_final: 0.7054 (mtm) REVERT: C 536 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6806 (tp30) REVERT: C 548 ASP cc_start: 0.7688 (t70) cc_final: 0.7315 (t0) REVERT: C 556 GLU cc_start: 0.7329 (tt0) cc_final: 0.7095 (tt0) REVERT: C 568 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7119 (ttm-80) REVERT: C 602 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6611 (t0) REVERT: C 695 MET cc_start: 0.7293 (mmm) cc_final: 0.7036 (tpp) REVERT: C 719 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7893 (mp) REVERT: C 722 ARG cc_start: 0.7357 (ttm170) cc_final: 0.7063 (ttt180) REVERT: D 68 ARG cc_start: 0.7693 (ptp90) cc_final: 0.7359 (ttp-110) REVERT: D 70 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6594 (mpt90) REVERT: D 74 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6942 (mm-30) REVERT: D 109 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.7842 (mp) REVERT: D 113 PHE cc_start: 0.7406 (m-80) cc_final: 0.7056 (m-80) REVERT: D 216 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7578 (t0) REVERT: D 217 MET cc_start: 0.8085 (mtp) cc_final: 0.7871 (mtp) REVERT: D 219 MET cc_start: 0.7155 (tpp) cc_final: 0.6640 (tpt) REVERT: D 220 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8129 (mmm-85) REVERT: D 223 MET cc_start: 0.5706 (OUTLIER) cc_final: 0.5004 (mpt) REVERT: D 234 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6937 (tpt-90) REVERT: D 261 GLU cc_start: 0.8856 (tp30) cc_final: 0.8296 (tp30) REVERT: D 287 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6485 (pm20) REVERT: D 300 TYR cc_start: 0.7187 (t80) cc_final: 0.6571 (t80) REVERT: D 444 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5197 (mtmt) REVERT: D 473 GLN cc_start: 0.6829 (tp40) cc_final: 0.6494 (tp40) REVERT: D 479 SER cc_start: 0.8268 (m) cc_final: 0.7998 (p) REVERT: D 541 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8107 (tt) REVERT: D 556 GLU cc_start: 0.6892 (pm20) cc_final: 0.6382 (pm20) REVERT: D 561 GLU cc_start: 0.6989 (pm20) cc_final: 0.6475 (pm20) REVERT: D 565 ASP cc_start: 0.7054 (m-30) cc_final: 0.6737 (m-30) REVERT: D 566 MET cc_start: 0.8157 (tmm) cc_final: 0.7637 (tmm) REVERT: D 606 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7079 (tp30) REVERT: D 672 GLU cc_start: 0.6941 (tp30) cc_final: 0.6531 (tp30) REVERT: D 686 TYR cc_start: 0.7768 (t80) cc_final: 0.7149 (t80) REVERT: E 69 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7071 (p) REVERT: E 155 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7641 (mtpt) REVERT: E 161 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6632 (ppp) REVERT: E 174 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: E 181 LYS cc_start: 0.8725 (mttt) cc_final: 0.8278 (mttt) REVERT: E 229 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6370 (tm-30) REVERT: E 271 MET cc_start: 0.6334 (ptt) cc_final: 0.5726 (ppp) REVERT: E 484 ASP cc_start: 0.7222 (m-30) cc_final: 0.6905 (m-30) REVERT: E 517 ASP cc_start: 0.6538 (t70) cc_final: 0.6119 (t0) REVERT: E 523 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7763 (mtp85) REVERT: E 548 ASP cc_start: 0.8199 (t0) cc_final: 0.7697 (t0) REVERT: E 612 ASP cc_start: 0.7606 (t0) cc_final: 0.7256 (t0) REVERT: E 615 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7441 (mtpt) REVERT: E 635 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6696 (mmmt) REVERT: F 469 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7498 (ttpp) REVERT: F 483 ASP cc_start: 0.6991 (m-30) cc_final: 0.6716 (m-30) REVERT: F 484 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6335 (t0) REVERT: F 489 SER cc_start: 0.8460 (t) cc_final: 0.7758 (p) REVERT: F 490 PRO cc_start: 0.8572 (Cg_endo) cc_final: 0.8348 (Cg_exo) REVERT: F 548 ASP cc_start: 0.8074 (t70) cc_final: 0.7583 (t0) REVERT: F 556 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6327 (mm-30) REVERT: F 568 ARG cc_start: 0.6787 (ttm-80) cc_final: 0.6348 (ttm-80) REVERT: F 604 LEU cc_start: 0.7899 (tp) cc_final: 0.7665 (mt) REVERT: F 606 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6707 (mt-10) REVERT: F 608 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: F 613 ASP cc_start: 0.6768 (m-30) cc_final: 0.6547 (m-30) REVERT: F 614 TYR cc_start: 0.7702 (t80) cc_final: 0.7193 (t80) REVERT: F 679 ARG cc_start: 0.7525 (mtt90) cc_final: 0.7210 (mtt90) REVERT: F 680 GLN cc_start: 0.7073 (mp10) cc_final: 0.6542 (mp10) REVERT: F 695 MET cc_start: 0.7521 (mmt) cc_final: 0.7064 (mmm) REVERT: F 696 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: F 700 ASP cc_start: 0.7004 (m-30) cc_final: 0.6729 (m-30) REVERT: F 723 LEU cc_start: 0.8608 (tp) cc_final: 0.8374 (tp) REVERT: F 724 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7806 (mmtp) outliers start: 202 outliers final: 116 residues processed: 782 average time/residue: 0.4517 time to fit residues: 516.1168 Evaluate side-chains 784 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 630 time to evaluate : 2.731 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 169 ASP 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 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 647 GLN Chi-restraints excluded: chain A residue 649 LYS 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 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 333 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 475 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 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 718 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 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 270 THR 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 515 LEU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 529 ARG 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 666 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 719 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 216 ASP 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 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 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 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 158 GLN Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 174 GLU 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 507 THR Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 577 LEU 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 529 ARG Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 577 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 672 GLU 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 98 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 177 optimal weight: 0.2980 chunk 230 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 207 optimal weight: 0.3980 chunk 262 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 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 430 HIS A 642 HIS ** A 647 GLN ** 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 609 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN C 332 GLN ** 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 616 ASN D 647 GLN ** 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 562 GLN F 463 HIS F 499 HIS F 569 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.176058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135050 restraints weight = 45469.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137552 restraints weight = 20426.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138927 restraints weight = 10338.017| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26073 Z= 0.159 Angle : 0.651 14.846 35237 Z= 0.333 Chirality : 0.040 0.182 3882 Planarity : 0.005 0.121 4545 Dihedral : 7.493 59.816 3564 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.85 % Favored : 93.54 % Rotamer: Outliers : 7.24 % Allowed : 30.37 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 3094 helix: 0.49 (0.11), residues: 2283 sheet: -6.31 (0.32), residues: 10 loop : -2.24 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 73 HIS 0.013 0.001 HIS F 499 PHE 0.039 0.002 PHE A 113 TYR 0.034 0.002 TYR D 325 ARG 0.012 0.001 ARG E 717 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 1510) hydrogen bonds : angle 4.83265 ( 4482) covalent geometry : bond 0.00346 (26073) covalent geometry : angle 0.65134 (35237) *********************** 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 845 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 642 time to evaluate : 2.696 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: 0.6863 (OUTLIER) cc_final: 0.6577 (pp20) REVERT: A 110 CYS cc_start: 0.8360 (m) cc_final: 0.8097 (m) REVERT: A 158 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7292 (mm-40) REVERT: A 194 ARG cc_start: 0.1816 (OUTLIER) cc_final: -0.0116 (tmm160) REVERT: A 218 LEU cc_start: 0.8808 (mt) cc_final: 0.8581 (mt) REVERT: A 240 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.8018 (tptt) REVERT: A 243 TYR cc_start: 0.6484 (m-10) cc_final: 0.5987 (m-80) REVERT: A 346 TYR cc_start: 0.5556 (OUTLIER) cc_final: 0.5323 (p90) REVERT: A 436 GLU cc_start: 0.7256 (tt0) cc_final: 0.6854 (tm-30) REVERT: A 470 SER cc_start: 0.8040 (m) cc_final: 0.7775 (t) REVERT: A 538 MET cc_start: 0.7379 (mmm) cc_final: 0.7081 (mmp) REVERT: A 548 ASP cc_start: 0.8074 (t0) cc_final: 0.7788 (t0) REVERT: A 570 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7819 (ttpp) REVERT: A 575 PHE cc_start: 0.8313 (m-80) cc_final: 0.7714 (m-80) REVERT: A 582 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7354 (tpp) REVERT: A 583 VAL cc_start: 0.8373 (t) cc_final: 0.8109 (p) REVERT: A 591 LYS cc_start: 0.6019 (OUTLIER) cc_final: 0.5798 (mttp) REVERT: A 608 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7453 (t80) REVERT: A 614 TYR cc_start: 0.7186 (t80) cc_final: 0.6897 (t80) REVERT: A 633 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.5265 (tm-30) REVERT: A 654 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8136 (mmt180) REVERT: A 671 LYS cc_start: 0.7885 (mmtm) cc_final: 0.7647 (mmmm) REVERT: A 691 MET cc_start: 0.7178 (tpp) cc_final: 0.6744 (ttm) REVERT: A 708 GLU cc_start: 0.7672 (tp30) cc_final: 0.7438 (tp30) REVERT: A 717 ARG cc_start: 0.7644 (tpp80) cc_final: 0.7223 (ttm-80) REVERT: A 722 ARG cc_start: 0.7545 (tpp80) cc_final: 0.7110 (tpp80) REVERT: B 69 CYS cc_start: 0.6735 (t) cc_final: 0.6424 (m) REVERT: B 73 TRP cc_start: 0.7799 (t-100) cc_final: 0.7449 (t-100) REVERT: B 113 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: B 114 GLU cc_start: 0.7985 (tt0) cc_final: 0.7693 (tm-30) REVERT: B 117 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7229 (t80) REVERT: B 119 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: B 217 MET cc_start: 0.7232 (mpp) cc_final: 0.6645 (mpp) REVERT: B 324 THR cc_start: 0.2962 (OUTLIER) cc_final: 0.2704 (t) REVERT: B 432 LEU cc_start: 0.8418 (mt) cc_final: 0.8146 (mp) REVERT: B 448 GLU cc_start: 0.7090 (mp0) cc_final: 0.6805 (mp0) REVERT: B 570 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8092 (ttpp) REVERT: B 589 GLN cc_start: 0.5166 (OUTLIER) cc_final: 0.4716 (tm-30) REVERT: B 593 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6925 (pp) REVERT: B 607 PHE cc_start: 0.7953 (t80) cc_final: 0.7637 (t80) REVERT: B 608 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7005 (t80) REVERT: B 672 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7420 (mm-30) REVERT: B 680 GLN cc_start: 0.6762 (tm-30) cc_final: 0.6234 (tm-30) REVERT: B 698 ILE cc_start: 0.7553 (mt) cc_final: 0.7320 (tt) REVERT: B 721 HIS cc_start: 0.8326 (t70) cc_final: 0.8112 (t70) REVERT: C 69 CYS cc_start: 0.8351 (m) cc_final: 0.7881 (m) REVERT: C 81 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5628 (tm-30) REVERT: C 102 LYS cc_start: 0.5758 (OUTLIER) cc_final: 0.5445 (mtpt) REVERT: C 155 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7617 (mmtm) REVERT: C 158 GLN cc_start: 0.7911 (tp40) cc_final: 0.7290 (mm-40) REVERT: C 161 MET cc_start: 0.6855 (mtm) cc_final: 0.6388 (mtm) REVERT: C 183 MET cc_start: 0.7913 (tmm) cc_final: 0.7529 (tmm) REVERT: C 199 LEU cc_start: 0.0665 (OUTLIER) cc_final: 0.0207 (mt) REVERT: C 219 MET cc_start: 0.8237 (ttp) cc_final: 0.7955 (ttp) REVERT: C 255 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6329 (t80) REVERT: C 271 MET cc_start: 0.3855 (ttt) cc_final: 0.3648 (ttt) REVERT: C 279 MET cc_start: 0.7787 (mmm) cc_final: 0.7523 (mmm) REVERT: C 479 SER cc_start: 0.7556 (m) cc_final: 0.7210 (p) REVERT: C 536 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6785 (tp30) REVERT: C 548 ASP cc_start: 0.7660 (t70) cc_final: 0.7296 (t0) REVERT: C 568 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7243 (ttm-80) REVERT: C 602 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6610 (t0) REVERT: C 667 ASP cc_start: 0.7115 (t0) cc_final: 0.6904 (t0) REVERT: C 695 MET cc_start: 0.7298 (mmm) cc_final: 0.7046 (tpp) REVERT: C 719 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7896 (mp) REVERT: C 722 ARG cc_start: 0.7373 (ttm170) cc_final: 0.7078 (ttt180) REVERT: D 68 ARG cc_start: 0.7689 (ptp90) cc_final: 0.7081 (ttp-110) REVERT: D 70 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6497 (mpt90) REVERT: D 74 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6919 (mm-30) REVERT: D 109 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7805 (mp) REVERT: D 113 PHE cc_start: 0.7467 (m-80) cc_final: 0.7128 (m-80) REVERT: D 217 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7857 (mtm) REVERT: D 219 MET cc_start: 0.7225 (tpp) cc_final: 0.6752 (tpt) REVERT: D 220 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8263 (mmm-85) REVERT: D 223 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.4940 (mpt) REVERT: D 234 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6980 (tpt-90) REVERT: D 287 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6299 (pm20) REVERT: D 300 TYR cc_start: 0.7232 (t80) cc_final: 0.6628 (t80) REVERT: D 444 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.5582 (mtmt) REVERT: D 473 GLN cc_start: 0.6839 (tp40) cc_final: 0.6507 (tp40) REVERT: D 479 SER cc_start: 0.8300 (m) cc_final: 0.7966 (p) REVERT: D 541 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8106 (tt) REVERT: D 561 GLU cc_start: 0.7041 (pm20) cc_final: 0.6502 (pm20) REVERT: D 565 ASP cc_start: 0.7053 (m-30) cc_final: 0.6712 (m-30) REVERT: D 606 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7113 (tp30) REVERT: D 672 GLU cc_start: 0.7011 (tp30) cc_final: 0.6712 (tp30) REVERT: D 686 TYR cc_start: 0.7820 (t80) cc_final: 0.7153 (t80) REVERT: D 695 MET cc_start: 0.6844 (tpt) cc_final: 0.6566 (tpt) REVERT: E 57 HIS cc_start: 0.7228 (m-70) cc_final: 0.6866 (m170) REVERT: E 69 CYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7077 (p) REVERT: E 155 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7670 (mtpt) REVERT: E 161 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6631 (ppp) REVERT: E 174 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7542 (pp20) REVERT: E 181 LYS cc_start: 0.8790 (mttt) cc_final: 0.8332 (mttt) REVERT: E 271 MET cc_start: 0.6309 (ptt) cc_final: 0.5783 (ppp) REVERT: E 484 ASP cc_start: 0.7211 (m-30) cc_final: 0.6868 (m-30) REVERT: E 517 ASP cc_start: 0.6541 (t70) cc_final: 0.6132 (t0) REVERT: E 611 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7369 (ttp-170) REVERT: E 612 ASP cc_start: 0.7621 (t0) cc_final: 0.7250 (t0) REVERT: E 615 LYS cc_start: 0.7810 (mtpt) cc_final: 0.7595 (mtpt) REVERT: E 635 LYS cc_start: 0.6956 (mmmt) cc_final: 0.6676 (mmmt) REVERT: E 699 THR cc_start: 0.7723 (m) cc_final: 0.7382 (p) REVERT: F 429 GLU cc_start: 0.6518 (tm-30) cc_final: 0.5936 (tm-30) REVERT: F 432 LEU cc_start: 0.8095 (mm) cc_final: 0.7801 (mm) REVERT: F 469 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7436 (ttpp) REVERT: F 483 ASP cc_start: 0.6911 (m-30) cc_final: 0.6616 (m-30) REVERT: F 484 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6371 (t0) REVERT: F 489 SER cc_start: 0.8510 (t) cc_final: 0.7873 (p) REVERT: F 490 PRO cc_start: 0.8552 (Cg_endo) cc_final: 0.8329 (Cg_exo) REVERT: F 548 ASP cc_start: 0.8093 (t70) cc_final: 0.7640 (t0) REVERT: F 551 TRP cc_start: 0.8377 (m-10) cc_final: 0.8146 (m-10) REVERT: F 604 LEU cc_start: 0.7909 (tp) cc_final: 0.7682 (mt) REVERT: F 608 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: F 613 ASP cc_start: 0.6777 (m-30) cc_final: 0.6534 (m-30) REVERT: F 614 TYR cc_start: 0.7711 (t80) cc_final: 0.7236 (t80) REVERT: F 679 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7256 (mtt90) REVERT: F 680 GLN cc_start: 0.7095 (mp10) cc_final: 0.6579 (mp10) REVERT: F 695 MET cc_start: 0.7512 (mmt) cc_final: 0.7072 (mmm) REVERT: F 696 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: F 700 ASP cc_start: 0.7055 (m-30) cc_final: 0.6783 (m-30) REVERT: F 723 LEU cc_start: 0.8598 (tp) cc_final: 0.8349 (tp) REVERT: F 724 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7788 (mmtp) outliers start: 203 outliers final: 132 residues processed: 775 average time/residue: 0.4572 time to fit residues: 521.7857 Evaluate side-chains 809 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 638 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 169 ASP 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 240 LYS 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 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 654 ARG 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 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 324 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 475 LEU 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 616 ASN 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 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 199 LEU Chi-restraints excluded: chain C residue 208 ILE 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 426 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 ASP 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 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 C residue 719 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 160 LYS Chi-restraints excluded: chain D residue 175 VAL 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 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP 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 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 161 MET Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 174 GLU 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 454 LEU Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 487 ASP 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 577 LEU 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 462 ASP Chi-restraints excluded: chain F residue 469 LYS 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 579 THR Chi-restraints excluded: chain F residue 581 MET 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 672 GLU 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 263 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 285 optimal weight: 0.2980 chunk 147 optimal weight: 0.8980 chunk 311 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** 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 332 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** 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 590 GLN F 463 HIS ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.175690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134234 restraints weight = 45564.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136962 restraints weight = 20477.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138147 restraints weight = 10313.285| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26073 Z= 0.173 Angle : 0.655 10.757 35237 Z= 0.336 Chirality : 0.041 0.184 3882 Planarity : 0.005 0.054 4545 Dihedral : 7.122 59.535 3554 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.91 % Favored : 93.54 % Rotamer: Outliers : 7.49 % Allowed : 29.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 3094 helix: 0.61 (0.11), residues: 2278 sheet: -6.21 (0.36), residues: 10 loop : -2.21 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 89 HIS 0.015 0.001 HIS E 430 PHE 0.041 0.002 PHE A 113 TYR 0.030 0.002 TYR F 550 ARG 0.010 0.001 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 1510) hydrogen bonds : angle 4.73514 ( 4482) covalent geometry : bond 0.00379 (26073) covalent geometry : angle 0.65523 (35237) *********************** 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 859 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 649 time to evaluate : 4.065 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 64 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6620 (pp20) REVERT: A 110 CYS cc_start: 0.8412 (m) cc_final: 0.8124 (m) REVERT: A 114 GLU cc_start: 0.8050 (tp30) cc_final: 0.7583 (tp30) REVERT: A 158 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7336 (mm-40) REVERT: A 218 LEU cc_start: 0.8775 (mt) cc_final: 0.8523 (mt) REVERT: A 240 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8022 (tptt) REVERT: A 243 TYR cc_start: 0.6453 (m-10) cc_final: 0.6144 (m-80) REVERT: A 346 TYR cc_start: 0.5615 (OUTLIER) cc_final: 0.5321 (p90) REVERT: A 360 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7305 (tp40) REVERT: A 436 GLU cc_start: 0.7262 (tt0) cc_final: 0.6875 (tm-30) REVERT: A 470 SER cc_start: 0.8050 (m) cc_final: 0.7781 (t) REVERT: A 538 MET cc_start: 0.7397 (mmm) cc_final: 0.7104 (mmp) REVERT: A 548 ASP cc_start: 0.8074 (t0) cc_final: 0.7768 (t0) REVERT: A 570 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7806 (ttpp) REVERT: A 575 PHE cc_start: 0.8312 (m-80) cc_final: 0.7719 (m-80) REVERT: A 582 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7359 (tpp) REVERT: A 583 VAL cc_start: 0.8423 (t) cc_final: 0.8146 (p) REVERT: A 591 LYS cc_start: 0.6045 (OUTLIER) cc_final: 0.5820 (mttp) REVERT: A 608 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7431 (t80) REVERT: A 614 TYR cc_start: 0.7225 (t80) cc_final: 0.6930 (t80) REVERT: A 633 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5286 (tm-30) REVERT: A 671 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7656 (mmmm) REVERT: A 690 LYS cc_start: 0.7803 (tptp) cc_final: 0.7597 (tptm) REVERT: A 691 MET cc_start: 0.7197 (tpp) cc_final: 0.6772 (ttm) REVERT: A 717 ARG cc_start: 0.7637 (tpp80) cc_final: 0.7194 (ttm-80) REVERT: A 722 ARG cc_start: 0.7574 (tpp80) cc_final: 0.7124 (tpp80) REVERT: B 54 ARG cc_start: 0.4825 (OUTLIER) cc_final: 0.4563 (mtp180) REVERT: B 69 CYS cc_start: 0.6677 (t) cc_final: 0.6324 (m) REVERT: B 73 TRP cc_start: 0.7765 (t-100) cc_final: 0.7457 (t-100) REVERT: B 113 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7711 (m-10) REVERT: B 114 GLU cc_start: 0.8023 (tt0) cc_final: 0.7798 (tm-30) REVERT: B 324 THR cc_start: 0.2838 (OUTLIER) cc_final: 0.2580 (t) REVERT: B 448 GLU cc_start: 0.7078 (mp0) cc_final: 0.6818 (mp0) REVERT: B 539 ARG cc_start: 0.6981 (ttt-90) cc_final: 0.6690 (ttt90) REVERT: B 589 GLN cc_start: 0.5142 (OUTLIER) cc_final: 0.4696 (tm-30) REVERT: B 593 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6970 (pp) REVERT: B 607 PHE cc_start: 0.7955 (t80) cc_final: 0.7602 (t80) REVERT: B 608 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6992 (t80) REVERT: B 672 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 680 GLN cc_start: 0.6771 (tm-30) cc_final: 0.6223 (tm-30) REVERT: B 698 ILE cc_start: 0.7519 (mt) cc_final: 0.7274 (tt) REVERT: C 69 CYS cc_start: 0.8388 (m) cc_final: 0.7913 (m) REVERT: C 81 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5521 (tm-30) REVERT: C 102 LYS cc_start: 0.5863 (OUTLIER) cc_final: 0.5571 (mtpt) REVERT: C 155 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7597 (mmtm) REVERT: C 158 GLN cc_start: 0.7857 (tp40) cc_final: 0.7312 (tp40) REVERT: C 161 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6618 (mtm) REVERT: C 183 MET cc_start: 0.7915 (tmm) cc_final: 0.7524 (tmm) REVERT: C 199 LEU cc_start: 0.0563 (OUTLIER) cc_final: 0.0124 (mt) REVERT: C 217 MET cc_start: 0.7770 (ptt) cc_final: 0.7487 (ppp) REVERT: C 219 MET cc_start: 0.8141 (ttp) cc_final: 0.7864 (ttp) REVERT: C 223 MET cc_start: 0.7148 (pmt) cc_final: 0.6651 (pmt) REVERT: C 255 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6306 (t80) REVERT: C 271 MET cc_start: 0.3718 (ttt) cc_final: 0.2325 (ptm) REVERT: C 447 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7107 (mtm-85) REVERT: C 479 SER cc_start: 0.7636 (m) cc_final: 0.7270 (p) REVERT: C 519 MET cc_start: 0.7396 (mtp) cc_final: 0.7118 (mtm) REVERT: C 536 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6764 (tp30) REVERT: C 556 GLU cc_start: 0.7448 (tt0) cc_final: 0.7183 (tt0) REVERT: C 568 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7227 (ttm-80) REVERT: C 602 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6618 (t0) REVERT: C 695 MET cc_start: 0.7306 (mmm) cc_final: 0.7068 (tpp) REVERT: C 722 ARG cc_start: 0.7405 (ttm170) cc_final: 0.6981 (ttt180) REVERT: D 68 ARG cc_start: 0.7670 (ptp90) cc_final: 0.7132 (ttp-110) REVERT: D 70 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6497 (mpt90) REVERT: D 74 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7072 (mm-30) REVERT: D 109 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7886 (mp) REVERT: D 113 PHE cc_start: 0.7519 (m-80) cc_final: 0.7128 (m-80) REVERT: D 216 ASP cc_start: 0.7823 (t70) cc_final: 0.7609 (t0) REVERT: D 219 MET cc_start: 0.7099 (tpp) cc_final: 0.6653 (tpt) REVERT: D 220 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8298 (mtp85) REVERT: D 223 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5020 (mpt) REVERT: D 234 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7052 (tpt-90) REVERT: D 261 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8279 (mm-30) REVERT: D 287 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6253 (pm20) REVERT: D 300 TYR cc_start: 0.7234 (t80) cc_final: 0.6610 (t80) REVERT: D 444 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.5702 (mtmt) REVERT: D 473 GLN cc_start: 0.6858 (tp40) cc_final: 0.6518 (tp40) REVERT: D 479 SER cc_start: 0.8245 (m) cc_final: 0.7980 (p) REVERT: D 541 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8169 (tt) REVERT: D 554 ASN cc_start: 0.8333 (t0) cc_final: 0.8105 (m110) REVERT: D 561 GLU cc_start: 0.7094 (pm20) cc_final: 0.6572 (pm20) REVERT: D 564 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8145 (mm) REVERT: D 565 ASP cc_start: 0.7051 (m-30) cc_final: 0.6704 (m-30) REVERT: D 606 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6910 (tp30) REVERT: D 633 GLU cc_start: 0.4421 (OUTLIER) cc_final: 0.4145 (tt0) REVERT: D 686 TYR cc_start: 0.7874 (t80) cc_final: 0.7202 (t80) REVERT: E 57 HIS cc_start: 0.7208 (m-70) cc_final: 0.6855 (m170) REVERT: E 69 CYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7086 (p) REVERT: E 155 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7697 (mtpt) REVERT: E 161 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6579 (ppp) REVERT: E 181 LYS cc_start: 0.8799 (mttt) cc_final: 0.8321 (mttt) REVERT: E 220 ARG cc_start: 0.7886 (ttt180) cc_final: 0.7669 (ttt180) REVERT: E 271 MET cc_start: 0.6338 (ptt) cc_final: 0.5811 (ppp) REVERT: E 484 ASP cc_start: 0.7212 (m-30) cc_final: 0.6873 (m-30) REVERT: E 517 ASP cc_start: 0.6573 (t70) cc_final: 0.6139 (t0) REVERT: E 523 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7499 (mtm180) REVERT: E 584 GLN cc_start: 0.7333 (tt0) cc_final: 0.7082 (tt0) REVERT: E 612 ASP cc_start: 0.7669 (t0) cc_final: 0.7323 (t0) REVERT: E 615 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7409 (mtpt) REVERT: E 635 LYS cc_start: 0.6957 (mmmt) cc_final: 0.6711 (mmmt) REVERT: E 699 THR cc_start: 0.7715 (m) cc_final: 0.7364 (p) REVERT: F 429 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6097 (tm-30) REVERT: F 432 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7827 (mm) REVERT: F 483 ASP cc_start: 0.6891 (m-30) cc_final: 0.6606 (m-30) REVERT: F 484 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.6383 (t0) REVERT: F 489 SER cc_start: 0.8489 (t) cc_final: 0.7801 (p) REVERT: F 490 PRO cc_start: 0.8537 (Cg_endo) cc_final: 0.8308 (Cg_exo) REVERT: F 548 ASP cc_start: 0.8102 (t70) cc_final: 0.7694 (t0) REVERT: F 551 TRP cc_start: 0.8393 (m-10) cc_final: 0.8125 (m-10) REVERT: F 604 LEU cc_start: 0.7928 (tp) cc_final: 0.7693 (mt) REVERT: F 608 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: F 609 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7313 (tp-100) REVERT: F 613 ASP cc_start: 0.6766 (m-30) cc_final: 0.6466 (m-30) REVERT: F 614 TYR cc_start: 0.7703 (t80) cc_final: 0.7182 (t80) REVERT: F 679 ARG cc_start: 0.7593 (mtt90) cc_final: 0.7300 (mtt90) REVERT: F 680 GLN cc_start: 0.7123 (mp10) cc_final: 0.6592 (mp10) REVERT: F 695 MET cc_start: 0.7524 (mmt) cc_final: 0.7074 (mmm) REVERT: F 696 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: F 700 ASP cc_start: 0.7054 (m-30) cc_final: 0.6789 (m-30) REVERT: F 723 LEU cc_start: 0.8591 (tp) cc_final: 0.8353 (tp) REVERT: F 724 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7976 (mmtp) outliers start: 210 outliers final: 135 residues processed: 784 average time/residue: 0.4699 time to fit residues: 540.8920 Evaluate side-chains 807 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 634 time to evaluate : 4.075 ------------------------------------------------------------------------------- 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 169 ASP Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 240 LYS 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 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 649 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 699 THR 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 324 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU 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 616 ASN 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 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 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 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 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 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 C residue 719 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 160 LYS 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 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP 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 633 GLU 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 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 161 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 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 532 ASP Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 590 GLN 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 668 VAL Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 432 LEU 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 529 ARG Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 579 THR 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 672 GLU 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 56 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 303 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** 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 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 329 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 E 156 GLN ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 HIS F 463 HIS ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 ASN F 569 GLN F 647 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.175861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134402 restraints weight = 45464.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137645 restraints weight = 20159.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138958 restraints weight = 9931.947| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26073 Z= 0.182 Angle : 0.669 10.230 35237 Z= 0.342 Chirality : 0.042 0.182 3882 Planarity : 0.005 0.054 4545 Dihedral : 6.872 59.984 3543 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.69 % Favored : 93.76 % Rotamer: Outliers : 7.38 % Allowed : 29.84 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3094 helix: 0.62 (0.11), residues: 2286 sheet: -6.05 (0.42), residues: 10 loop : -2.21 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 89 HIS 0.014 0.001 HIS F 499 PHE 0.044 0.002 PHE A 113 TYR 0.031 0.002 TYR B 550 ARG 0.011 0.001 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 1510) hydrogen bonds : angle 4.67333 ( 4482) covalent geometry : bond 0.00401 (26073) covalent geometry : angle 0.66881 (35237) *********************** 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 852 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 645 time to evaluate : 9.698 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 64 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6621 (pp20) REVERT: A 110 CYS cc_start: 0.8397 (m) cc_final: 0.8064 (m) REVERT: A 114 GLU cc_start: 0.7961 (tp30) cc_final: 0.7467 (tp30) REVERT: A 158 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7405 (mm-40) REVERT: A 194 ARG cc_start: 0.1699 (OUTLIER) cc_final: -0.0280 (tmm160) REVERT: A 218 LEU cc_start: 0.8758 (mt) cc_final: 0.8509 (mt) REVERT: A 240 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8023 (tptt) REVERT: A 243 TYR cc_start: 0.6417 (m-10) cc_final: 0.6096 (m-80) REVERT: A 279 MET cc_start: 0.5163 (OUTLIER) cc_final: 0.4727 (mmm) REVERT: A 346 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.5446 (p90) REVERT: A 360 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7173 (tp40) REVERT: A 436 GLU cc_start: 0.7265 (tt0) cc_final: 0.6849 (tm-30) REVERT: A 470 SER cc_start: 0.8036 (m) cc_final: 0.7758 (t) REVERT: A 548 ASP cc_start: 0.8074 (t0) cc_final: 0.7789 (t0) REVERT: A 570 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7785 (ttpp) REVERT: A 575 PHE cc_start: 0.8309 (m-80) cc_final: 0.7716 (m-80) REVERT: A 582 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7379 (tpp) REVERT: A 583 VAL cc_start: 0.8411 (t) cc_final: 0.8145 (p) REVERT: A 591 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5793 (mttp) REVERT: A 608 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7451 (t80) REVERT: A 614 TYR cc_start: 0.7248 (t80) cc_final: 0.6924 (t80) REVERT: A 633 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.5289 (tm-30) REVERT: A 654 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8143 (mmt180) REVERT: A 671 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7635 (mmmm) REVERT: A 691 MET cc_start: 0.7186 (tpp) cc_final: 0.6793 (ttm) REVERT: A 717 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7382 (ttm-80) REVERT: A 722 ARG cc_start: 0.7598 (tpp80) cc_final: 0.7117 (tpp80) REVERT: B 69 CYS cc_start: 0.6708 (t) cc_final: 0.6326 (m) REVERT: B 73 TRP cc_start: 0.7780 (t-100) cc_final: 0.7458 (t-100) REVERT: B 113 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7709 (m-10) REVERT: B 324 THR cc_start: 0.2673 (OUTLIER) cc_final: 0.2431 (t) REVERT: B 589 GLN cc_start: 0.5037 (OUTLIER) cc_final: 0.4601 (tm-30) REVERT: B 593 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6972 (pp) REVERT: B 672 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7421 (mm-30) REVERT: B 680 GLN cc_start: 0.6760 (tm-30) cc_final: 0.6212 (tm-30) REVERT: B 685 GLU cc_start: 0.6993 (mp0) cc_final: 0.6602 (mp0) REVERT: B 698 ILE cc_start: 0.7533 (mt) cc_final: 0.7306 (tt) REVERT: C 69 CYS cc_start: 0.8393 (m) cc_final: 0.7897 (m) REVERT: C 81 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5526 (tm-30) REVERT: C 102 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5622 (mtpt) REVERT: C 155 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7583 (mmtm) REVERT: C 158 GLN cc_start: 0.7841 (tp40) cc_final: 0.7338 (mm-40) REVERT: C 161 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6520 (mtm) REVERT: C 183 MET cc_start: 0.7939 (tmm) cc_final: 0.7553 (tmm) REVERT: C 199 LEU cc_start: 0.0511 (OUTLIER) cc_final: 0.0091 (mt) REVERT: C 219 MET cc_start: 0.8150 (ttp) cc_final: 0.7858 (ttp) REVERT: C 223 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6684 (pmt) REVERT: C 255 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.6278 (t80) REVERT: C 271 MET cc_start: 0.3699 (ttt) cc_final: 0.2319 (ptm) REVERT: C 479 SER cc_start: 0.7642 (m) cc_final: 0.7345 (p) REVERT: C 519 MET cc_start: 0.7403 (mtp) cc_final: 0.7127 (mtm) REVERT: C 536 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6746 (tp30) REVERT: C 556 GLU cc_start: 0.7432 (tt0) cc_final: 0.7165 (tt0) REVERT: C 568 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7221 (ttm-80) REVERT: C 602 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6627 (t0) REVERT: C 695 MET cc_start: 0.7318 (mmm) cc_final: 0.7108 (tpp) REVERT: C 722 ARG cc_start: 0.7393 (ttm170) cc_final: 0.6980 (ttt180) REVERT: D 68 ARG cc_start: 0.7640 (ptp90) cc_final: 0.7014 (ttp80) REVERT: D 70 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6423 (mpt90) REVERT: D 74 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7065 (mm-30) REVERT: D 109 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7855 (mp) REVERT: D 113 PHE cc_start: 0.7469 (m-80) cc_final: 0.7089 (m-80) REVERT: D 217 MET cc_start: 0.8202 (mtp) cc_final: 0.7955 (mtp) REVERT: D 219 MET cc_start: 0.7110 (tpp) cc_final: 0.6628 (tpt) REVERT: D 223 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.4970 (mpt) REVERT: D 234 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7074 (tpt-90) REVERT: D 261 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8334 (mm-30) REVERT: D 287 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6195 (pm20) REVERT: D 295 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8266 (tp30) REVERT: D 300 TYR cc_start: 0.7189 (t80) cc_final: 0.6584 (t80) REVERT: D 444 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.5681 (mtmt) REVERT: D 448 GLU cc_start: 0.6540 (mp0) cc_final: 0.6268 (mp0) REVERT: D 473 GLN cc_start: 0.6835 (tp40) cc_final: 0.6516 (tp40) REVERT: D 479 SER cc_start: 0.8260 (m) cc_final: 0.7974 (p) REVERT: D 487 ASP cc_start: 0.6805 (t0) cc_final: 0.6535 (t0) REVERT: D 541 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8162 (tt) REVERT: D 554 ASN cc_start: 0.8339 (t0) cc_final: 0.8125 (m110) REVERT: D 561 GLU cc_start: 0.7089 (pm20) cc_final: 0.6818 (pm20) REVERT: D 566 MET cc_start: 0.8094 (tmm) cc_final: 0.7709 (tmm) REVERT: D 606 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6904 (tp30) REVERT: D 633 GLU cc_start: 0.4381 (OUTLIER) cc_final: 0.4153 (tt0) REVERT: D 650 ASN cc_start: 0.7742 (t0) cc_final: 0.7324 (t0) REVERT: D 672 GLU cc_start: 0.7096 (tp30) cc_final: 0.6706 (tp30) REVERT: D 686 TYR cc_start: 0.7875 (t80) cc_final: 0.7230 (t80) REVERT: E 69 CYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7121 (p) REVERT: E 155 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7656 (mtpt) REVERT: E 161 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6484 (ppp) REVERT: E 174 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7557 (pp20) REVERT: E 181 LYS cc_start: 0.8809 (mttt) cc_final: 0.8329 (mttt) REVERT: E 271 MET cc_start: 0.6153 (ptt) cc_final: 0.5659 (ppp) REVERT: E 484 ASP cc_start: 0.7232 (m-30) cc_final: 0.6865 (m-30) REVERT: E 506 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: E 517 ASP cc_start: 0.6572 (t70) cc_final: 0.6168 (t0) REVERT: E 523 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7431 (mtm180) REVERT: E 584 GLN cc_start: 0.7392 (tt0) cc_final: 0.7126 (tt0) REVERT: E 611 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7269 (ttp80) REVERT: E 612 ASP cc_start: 0.7670 (t0) cc_final: 0.7312 (t0) REVERT: E 615 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7553 (mtpt) REVERT: E 635 LYS cc_start: 0.7298 (mmmt) cc_final: 0.6941 (mmmt) REVERT: E 699 THR cc_start: 0.7695 (m) cc_final: 0.7376 (p) REVERT: F 432 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7821 (mm) REVERT: F 469 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7487 (ttpp) REVERT: F 483 ASP cc_start: 0.6896 (m-30) cc_final: 0.6622 (m-30) REVERT: F 489 SER cc_start: 0.8455 (t) cc_final: 0.7843 (p) REVERT: F 548 ASP cc_start: 0.8094 (t70) cc_final: 0.7700 (t0) REVERT: F 551 TRP cc_start: 0.8355 (m-10) cc_final: 0.8117 (m-10) REVERT: F 608 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: F 609 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7265 (tp-100) REVERT: F 613 ASP cc_start: 0.6767 (m-30) cc_final: 0.6457 (m-30) REVERT: F 614 TYR cc_start: 0.7717 (t80) cc_final: 0.7245 (t80) REVERT: F 679 ARG cc_start: 0.7587 (mtt90) cc_final: 0.7282 (mtt90) REVERT: F 680 GLN cc_start: 0.7136 (mp10) cc_final: 0.6601 (mp10) REVERT: F 695 MET cc_start: 0.7548 (mmt) cc_final: 0.7113 (mmm) REVERT: F 696 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: F 700 ASP cc_start: 0.7060 (m-30) cc_final: 0.6798 (m-30) REVERT: F 723 LEU cc_start: 0.8596 (tp) cc_final: 0.8372 (tp) REVERT: F 724 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7984 (mmtp) outliers start: 207 outliers final: 139 residues processed: 779 average time/residue: 0.7352 time to fit residues: 855.0713 Evaluate side-chains 809 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 629 time to evaluate : 3.262 ------------------------------------------------------------------------------- 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 240 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 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 637 SER Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 699 THR 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 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 324 THR 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 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 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 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 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 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 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 602 ASP 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 C residue 719 LEU Chi-restraints excluded: chain C residue 720 ILE 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 160 LYS 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 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP 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 633 GLU 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 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 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 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 454 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 593 LEU 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 668 VAL Chi-restraints excluded: chain E residue 721 HIS Chi-restraints excluded: chain F residue 432 LEU 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 469 LYS Chi-restraints excluded: chain F residue 516 ILE Chi-restraints excluded: chain F residue 529 ARG Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 571 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 22 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 chunk 226 optimal weight: 0.6980 chunk 225 optimal weight: 0.0770 chunk 203 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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** ** 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 584 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 329 GLN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 ASN D 512 ASN D 616 ASN ** 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 590 GLN F 463 HIS F 499 HIS F 569 GLN F 647 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.177082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135740 restraints weight = 45482.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.139279 restraints weight = 19457.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140850 restraints weight = 9683.481| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4493 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= 0.144 Angle : 0.657 10.392 35237 Z= 0.334 Chirality : 0.040 0.196 3882 Planarity : 0.005 0.053 4545 Dihedral : 6.709 59.742 3543 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.40 % Favored : 94.09 % Rotamer: Outliers : 6.49 % Allowed : 30.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 3094 helix: 0.82 (0.11), residues: 2278 sheet: -6.01 (0.45), residues: 10 loop : -2.13 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 89 HIS 0.013 0.001 HIS F 499 PHE 0.042 0.002 PHE A 113 TYR 0.028 0.002 TYR B 550 ARG 0.010 0.001 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 1510) hydrogen bonds : angle 4.52779 ( 4482) covalent geometry : bond 0.00319 (26073) covalent geometry : angle 0.65665 (35237) *********************** 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 833 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 651 time to evaluate : 2.866 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: 0.6924 (OUTLIER) cc_final: 0.6631 (pp20) REVERT: A 110 CYS cc_start: 0.8395 (m) cc_final: 0.8105 (m) REVERT: A 114 GLU cc_start: 0.7924 (tp30) cc_final: 0.7432 (tp30) REVERT: A 158 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7421 (mm-40) REVERT: A 194 ARG cc_start: 0.1615 (OUTLIER) cc_final: -0.0301 (mmm160) REVERT: A 218 LEU cc_start: 0.8714 (mt) cc_final: 0.8469 (mt) REVERT: A 243 TYR cc_start: 0.6457 (m-10) cc_final: 0.6112 (m-80) REVERT: A 346 TYR cc_start: 0.5453 (OUTLIER) cc_final: 0.5186 (p90) REVERT: A 360 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7008 (tp40) REVERT: A 429 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 436 GLU cc_start: 0.7231 (tt0) cc_final: 0.6869 (tm-30) REVERT: A 538 MET cc_start: 0.7352 (mmm) cc_final: 0.7107 (mmp) REVERT: A 548 ASP cc_start: 0.8087 (t0) cc_final: 0.7771 (t0) REVERT: A 570 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7750 (ttpp) REVERT: A 575 PHE cc_start: 0.8270 (m-80) cc_final: 0.7671 (m-80) REVERT: A 582 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7344 (tpp) REVERT: A 583 VAL cc_start: 0.8375 (t) cc_final: 0.8095 (p) REVERT: A 608 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7456 (t80) REVERT: A 614 TYR cc_start: 0.7213 (t80) cc_final: 0.6933 (t80) REVERT: A 633 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5285 (tm-30) REVERT: A 638 TYR cc_start: 0.7802 (t80) cc_final: 0.7026 (t80) REVERT: A 654 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8108 (mmt180) REVERT: A 671 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7630 (mmmm) REVERT: A 686 TYR cc_start: 0.7891 (t80) cc_final: 0.7527 (t80) REVERT: A 691 MET cc_start: 0.7143 (tpp) cc_final: 0.6697 (ttm) REVERT: A 717 ARG cc_start: 0.7579 (tpp80) cc_final: 0.7344 (ttm-80) REVERT: A 722 ARG cc_start: 0.7531 (tpp80) cc_final: 0.7105 (tpp80) REVERT: B 73 TRP cc_start: 0.7763 (t-100) cc_final: 0.7549 (t-100) REVERT: B 113 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7734 (m-10) REVERT: B 217 MET cc_start: 0.7361 (mpp) cc_final: 0.6820 (mpp) REVERT: B 324 THR cc_start: 0.2831 (OUTLIER) cc_final: 0.2581 (t) REVERT: B 505 GLU cc_start: 0.7032 (mp0) cc_final: 0.6763 (mp0) REVERT: B 539 ARG cc_start: 0.6954 (ttt-90) cc_final: 0.6655 (ttt90) REVERT: B 589 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.4524 (tm-30) REVERT: B 593 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6885 (pp) REVERT: B 607 PHE cc_start: 0.7861 (t80) cc_final: 0.7434 (t80) REVERT: B 672 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 680 GLN cc_start: 0.6739 (tm-30) cc_final: 0.6196 (tm-30) REVERT: C 69 CYS cc_start: 0.8388 (m) cc_final: 0.7903 (m) REVERT: C 81 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.5502 (tm-30) REVERT: C 102 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5817 (mtpt) REVERT: C 155 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7609 (mmtm) REVERT: C 158 GLN cc_start: 0.7839 (tp40) cc_final: 0.7331 (tp40) REVERT: C 183 MET cc_start: 0.7935 (tmm) cc_final: 0.7553 (tmm) REVERT: C 217 MET cc_start: 0.7772 (ptt) cc_final: 0.7484 (ppp) REVERT: C 219 MET cc_start: 0.8022 (ttp) cc_final: 0.7800 (ttp) REVERT: C 223 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6622 (pmt) REVERT: C 255 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6542 (t80) REVERT: C 271 MET cc_start: 0.3903 (ttt) cc_final: 0.2757 (ptm) REVERT: C 479 SER cc_start: 0.7664 (m) cc_final: 0.7329 (p) REVERT: C 536 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6738 (tp30) REVERT: C 556 GLU cc_start: 0.7395 (tt0) cc_final: 0.7109 (tt0) REVERT: C 596 GLN cc_start: 0.7142 (mt0) cc_final: 0.6832 (mt0) REVERT: C 602 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6566 (t0) REVERT: C 719 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7897 (mp) REVERT: C 722 ARG cc_start: 0.7365 (ttm170) cc_final: 0.7061 (ttt180) REVERT: D 68 ARG cc_start: 0.7586 (ptp90) cc_final: 0.7077 (ttp80) REVERT: D 70 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6434 (mpt90) REVERT: D 74 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7053 (mm-30) REVERT: D 109 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7971 (pt) REVERT: D 113 PHE cc_start: 0.7479 (m-80) cc_final: 0.7231 (m-80) REVERT: D 217 MET cc_start: 0.8195 (mtp) cc_final: 0.7980 (mtp) REVERT: D 219 MET cc_start: 0.7121 (tpp) cc_final: 0.6623 (tpt) REVERT: D 223 MET cc_start: 0.5881 (OUTLIER) cc_final: 0.4908 (mpt) REVERT: D 234 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7050 (tpt-90) REVERT: D 261 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8342 (mm-30) REVERT: D 287 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6064 (pm20) REVERT: D 300 TYR cc_start: 0.7183 (t80) cc_final: 0.6604 (t80) REVERT: D 444 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.5429 (mtmt) REVERT: D 473 GLN cc_start: 0.6765 (tp40) cc_final: 0.6430 (tp40) REVERT: D 479 SER cc_start: 0.8232 (m) cc_final: 0.7913 (p) REVERT: D 541 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8049 (tt) REVERT: D 554 ASN cc_start: 0.8326 (t0) cc_final: 0.8097 (m110) REVERT: D 561 GLU cc_start: 0.7095 (pm20) cc_final: 0.6551 (pm20) REVERT: D 565 ASP cc_start: 0.7057 (m-30) cc_final: 0.6733 (m-30) REVERT: D 566 MET cc_start: 0.8098 (tmm) cc_final: 0.7738 (tmm) REVERT: D 606 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6915 (tp30) REVERT: D 650 ASN cc_start: 0.7698 (t0) cc_final: 0.7283 (t0) REVERT: D 672 GLU cc_start: 0.7061 (tp30) cc_final: 0.6797 (tp30) REVERT: D 686 TYR cc_start: 0.7810 (t80) cc_final: 0.7191 (t80) REVERT: E 69 CYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7098 (p) REVERT: E 155 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7687 (mtpt) REVERT: E 161 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6479 (ppp) REVERT: E 174 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: E 181 LYS cc_start: 0.8763 (mttt) cc_final: 0.8285 (mttt) REVERT: E 220 ARG cc_start: 0.7809 (ttt180) cc_final: 0.7591 (ttt180) REVERT: E 271 MET cc_start: 0.6134 (ptt) cc_final: 0.5672 (ppp) REVERT: E 484 ASP cc_start: 0.7204 (m-30) cc_final: 0.6846 (m-30) REVERT: E 506 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: E 517 ASP cc_start: 0.6556 (t70) cc_final: 0.6143 (t0) REVERT: E 522 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8182 (m) REVERT: E 584 GLN cc_start: 0.7300 (tt0) cc_final: 0.7057 (mt0) REVERT: E 611 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7311 (ttp80) REVERT: E 612 ASP cc_start: 0.7674 (t0) cc_final: 0.7364 (t0) REVERT: E 615 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7538 (mtpt) REVERT: E 635 LYS cc_start: 0.7269 (mmmt) cc_final: 0.6929 (mmmt) REVERT: E 699 THR cc_start: 0.7566 (m) cc_final: 0.7268 (p) REVERT: E 717 ARG cc_start: 0.7283 (ptt-90) cc_final: 0.7031 (ptt-90) REVERT: F 432 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7841 (mm) REVERT: F 469 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7417 (ttpp) REVERT: F 483 ASP cc_start: 0.6855 (m-30) cc_final: 0.6544 (m-30) REVERT: F 489 SER cc_start: 0.8446 (t) cc_final: 0.8075 (p) REVERT: F 548 ASP cc_start: 0.8086 (t70) cc_final: 0.7620 (t0) REVERT: F 551 TRP cc_start: 0.8258 (m-10) cc_final: 0.8054 (m-10) REVERT: F 608 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: F 609 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7266 (tp-100) REVERT: F 613 ASP cc_start: 0.6771 (m-30) cc_final: 0.6426 (m-30) REVERT: F 614 TYR cc_start: 0.7724 (t80) cc_final: 0.7297 (t80) REVERT: F 679 ARG cc_start: 0.7552 (mtt90) cc_final: 0.7253 (mtt90) REVERT: F 680 GLN cc_start: 0.7114 (mp10) cc_final: 0.6569 (mp10) REVERT: F 695 MET cc_start: 0.7572 (mmt) cc_final: 0.7121 (mmm) REVERT: F 696 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: F 700 ASP cc_start: 0.7092 (m-30) cc_final: 0.6813 (m-30) REVERT: F 723 LEU cc_start: 0.8577 (tp) cc_final: 0.8347 (tp) REVERT: F 724 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7984 (mmtp) outliers start: 182 outliers final: 123 residues processed: 765 average time/residue: 0.4503 time to fit residues: 504.8886 Evaluate side-chains 781 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 622 time to evaluate : 2.965 ------------------------------------------------------------------------------- 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 169 ASP 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 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 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 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 102 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 432 LEU 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 615 LYS 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 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 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 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 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 602 ASP 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 719 LEU 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 160 LYS 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 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP 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 677 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 161 MET Chi-restraints excluded: chain E residue 174 GLU 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 454 LEU Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 590 GLN 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 432 LEU 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 469 LYS 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 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 212 optimal weight: 0.3980 chunk 291 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 HIS ** 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 294 GLN ** 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 488 HIS D 616 ASN ** 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 590 GLN F 463 HIS F 499 HIS F 554 ASN F 569 GLN F 647 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.176658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135741 restraints weight = 45425.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138337 restraints weight = 20132.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.139555 restraints weight = 10364.171| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26073 Z= 0.174 Angle : 0.689 11.690 35237 Z= 0.350 Chirality : 0.041 0.187 3882 Planarity : 0.005 0.052 4545 Dihedral : 6.561 59.523 3536 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.75 % Favored : 93.76 % Rotamer: Outliers : 6.10 % Allowed : 31.48 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 3094 helix: 0.84 (0.11), residues: 2282 sheet: -5.99 (0.45), residues: 10 loop : -2.09 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 89 HIS 0.013 0.001 HIS F 499 PHE 0.044 0.002 PHE A 113 TYR 0.033 0.002 TYR D 325 ARG 0.010 0.001 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 1510) hydrogen bonds : angle 4.54655 ( 4482) covalent geometry : bond 0.00387 (26073) covalent geometry : angle 0.68876 (35237) ********************** 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 817 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 646 time to evaluate : 2.963 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: 0.6885 (OUTLIER) cc_final: 0.6607 (pp20) REVERT: A 110 CYS cc_start: 0.8398 (m) cc_final: 0.8141 (m) REVERT: A 114 GLU cc_start: 0.7927 (tp30) cc_final: 0.7425 (tp30) REVERT: A 158 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7408 (mm-40) REVERT: A 194 ARG cc_start: 0.1673 (OUTLIER) cc_final: -0.0324 (mmm160) REVERT: A 218 LEU cc_start: 0.8680 (mt) cc_final: 0.8445 (mt) REVERT: A 233 LYS cc_start: 0.8431 (mttp) cc_final: 0.8172 (mttp) REVERT: A 243 TYR cc_start: 0.6470 (m-10) cc_final: 0.6121 (m-80) REVERT: A 279 MET cc_start: 0.5543 (mmt) cc_final: 0.5155 (mmm) REVERT: A 346 TYR cc_start: 0.5610 (OUTLIER) cc_final: 0.5310 (p90) REVERT: A 360 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7121 (tp40) REVERT: A 429 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7206 (tm-30) REVERT: A 436 GLU cc_start: 0.7257 (tt0) cc_final: 0.6891 (tm-30) REVERT: A 470 SER cc_start: 0.8015 (m) cc_final: 0.7734 (t) REVERT: A 548 ASP cc_start: 0.8068 (t0) cc_final: 0.7777 (t0) REVERT: A 570 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7772 (ttpp) REVERT: A 575 PHE cc_start: 0.8281 (m-80) cc_final: 0.7697 (m-80) REVERT: A 582 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7345 (tpp) REVERT: A 583 VAL cc_start: 0.8431 (t) cc_final: 0.8119 (p) REVERT: A 608 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7455 (t80) REVERT: A 614 TYR cc_start: 0.7250 (t80) cc_final: 0.6931 (t80) REVERT: A 633 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5294 (tm-30) REVERT: A 638 TYR cc_start: 0.7859 (t80) cc_final: 0.7099 (t80) REVERT: A 654 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8149 (mmt180) REVERT: A 671 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7622 (mmmm) REVERT: A 691 MET cc_start: 0.7230 (tpp) cc_final: 0.6709 (ttm) REVERT: A 717 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7122 (tpp80) REVERT: A 722 ARG cc_start: 0.7558 (tpp80) cc_final: 0.7125 (tpp80) REVERT: B 73 TRP cc_start: 0.7687 (t-100) cc_final: 0.7482 (t-100) REVERT: B 113 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: B 217 MET cc_start: 0.7383 (mpp) cc_final: 0.6890 (mpp) REVERT: B 324 THR cc_start: 0.2693 (OUTLIER) cc_final: 0.2467 (t) REVERT: B 539 ARG cc_start: 0.6974 (ttt-90) cc_final: 0.6664 (ttt90) REVERT: B 593 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6958 (pp) REVERT: B 607 PHE cc_start: 0.7919 (t80) cc_final: 0.7472 (t80) REVERT: B 672 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 680 GLN cc_start: 0.6738 (tm-30) cc_final: 0.6191 (tm-30) REVERT: B 719 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8126 (mp) REVERT: C 69 CYS cc_start: 0.8390 (m) cc_final: 0.7906 (m) REVERT: C 81 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5588 (tm-30) REVERT: C 102 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.6244 (mtpt) REVERT: C 155 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7653 (mmtm) REVERT: C 158 GLN cc_start: 0.8037 (tp40) cc_final: 0.7227 (tp40) REVERT: C 161 MET cc_start: 0.7120 (mtm) cc_final: 0.6602 (mtm) REVERT: C 183 MET cc_start: 0.7948 (tmm) cc_final: 0.7558 (tmm) REVERT: C 217 MET cc_start: 0.7754 (ptt) cc_final: 0.7415 (ppp) REVERT: C 223 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6665 (pmt) REVERT: C 271 MET cc_start: 0.3819 (ttt) cc_final: 0.2453 (ptm) REVERT: C 447 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7067 (mtm-85) REVERT: C 479 SER cc_start: 0.7759 (m) cc_final: 0.7403 (p) REVERT: C 484 ASP cc_start: 0.6658 (m-30) cc_final: 0.6407 (m-30) REVERT: C 519 MET cc_start: 0.7328 (mtp) cc_final: 0.7043 (mtm) REVERT: C 536 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6753 (tp30) REVERT: C 596 GLN cc_start: 0.7205 (mt0) cc_final: 0.6885 (mt0) REVERT: C 602 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6577 (t0) REVERT: C 722 ARG cc_start: 0.7387 (ttm170) cc_final: 0.7064 (ttt180) REVERT: D 68 ARG cc_start: 0.7505 (ptp90) cc_final: 0.7017 (ttp80) REVERT: D 70 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6377 (mpt90) REVERT: D 74 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7091 (mm-30) REVERT: D 109 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7658 (mp) REVERT: D 113 PHE cc_start: 0.7441 (m-80) cc_final: 0.7110 (m-80) REVERT: D 217 MET cc_start: 0.8198 (mtp) cc_final: 0.7954 (mtp) REVERT: D 219 MET cc_start: 0.7124 (tpp) cc_final: 0.6636 (tpt) REVERT: D 223 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.4924 (mpt) REVERT: D 234 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7052 (tpt-90) REVERT: D 261 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8318 (mm-30) REVERT: D 287 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5989 (pm20) REVERT: D 300 TYR cc_start: 0.7217 (t80) cc_final: 0.6614 (t80) REVERT: D 444 LYS cc_start: 0.6587 (OUTLIER) cc_final: 0.5618 (mtmt) REVERT: D 473 GLN cc_start: 0.6780 (tp40) cc_final: 0.6509 (tp40) REVERT: D 479 SER cc_start: 0.8283 (m) cc_final: 0.7973 (p) REVERT: D 493 ARG cc_start: 0.7182 (mtp85) cc_final: 0.6907 (ttm-80) REVERT: D 541 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8061 (tt) REVERT: D 561 GLU cc_start: 0.7124 (pm20) cc_final: 0.6597 (pm20) REVERT: D 565 ASP cc_start: 0.7091 (m-30) cc_final: 0.6763 (m-30) REVERT: D 606 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6922 (tp30) REVERT: D 650 ASN cc_start: 0.7743 (t0) cc_final: 0.7237 (t0) REVERT: D 672 GLU cc_start: 0.7082 (tp30) cc_final: 0.6843 (tp30) REVERT: D 686 TYR cc_start: 0.7880 (t80) cc_final: 0.7284 (t80) REVERT: E 69 CYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7108 (p) REVERT: E 155 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7769 (mtpt) REVERT: E 161 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6511 (ppp) REVERT: E 174 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7546 (pp20) REVERT: E 181 LYS cc_start: 0.8776 (mttt) cc_final: 0.8295 (mttt) REVERT: E 271 MET cc_start: 0.6099 (ptt) cc_final: 0.5623 (ppp) REVERT: E 484 ASP cc_start: 0.7207 (m-30) cc_final: 0.6841 (m-30) REVERT: E 505 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7015 (mm-30) REVERT: E 517 ASP cc_start: 0.6556 (t70) cc_final: 0.6126 (t0) REVERT: E 522 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8091 (m) REVERT: E 584 GLN cc_start: 0.7377 (tt0) cc_final: 0.7125 (tt0) REVERT: E 612 ASP cc_start: 0.7690 (t0) cc_final: 0.7378 (t0) REVERT: E 615 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7453 (mtpt) REVERT: E 635 LYS cc_start: 0.7253 (mmmt) cc_final: 0.6931 (mmmt) REVERT: E 699 THR cc_start: 0.7600 (m) cc_final: 0.7328 (p) REVERT: F 432 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7832 (mm) REVERT: F 469 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7444 (ttpp) REVERT: F 489 SER cc_start: 0.8484 (t) cc_final: 0.8101 (p) REVERT: F 548 ASP cc_start: 0.8084 (t70) cc_final: 0.7662 (t0) REVERT: F 551 TRP cc_start: 0.8322 (m-10) cc_final: 0.8098 (m-10) REVERT: F 608 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: F 609 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7228 (tp-100) REVERT: F 613 ASP cc_start: 0.6763 (m-30) cc_final: 0.6446 (m-30) REVERT: F 614 TYR cc_start: 0.7692 (t80) cc_final: 0.7230 (t80) REVERT: F 679 ARG cc_start: 0.7584 (mtt90) cc_final: 0.7278 (mtt90) REVERT: F 680 GLN cc_start: 0.7142 (mp10) cc_final: 0.6584 (mp10) REVERT: F 695 MET cc_start: 0.7583 (mmt) cc_final: 0.7170 (mmm) REVERT: F 696 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: F 700 ASP cc_start: 0.7070 (m-30) cc_final: 0.6800 (m-30) REVERT: F 723 LEU cc_start: 0.8580 (tp) cc_final: 0.8363 (tp) REVERT: F 724 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7988 (mmtp) outliers start: 171 outliers final: 119 residues processed: 752 average time/residue: 0.4384 time to fit residues: 483.1432 Evaluate side-chains 782 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 629 time to evaluate : 2.880 ------------------------------------------------------------------------------- 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 270 THR 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 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 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 102 LYS Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 452 ASP 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 615 LYS 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 81 GLU 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 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 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 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 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 C residue 719 LEU Chi-restraints excluded: chain C residue 720 ILE 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 160 LYS 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 302 GLN Chi-restraints excluded: chain D residue 343 CYS Chi-restraints excluded: chain D residue 349 TRP 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 677 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 161 MET Chi-restraints excluded: chain E residue 174 GLU 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 454 LEU 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 532 ASP Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 590 GLN 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 432 LEU 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 469 LYS Chi-restraints excluded: chain F residue 492 ARG 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 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 70 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 255 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 212 optimal weight: 0.2980 chunk 247 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 183 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 121 ASN ** 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 596 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN ** C 294 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 488 HIS D 554 ASN D 616 ASN D 647 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS F 499 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.176488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135034 restraints weight = 45176.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138431 restraints weight = 19544.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139325 restraints weight = 9850.567| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 26073 Z= 0.186 Angle : 0.842 59.160 35237 Z= 0.455 Chirality : 0.044 1.000 3882 Planarity : 0.006 0.158 4545 Dihedral : 6.542 59.456 3534 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.75 % Favored : 93.76 % Rotamer: Outliers : 5.99 % Allowed : 31.48 % Favored : 62.53 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 3094 helix: 0.85 (0.11), residues: 2282 sheet: -5.98 (0.44), residues: 10 loop : -2.10 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 89 HIS 0.067 0.002 HIS C 430 PHE 0.043 0.002 PHE A 113 TYR 0.033 0.002 TYR D 550 ARG 0.044 0.001 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 1510) hydrogen bonds : angle 4.54881 ( 4482) covalent geometry : bond 0.00422 (26073) covalent geometry : angle 0.84192 (35237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11640.05 seconds wall clock time: 205 minutes 52.49 seconds (12352.49 seconds total)