Starting phenix.real_space_refine on Tue Aug 26 14:04:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygp_39259/08_2025/8ygp_39259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygp_39259/08_2025/8ygp_39259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ygp_39259/08_2025/8ygp_39259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygp_39259/08_2025/8ygp_39259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ygp_39259/08_2025/8ygp_39259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygp_39259/08_2025/8ygp_39259.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 140 5.16 5 C 24200 2.51 5 N 6044 2.21 5 O 7140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37524 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "B" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "C" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "D" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "E" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "F" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "G" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "H" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Time building chain proxies: 9.01, per 1000 atoms: 0.24 Number of scatterers: 37524 At special positions: 0 Unit cell: (104.58, 138.61, 267.26, 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 140 16.00 O 7140 8.00 N 6044 7.00 C 24200 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: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8632 Finding SS restraints... Secondary structure from input PDB file: 232 helices and 19 sheets defined 57.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.947A pdb=" N ARG A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.866A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.632A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 115 through 123 removed outlier: 4.277A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.576A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 160' Processing helix chain 'A' and resid 186 through 197 removed outlier: 5.166A pdb=" N ASP A 194 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.712A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 281 through 296 removed outlier: 4.001A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.589A pdb=" N ILE A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.510A pdb=" N LEU A 330 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.559A pdb=" N ARG A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 417 through 425 removed outlier: 3.775A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.554A pdb=" N ASP A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 removed outlier: 4.152A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 493 removed outlier: 3.627A pdb=" N ARG A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.509A pdb=" N PHE A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 removed outlier: 4.255A pdb=" N ASN A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 548 through 572 removed outlier: 3.962A pdb=" N TYR A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.533A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 595 " --> pdb=" O ASN A 591 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.830A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 627 removed outlier: 4.104A pdb=" N SER A 615 " --> pdb=" O TYR A 611 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 680 through 694 removed outlier: 3.791A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU A 694 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 712 removed outlier: 3.671A pdb=" N TYR A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 722 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 750 through 761 Processing helix chain 'A' and resid 771 through 786 removed outlier: 4.949A pdb=" N ASP A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N HIS A 786 " --> pdb=" O GLN A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.553A pdb=" N LYS A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 827 Processing helix chain 'A' and resid 831 through 840 removed outlier: 3.660A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.812A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 928 through 934 removed outlier: 3.708A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 932 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 933 " --> pdb=" O MET A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 962 removed outlier: 3.852A pdb=" N LEU A 959 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 979 through 990 Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 24 through 39 removed outlier: 3.984A pdb=" N ASN B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 82 through 96 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.509A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.844A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.570A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.567A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.626A pdb=" N TYR B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.558A pdb=" N PHE B 301 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 302 " --> pdb=" O ASN B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 302' Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.925A pdb=" N ILE B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 4.441A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.851A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.509A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 374 through 392 removed outlier: 4.386A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.508A pdb=" N GLY B 416 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.748A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 removed outlier: 3.781A pdb=" N GLY B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 466 removed outlier: 4.738A pdb=" N ILE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 493 removed outlier: 3.825A pdb=" N TYR B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 523 through 529 removed outlier: 3.983A pdb=" N ASP B 526 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 528 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 removed outlier: 3.596A pdb=" N GLU B 543 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 550 removed outlier: 3.788A pdb=" N PHE B 550 " --> pdb=" O ASP B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 551 through 569 removed outlier: 3.667A pdb=" N VAL B 556 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN B 563 " --> pdb=" O PHE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 591 removed outlier: 3.658A pdb=" N LEU B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 599 removed outlier: 4.648A pdb=" N LEU B 595 " --> pdb=" O ASN B 591 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.666A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.708A pdb=" N PHE B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.982A pdb=" N GLU B 694 " --> pdb=" O GLY B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 removed outlier: 4.815A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 743 removed outlier: 4.637A pdb=" N LYS B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.690A pdb=" N THR B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.549A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 846 through 856 Processing helix chain 'B' and resid 861 through 871 removed outlier: 4.036A pdb=" N LEU B 865 " --> pdb=" O ASN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 903 removed outlier: 3.878A pdb=" N VAL B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.646A pdb=" N THR B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.997A pdb=" N GLU B 932 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.777A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 954 " --> pdb=" O TYR B 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 950 through 954' Processing helix chain 'B' and resid 955 through 960 removed outlier: 3.539A pdb=" N LEU B 959 " --> pdb=" O PRO B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 972 removed outlier: 4.021A pdb=" N GLY B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.593A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 999 Processing helix chain 'C' and resid 69 through 78 removed outlier: 4.578A pdb=" N MET C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.670A pdb=" N GLY D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 39 removed outlier: 3.699A pdb=" N ASN E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 removed outlier: 4.583A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 71 removed outlier: 4.315A pdb=" N ASP E 64 " --> pdb=" O TRP E 60 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 95 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 115 through 124 removed outlier: 4.058A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET E 124 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 154 through 159 removed outlier: 3.832A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.901A pdb=" N TYR E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 removed outlier: 3.751A pdb=" N TYR E 197 " --> pdb=" O TYR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.553A pdb=" N SER E 201 " --> pdb=" O TYR E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 234 removed outlier: 3.771A pdb=" N ASN E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 283 through 295 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.963A pdb=" N ILE E 309 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 removed outlier: 4.013A pdb=" N ALA E 321 " --> pdb=" O PRO E 318 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU E 322 " --> pdb=" O LEU E 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 318 through 322' Processing helix chain 'E' and resid 355 through 366 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 374 through 392 removed outlier: 6.268A pdb=" N ASN E 386 " --> pdb=" O ASN E 382 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 removed outlier: 3.543A pdb=" N ASP E 399 " --> pdb=" O MET E 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 400 " --> pdb=" O ALA E 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 396 through 400' Processing helix chain 'E' and resid 418 through 425 Processing helix chain 'E' and resid 431 through 446 Processing helix chain 'E' and resid 447 through 461 removed outlier: 3.823A pdb=" N ASP E 453 " --> pdb=" O GLU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 495 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'E' and resid 508 through 520 removed outlier: 3.598A pdb=" N LEU E 512 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 513 " --> pdb=" O ASP E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 538 Processing helix chain 'E' and resid 539 through 544 removed outlier: 3.614A pdb=" N PHE E 544 " --> pdb=" O ILE E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 572 removed outlier: 3.798A pdb=" N TYR E 552 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS E 557 " --> pdb=" O ASP E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 598 removed outlier: 3.856A pdb=" N ASN E 598 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 3.718A pdb=" N VAL E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 625 removed outlier: 4.044A pdb=" N LYS E 622 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 624 " --> pdb=" O ILE E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 659 removed outlier: 4.132A pdb=" N ASN E 654 " --> pdb=" O TYR E 650 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE E 655 " --> pdb=" O ASP E 651 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE E 659 " --> pdb=" O ILE E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 670 removed outlier: 3.693A pdb=" N SER E 670 " --> pdb=" O ASN E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 701 removed outlier: 4.091A pdb=" N ILE E 684 " --> pdb=" O GLU E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 711 removed outlier: 3.626A pdb=" N GLN E 711 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 722 removed outlier: 3.597A pdb=" N ALA E 719 " --> pdb=" O GLU E 715 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 720 " --> pdb=" O ALA E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 734 Processing helix chain 'E' and resid 735 through 743 Processing helix chain 'E' and resid 750 through 765 removed outlier: 3.936A pdb=" N ARG E 754 " --> pdb=" O ASP E 750 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR E 755 " --> pdb=" O ILE E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 786 removed outlier: 4.048A pdb=" N ILE E 772 " --> pdb=" O PRO E 768 " (cutoff:3.500A) Processing helix chain 'E' and resid 799 through 812 removed outlier: 3.872A pdb=" N ASP E 803 " --> pdb=" O LEU E 799 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR E 804 " --> pdb=" O TYR E 800 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE E 808 " --> pdb=" O TYR E 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 826 removed outlier: 3.599A pdb=" N SER E 821 " --> pdb=" O SER E 817 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE E 823 " --> pdb=" O ARG E 819 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS E 826 " --> pdb=" O GLU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 841 Processing helix chain 'E' and resid 842 through 845 Processing helix chain 'E' and resid 846 through 852 Processing helix chain 'E' and resid 861 through 871 Processing helix chain 'E' and resid 878 through 903 removed outlier: 3.645A pdb=" N GLU E 901 " --> pdb=" O ILE E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 922 removed outlier: 4.177A pdb=" N PHE E 916 " --> pdb=" O TYR E 912 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY E 917 " --> pdb=" O MET E 913 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU E 922 " --> pdb=" O ILE E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 927 through 933 removed outlier: 4.013A pdb=" N MET E 930 " --> pdb=" O ASN E 927 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 944 Processing helix chain 'E' and resid 955 through 962 removed outlier: 4.016A pdb=" N LYS E 960 " --> pdb=" O SER E 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 971 removed outlier: 4.214A pdb=" N LYS E 969 " --> pdb=" O LYS E 965 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 977 Processing helix chain 'E' and resid 978 through 989 removed outlier: 4.001A pdb=" N LEU E 984 " --> pdb=" O VAL E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1001 removed outlier: 3.549A pdb=" N GLU E 998 " --> pdb=" O LYS E 994 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 39 removed outlier: 3.511A pdb=" N ASN F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.524A pdb=" N SER F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 71 Processing helix chain 'F' and resid 80 through 85 Processing helix chain 'F' and resid 85 through 95 removed outlier: 4.812A pdb=" N GLN F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN F 93 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 removed outlier: 3.592A pdb=" N GLN F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 124 removed outlier: 3.555A pdb=" N ASP F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU F 122 " --> pdb=" O HIS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.853A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 186 through 192 removed outlier: 3.620A pdb=" N TYR F 190 " --> pdb=" O LYS F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'F' and resid 197 through 211 removed outlier: 3.849A pdb=" N SER F 201 " --> pdb=" O TYR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 227 Processing helix chain 'F' and resid 229 through 236 removed outlier: 3.819A pdb=" N LEU F 235 " --> pdb=" O TRP F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 298 through 302 removed outlier: 4.199A pdb=" N PHE F 301 " --> pdb=" O GLU F 298 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE F 302 " --> pdb=" O ASN F 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 298 through 302' Processing helix chain 'F' and resid 304 through 317 Processing helix chain 'F' and resid 318 through 322 Processing helix chain 'F' and resid 327 through 333 Processing helix chain 'F' and resid 355 through 363 Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.968A pdb=" N SER F 371 " --> pdb=" O ASP F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 391 Processing helix chain 'F' and resid 417 through 427 removed outlier: 3.605A pdb=" N GLU F 427 " --> pdb=" O LYS F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 446 Processing helix chain 'F' and resid 447 through 462 Processing helix chain 'F' and resid 468 through 494 Processing helix chain 'F' and resid 495 through 500 Processing helix chain 'F' and resid 508 through 519 Processing helix chain 'F' and resid 524 through 529 removed outlier: 4.378A pdb=" N PHE F 528 " --> pdb=" O ILE F 524 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN F 529 " --> pdb=" O ASP F 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 529' Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 540 through 544 Processing helix chain 'F' and resid 549 through 569 removed outlier: 4.505A pdb=" N ASP F 554 " --> pdb=" O PHE F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 removed outlier: 4.178A pdb=" N ASN F 598 " --> pdb=" O PHE F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 604 removed outlier: 3.899A pdb=" N VAL F 603 " --> pdb=" O LEU F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 628 removed outlier: 3.669A pdb=" N HIS F 609 " --> pdb=" O PHE F 605 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU F 621 " --> pdb=" O SER F 617 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS F 622 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU F 624 " --> pdb=" O ILE F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 658 Processing helix chain 'F' and resid 660 through 671 Processing helix chain 'F' and resid 672 through 676 Processing helix chain 'F' and resid 680 through 701 removed outlier: 4.074A pdb=" N ILE F 684 " --> pdb=" O GLU F 680 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU F 685 " --> pdb=" O GLN F 681 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU F 686 " --> pdb=" O GLU F 682 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA F 701 " --> pdb=" O LYS F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 710 Processing helix chain 'F' and resid 712 through 722 removed outlier: 3.532A pdb=" N LYS F 717 " --> pdb=" O ILE F 713 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE F 722 " --> pdb=" O ALA F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 743 removed outlier: 3.699A pdb=" N ALA F 739 " --> pdb=" O LYS F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 762 removed outlier: 3.580A pdb=" N GLU F 759 " --> pdb=" O TYR F 755 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG F 760 " --> pdb=" O VAL F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 787 removed outlier: 3.618A pdb=" N ILE F 787 " --> pdb=" O ALA F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 802 through 811 Processing helix chain 'F' and resid 819 through 826 Processing helix chain 'F' and resid 832 through 838 removed outlier: 3.695A pdb=" N ASP F 836 " --> pdb=" O GLN F 832 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 845 removed outlier: 3.974A pdb=" N LEU F 842 " --> pdb=" O PHE F 839 " (cutoff:3.500A) Proline residue: F 843 - end of helix No H-bonds generated for 'chain 'F' and resid 839 through 845' Processing helix chain 'F' and resid 846 through 855 removed outlier: 4.020A pdb=" N LYS F 850 " --> pdb=" O SER F 846 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 872 removed outlier: 4.241A pdb=" N ARG F 870 " --> pdb=" O MET F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 882 through 903 removed outlier: 3.878A pdb=" N ILE F 886 " --> pdb=" O GLU F 882 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL F 894 " --> pdb=" O GLU F 890 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN F 895 " --> pdb=" O THR F 891 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS F 902 " --> pdb=" O VAL F 898 " (cutoff:3.500A) Processing helix chain 'F' and resid 912 through 922 removed outlier: 3.663A pdb=" N TRP F 919 " --> pdb=" O THR F 915 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE F 921 " --> pdb=" O GLY F 917 " (cutoff:3.500A) Processing helix chain 'F' and resid 937 through 945 Processing helix chain 'F' and resid 957 through 961 Processing helix chain 'F' and resid 965 through 971 Processing helix chain 'F' and resid 977 through 990 removed outlier: 3.733A pdb=" N GLU F 982 " --> pdb=" O HIS F 978 " (cutoff:3.500A) Processing helix chain 'F' and resid 993 through 1002 removed outlier: 4.250A pdb=" N LEU F 997 " --> pdb=" O ASP F 993 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN F1002 " --> pdb=" O GLU F 998 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 removed outlier: 3.559A pdb=" N ALA G 74 " --> pdb=" O LEU G 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.521A pdb=" N LYS A 169 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 129 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 214 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 246 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 4.003A pdb=" N SER C 31 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR C 62 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 33 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 221 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 904 through 906 removed outlier: 3.634A pdb=" N GLN D 194 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER D 189 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR D 12 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG D 176 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP D 10 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.523A pdb=" N VAL B 129 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 130 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 43 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 214 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 247 removed outlier: 6.141A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 24 removed outlier: 4.314A pdb=" N LYS C 20 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG C 15 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL C 22 " --> pdb=" O PHE C 13 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER C 189 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 31 through 32 Processing sheet with id=AB1, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'E' and resid 150 through 152 removed outlier: 3.543A pdb=" N LYS E 169 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL E 43 " --> pdb=" O THR E 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AB4, first strand: chain 'E' and resid 904 through 908 removed outlier: 3.508A pdb=" N ALA H 232 " --> pdb=" O PHE E 907 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER H 189 " --> pdb=" O ALA H 179 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 193 " --> pdb=" O TYR H 175 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG H 176 " --> pdb=" O ASP H 10 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG H 15 " --> pdb=" O LYS H 20 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS H 20 " --> pdb=" O ARG H 15 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.591A pdb=" N SER F 150 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LYS F 169 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE F 152 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 129 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE F 130 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL F 43 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE F 216 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE F 45 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 244 through 245 Processing sheet with id=AB7, first strand: chain 'F' and resid 338 through 339 Processing sheet with id=AB8, first strand: chain 'F' and resid 574 through 575 removed outlier: 3.657A pdb=" N THR H 62 " --> pdb=" O SER H 31 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN H 60 " --> pdb=" O SER H 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU H 61 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 63 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.564A pdb=" N VAL G 11 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 193 " --> pdb=" O TYR G 175 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA G 179 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER G 189 " --> pdb=" O ALA G 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 62 through 63 1637 hydrogen bonds defined for protein. 4638 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: 8.61 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 5343 1.25 - 1.39: 10970 1.39 - 1.53: 20697 1.53 - 1.68: 1117 1.68 - 1.82: 241 Bond restraints: 38368 Sorted by residual: bond pdb=" C SER A 580 " pdb=" O SER A 580 " ideal model delta sigma weight residual 1.234 1.105 0.129 1.17e-02 7.31e+03 1.21e+02 bond pdb=" N ILE A 582 " pdb=" CA ILE A 582 " ideal model delta sigma weight residual 1.461 1.375 0.085 1.19e-02 7.06e+03 5.13e+01 bond pdb=" N VAL A 584 " pdb=" CA VAL A 584 " ideal model delta sigma weight residual 1.463 1.391 0.072 1.14e-02 7.69e+03 4.00e+01 bond pdb=" CA GLU A 607 " pdb=" C GLU A 607 " ideal model delta sigma weight residual 1.525 1.448 0.077 1.22e-02 6.72e+03 3.98e+01 bond pdb=" CA ASN F 961 " pdb=" C ASN F 961 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.30e-02 5.92e+03 3.91e+01 ... (remaining 38363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.53: 51517 7.53 - 15.06: 134 15.06 - 22.59: 31 22.59 - 30.11: 17 30.11 - 37.64: 9 Bond angle restraints: 51708 Sorted by residual: angle pdb=" N TRP B 601 " pdb=" CA TRP B 601 " pdb=" C TRP B 601 " ideal model delta sigma weight residual 112.54 149.99 -37.45 1.22e+00 6.72e-01 9.42e+02 angle pdb=" N ASP E 630 " pdb=" CA ASP E 630 " pdb=" C ASP E 630 " ideal model delta sigma weight residual 110.53 72.89 37.64 1.32e+00 5.74e-01 8.13e+02 angle pdb=" N ASN B 182 " pdb=" CA ASN B 182 " pdb=" C ASN B 182 " ideal model delta sigma weight residual 110.97 137.06 -26.09 1.09e+00 8.42e-01 5.73e+02 angle pdb=" N GLY F 392 " pdb=" CA GLY F 392 " pdb=" C GLY F 392 " ideal model delta sigma weight residual 115.31 144.42 -29.11 1.24e+00 6.50e-01 5.51e+02 angle pdb=" N GLU H 230 " pdb=" CA GLU H 230 " pdb=" C GLU H 230 " ideal model delta sigma weight residual 111.90 142.73 -30.83 1.32e+00 5.74e-01 5.46e+02 ... (remaining 51703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19214 18.00 - 36.00: 2827 36.00 - 54.00: 713 54.00 - 72.01: 119 72.01 - 90.01: 47 Dihedral angle restraints: 22920 sinusoidal: 9484 harmonic: 13436 Sorted by residual: dihedral pdb=" C THR H 24 " pdb=" N THR H 24 " pdb=" CA THR H 24 " pdb=" CB THR H 24 " ideal model delta harmonic sigma weight residual -122.00 -82.29 -39.71 0 2.50e+00 1.60e-01 2.52e+02 dihedral pdb=" N LYS A 738 " pdb=" C LYS A 738 " pdb=" CA LYS A 738 " pdb=" CB LYS A 738 " ideal model delta harmonic sigma weight residual 122.80 91.73 31.07 0 2.50e+00 1.60e-01 1.54e+02 dihedral pdb=" C PHE F 646 " pdb=" N PHE F 646 " pdb=" CA PHE F 646 " pdb=" CB PHE F 646 " ideal model delta harmonic sigma weight residual -122.60 -94.42 -28.18 0 2.50e+00 1.60e-01 1.27e+02 ... (remaining 22917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 5454 0.250 - 0.501: 27 0.501 - 0.751: 12 0.751 - 1.001: 3 1.001 - 1.251: 4 Chirality restraints: 5500 Sorted by residual: chirality pdb=" CA TRP B 601 " pdb=" N TRP B 601 " pdb=" C TRP B 601 " pdb=" CB TRP B 601 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.92e+01 chirality pdb=" CA TYR B 193 " pdb=" N TYR B 193 " pdb=" C TYR B 193 " pdb=" CB TYR B 193 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.88e+01 chirality pdb=" CA ASP B 663 " pdb=" N ASP B 663 " pdb=" C ASP B 663 " pdb=" CB ASP B 663 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.61e+01 ... (remaining 5497 not shown) Planarity restraints: 6636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 580 " 0.055 2.00e-02 2.50e+03 1.17e-01 1.37e+02 pdb=" C SER A 580 " -0.202 2.00e-02 2.50e+03 pdb=" O SER A 580 " 0.085 2.00e-02 2.50e+03 pdb=" N ASP A 581 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 72 " 0.039 2.00e-02 2.50e+03 4.28e-02 4.58e+01 pdb=" CG TRP G 72 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 TRP G 72 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP G 72 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 72 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP G 72 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP G 72 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 72 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 72 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP G 72 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 578 " 0.024 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C MET A 578 " -0.089 2.00e-02 2.50e+03 pdb=" O MET A 578 " 0.035 2.00e-02 2.50e+03 pdb=" N SER A 579 " 0.030 2.00e-02 2.50e+03 ... (remaining 6633 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 7 2.00 - 2.73: 3461 2.73 - 3.45: 60225 3.45 - 4.18: 90331 4.18 - 4.90: 150938 Nonbonded interactions: 304962 Sorted by model distance: nonbonded pdb=" O ASP B 663 " pdb=" OD1 ASP B 663 " model vdw 1.280 3.040 nonbonded pdb=" O TRP B 601 " pdb=" CD2 TRP B 601 " model vdw 1.722 3.260 nonbonded pdb=" N ASP E 630 " pdb=" O ASP E 630 " model vdw 1.814 2.496 nonbonded pdb=" O THR H 24 " pdb=" ND2 ASN H 65 " model vdw 1.885 3.120 nonbonded pdb=" O THR H 24 " pdb=" OG1 THR H 24 " model vdw 1.936 3.040 ... (remaining 304957 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } 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: 7.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.150 Find NCS groups from input model: 0.670 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 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 : 0.005 0.193 38368 Z= 0.322 Angle : 1.278 37.643 51708 Z= 0.778 Chirality : 0.074 1.251 5500 Planarity : 0.006 0.120 6636 Dihedral : 18.050 90.008 14288 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.77 % Favored : 87.85 % Rotamer: Outliers : 2.38 % Allowed : 26.89 % Favored : 70.73 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.12), residues: 4512 helix: -0.91 (0.11), residues: 2196 sheet: -0.62 (0.29), residues: 324 loop : -2.80 (0.12), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 326 TYR 0.048 0.002 TYR B 455 PHE 0.043 0.002 PHE F 943 TRP 0.104 0.004 TRP G 72 HIS 0.029 0.002 HIS E 606 Details of bonding type rmsd covalent geometry : bond 0.00537 (38368) covalent geometry : angle 1.27831 (51708) hydrogen bonds : bond 0.17837 ( 1637) hydrogen bonds : angle 7.62693 ( 4638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 804 time to evaluate : 1.555 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 25 ASN cc_start: 0.8537 (m110) cc_final: 0.8131 (p0) REVERT: A 467 ASN cc_start: 0.8005 (t0) cc_final: 0.7742 (m-40) REVERT: A 547 ASP cc_start: 0.4647 (OUTLIER) cc_final: 0.4255 (p0) REVERT: A 578 MET cc_start: 0.6627 (tpt) cc_final: 0.6413 (tpt) REVERT: A 594 PHE cc_start: 0.7571 (t80) cc_final: 0.7214 (t80) REVERT: B 32 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8135 (mm-30) REVERT: B 89 GLN cc_start: 0.6725 (tp40) cc_final: 0.4878 (tp40) REVERT: B 187 GLU cc_start: 0.7494 (pp20) cc_final: 0.7127 (pp20) REVERT: B 197 TYR cc_start: 0.7566 (p90) cc_final: 0.7267 (p90) REVERT: B 327 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8332 (mmtm) REVERT: E 105 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6935 (mmtt) REVERT: E 197 TYR cc_start: 0.7599 (m-80) cc_final: 0.7158 (m-80) REVERT: E 307 GLU cc_start: 0.7759 (tp30) cc_final: 0.7273 (tt0) REVERT: E 379 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8066 (mp0) REVERT: E 380 ARG cc_start: 0.8249 (mmt180) cc_final: 0.7839 (mmt180) REVERT: E 437 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7256 (tppt) REVERT: E 609 HIS cc_start: 0.7987 (m90) cc_final: 0.7730 (m90) REVERT: E 674 ASP cc_start: 0.7866 (m-30) cc_final: 0.7592 (m-30) REVERT: E 744 PHE cc_start: 0.7963 (t80) cc_final: 0.7514 (t80) REVERT: E 775 ILE cc_start: 0.8351 (mt) cc_final: 0.8151 (mt) REVERT: F 105 LYS cc_start: 0.7463 (tptt) cc_final: 0.7069 (tptt) REVERT: F 291 ASP cc_start: 0.8181 (m-30) cc_final: 0.7956 (m-30) REVERT: F 336 TYR cc_start: 0.7458 (m-80) cc_final: 0.7180 (m-80) REVERT: F 357 MET cc_start: 0.8495 (pmm) cc_final: 0.8227 (pmm) REVERT: F 421 MET cc_start: 0.8698 (ptt) cc_final: 0.8309 (ptt) REVERT: F 491 GLN cc_start: 0.6707 (tt0) cc_final: 0.6248 (tt0) REVERT: F 531 MET cc_start: 0.4721 (mmp) cc_final: 0.4383 (mmp) REVERT: F 534 GLU cc_start: 0.7529 (tp30) cc_final: 0.6797 (tp30) REVERT: F 538 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8137 (ptpp) REVERT: F 607 GLU cc_start: 0.8088 (tt0) cc_final: 0.7815 (tt0) REVERT: F 678 PHE cc_start: 0.7546 (m-10) cc_final: 0.7129 (m-10) REVERT: F 755 TYR cc_start: 0.7855 (t80) cc_final: 0.7560 (t80) REVERT: F 829 GLN cc_start: 0.2200 (OUTLIER) cc_final: 0.1836 (mt0) REVERT: F 862 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7707 (mm) REVERT: F 905 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6007 (mm110) REVERT: F 961 ASN cc_start: 0.8351 (m-40) cc_final: 0.7986 (m110) REVERT: H 65 ASN cc_start: 0.5488 (p0) cc_final: 0.4961 (p0) REVERT: H 69 ASP cc_start: 0.6027 (t70) cc_final: 0.5595 (t70) REVERT: H 199 SER cc_start: 0.6765 (m) cc_final: 0.6474 (t) REVERT: H 206 MET cc_start: 0.6715 (tpt) cc_final: 0.6368 (tpt) REVERT: H 207 SER cc_start: 0.6402 (OUTLIER) cc_final: 0.6112 (p) outliers start: 98 outliers final: 52 residues processed: 871 average time/residue: 0.2602 time to fit residues: 362.9739 Evaluate side-chains 834 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 777 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN B 939 GLN B 963 ASN B 992 ASN D 6 GLN D 194 GLN E 67 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 HIS E 377 GLN ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 705 ASN E1002 ASN F 115 ASN ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 782 GLN ** F 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 ASN G 6 GLN H 77 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.210836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.166765 restraints weight = 82994.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.172139 restraints weight = 54445.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.175991 restraints weight = 38936.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.178719 restraints weight = 29781.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.180843 restraints weight = 24044.231| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 38368 Z= 0.167 Angle : 0.742 11.086 51708 Z= 0.397 Chirality : 0.048 0.280 5500 Planarity : 0.005 0.095 6636 Dihedral : 6.113 81.807 4984 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.73 % Favored : 90.03 % Rotamer: Outliers : 0.27 % Allowed : 4.68 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.12), residues: 4512 helix: -0.74 (0.10), residues: 2263 sheet: -0.69 (0.29), residues: 309 loop : -2.63 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 170 TYR 0.028 0.002 TYR F 482 PHE 0.047 0.002 PHE A 659 TRP 0.042 0.002 TRP E 919 HIS 0.011 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00351 (38368) covalent geometry : angle 0.74244 (51708) hydrogen bonds : bond 0.05170 ( 1637) hydrogen bonds : angle 6.09375 ( 4638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 863 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 CYS cc_start: 0.8816 (m) cc_final: 0.8096 (t) REVERT: A 60 TRP cc_start: 0.7217 (p-90) cc_final: 0.6949 (p-90) REVERT: A 105 LYS cc_start: 0.7935 (mmtm) cc_final: 0.7465 (mmmm) REVERT: A 124 MET cc_start: 0.8396 (tpp) cc_final: 0.7857 (tpp) REVERT: A 125 ASN cc_start: 0.8743 (m110) cc_final: 0.8427 (m-40) REVERT: A 144 LYS cc_start: 0.8509 (ptpp) cc_final: 0.8281 (pttp) REVERT: A 396 MET cc_start: 0.6686 (ptp) cc_final: 0.6252 (ptp) REVERT: A 421 MET cc_start: 0.4640 (mpp) cc_final: 0.4374 (mpp) REVERT: A 467 ASN cc_start: 0.7986 (t0) cc_final: 0.7785 (m110) REVERT: A 583 VAL cc_start: 0.8830 (t) cc_final: 0.8583 (t) REVERT: A 609 HIS cc_start: 0.8736 (m-70) cc_final: 0.8314 (m-70) REVERT: A 616 MET cc_start: 0.7944 (tpt) cc_final: 0.7737 (tpt) REVERT: A 671 CYS cc_start: 0.8285 (p) cc_final: 0.7597 (t) REVERT: A 686 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 694 GLU cc_start: 0.6673 (mp0) cc_final: 0.6447 (mp0) REVERT: A 704 MET cc_start: 0.5569 (ttt) cc_final: 0.5352 (ttt) REVERT: A 711 GLN cc_start: 0.8292 (mp10) cc_final: 0.7921 (mm-40) REVERT: A 913 MET cc_start: -0.5484 (mmp) cc_final: -0.6286 (mmt) REVERT: B 28 GLU cc_start: 0.8550 (tt0) cc_final: 0.8347 (pt0) REVERT: B 31 LYS cc_start: 0.8705 (tmmt) cc_final: 0.8466 (ptmm) REVERT: B 32 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 36 SER cc_start: 0.8119 (m) cc_final: 0.7486 (m) REVERT: B 62 LEU cc_start: 0.8132 (tt) cc_final: 0.7806 (mt) REVERT: B 89 GLN cc_start: 0.6800 (tp40) cc_final: 0.6390 (tp40) REVERT: B 118 HIS cc_start: 0.7865 (m-70) cc_final: 0.7397 (m-70) REVERT: B 119 ASP cc_start: 0.8501 (m-30) cc_final: 0.8164 (m-30) REVERT: B 122 LEU cc_start: 0.8977 (mt) cc_final: 0.8600 (pp) REVERT: B 136 ASN cc_start: 0.8194 (p0) cc_final: 0.7985 (p0) REVERT: B 179 LYS cc_start: 0.7309 (mppt) cc_final: 0.6936 (mmtt) REVERT: B 188 ASP cc_start: 0.8132 (t0) cc_final: 0.7920 (t0) REVERT: B 190 TYR cc_start: 0.7981 (m-10) cc_final: 0.7566 (m-10) REVERT: B 193 TYR cc_start: 0.6913 (t80) cc_final: 0.6228 (t80) REVERT: B 197 TYR cc_start: 0.7506 (p90) cc_final: 0.7278 (p90) REVERT: B 228 LEU cc_start: 0.8102 (mt) cc_final: 0.7679 (mt) REVERT: B 258 LEU cc_start: 0.8641 (mt) cc_final: 0.8342 (mt) REVERT: B 387 PHE cc_start: 0.7445 (p90) cc_final: 0.7239 (p90) REVERT: B 421 MET cc_start: 0.6240 (mtm) cc_final: 0.5747 (mtm) REVERT: B 435 ASP cc_start: 0.8460 (m-30) cc_final: 0.8105 (m-30) REVERT: B 442 LEU cc_start: 0.8724 (mt) cc_final: 0.8460 (mt) REVERT: B 476 ILE cc_start: 0.8745 (mt) cc_final: 0.8468 (mm) REVERT: B 480 ARG cc_start: 0.8177 (mmt180) cc_final: 0.7472 (mmm-85) REVERT: B 482 TYR cc_start: 0.7192 (t80) cc_final: 0.6884 (t80) REVERT: B 521 ASN cc_start: 0.7544 (t160) cc_final: 0.7151 (t0) REVERT: B 523 ASN cc_start: 0.8027 (m-40) cc_final: 0.7552 (m-40) REVERT: B 524 ILE cc_start: 0.7850 (pt) cc_final: 0.7468 (mm) REVERT: B 560 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7416 (tm-30) REVERT: B 569 MET cc_start: 0.6457 (tmm) cc_final: 0.5936 (tmm) REVERT: B 597 GLU cc_start: 0.8276 (tt0) cc_final: 0.7977 (tt0) REVERT: B 605 PHE cc_start: 0.7670 (m-80) cc_final: 0.7346 (m-80) REVERT: B 618 LEU cc_start: 0.7974 (mm) cc_final: 0.7751 (mm) REVERT: B 674 ASP cc_start: 0.7972 (t0) cc_final: 0.7698 (t0) REVERT: B 757 TRP cc_start: 0.6309 (m-10) cc_final: 0.5978 (m-10) REVERT: E 92 TYR cc_start: 0.7528 (t80) cc_final: 0.7007 (t80) REVERT: E 118 HIS cc_start: 0.7930 (m90) cc_final: 0.7571 (m90) REVERT: E 124 MET cc_start: 0.8016 (pmm) cc_final: 0.6948 (ppp) REVERT: E 144 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7881 (pttm) REVERT: E 158 VAL cc_start: 0.8158 (t) cc_final: 0.7897 (p) REVERT: E 357 MET cc_start: 0.7879 (mmm) cc_final: 0.7186 (mmm) REVERT: E 419 ASP cc_start: 0.8164 (p0) cc_final: 0.7662 (m-30) REVERT: E 421 MET cc_start: 0.7912 (mmt) cc_final: 0.7203 (mmt) REVERT: E 437 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7802 (mmtm) REVERT: E 448 TRP cc_start: 0.7992 (m-90) cc_final: 0.7540 (m-90) REVERT: E 457 ASN cc_start: 0.8687 (m-40) cc_final: 0.8425 (t0) REVERT: E 476 ILE cc_start: 0.7394 (mm) cc_final: 0.7010 (mm) REVERT: E 477 ASN cc_start: 0.8104 (t0) cc_final: 0.7781 (t0) REVERT: E 478 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7545 (ttp-110) REVERT: E 483 GLN cc_start: 0.7610 (tp-100) cc_final: 0.7380 (tp-100) REVERT: E 522 PHE cc_start: 0.7621 (m-10) cc_final: 0.7365 (m-80) REVERT: E 590 ASP cc_start: 0.7704 (t0) cc_final: 0.7475 (t0) REVERT: E 607 GLU cc_start: 0.7788 (pm20) cc_final: 0.7484 (pm20) REVERT: E 629 ARG cc_start: 0.6961 (tpp80) cc_final: 0.6748 (tpp80) REVERT: E 634 LEU cc_start: 0.8162 (mm) cc_final: 0.7568 (tt) REVERT: E 636 PHE cc_start: 0.8070 (t80) cc_final: 0.7645 (t80) REVERT: E 645 PHE cc_start: 0.7826 (t80) cc_final: 0.6820 (t80) REVERT: E 651 ASP cc_start: 0.8154 (m-30) cc_final: 0.7948 (m-30) REVERT: E 652 PHE cc_start: 0.7147 (t80) cc_final: 0.6883 (t80) REVERT: E 662 ASP cc_start: 0.8208 (p0) cc_final: 0.7826 (p0) REVERT: E 666 ASN cc_start: 0.7788 (t0) cc_final: 0.7474 (t0) REVERT: E 674 ASP cc_start: 0.7576 (m-30) cc_final: 0.7266 (m-30) REVERT: E 722 PHE cc_start: 0.8010 (t80) cc_final: 0.7707 (t80) REVERT: E 738 LYS cc_start: 0.8399 (pttm) cc_final: 0.7741 (pttm) REVERT: E 837 PHE cc_start: 0.8619 (t80) cc_final: 0.8416 (t80) REVERT: E 883 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: E 913 MET cc_start: 0.7519 (mmm) cc_final: 0.6802 (mmm) REVERT: E 974 LYS cc_start: 0.9206 (tppt) cc_final: 0.8830 (tppt) REVERT: F 25 ASN cc_start: 0.8992 (p0) cc_final: 0.8633 (p0) REVERT: F 98 MET cc_start: 0.8509 (mmp) cc_final: 0.8262 (mmp) REVERT: F 105 LYS cc_start: 0.7486 (tptt) cc_final: 0.7091 (tptt) REVERT: F 201 SER cc_start: 0.8045 (p) cc_final: 0.7838 (m) REVERT: F 242 LYS cc_start: 0.8065 (ptmm) cc_final: 0.7566 (ptmm) REVERT: F 277 SER cc_start: 0.8759 (t) cc_final: 0.5685 (p) REVERT: F 284 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6837 (tm-30) REVERT: F 290 MET cc_start: 0.8595 (mmp) cc_final: 0.8263 (mmp) REVERT: F 329 ASP cc_start: 0.8134 (m-30) cc_final: 0.7731 (m-30) REVERT: F 419 ASP cc_start: 0.7801 (p0) cc_final: 0.7509 (p0) REVERT: F 422 LYS cc_start: 0.8746 (tmmt) cc_final: 0.8389 (tmmt) REVERT: F 453 ASP cc_start: 0.7848 (m-30) cc_final: 0.7597 (m-30) REVERT: F 471 TYR cc_start: 0.6554 (t80) cc_final: 0.5940 (t80) REVERT: F 485 ILE cc_start: 0.8007 (tt) cc_final: 0.7742 (tp) REVERT: F 487 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7404 (tm-30) REVERT: F 491 GLN cc_start: 0.6734 (tt0) cc_final: 0.5696 (tt0) REVERT: F 509 ASP cc_start: 0.8594 (p0) cc_final: 0.8350 (p0) REVERT: F 516 GLU cc_start: 0.8010 (tp30) cc_final: 0.7646 (tp30) REVERT: F 521 ASN cc_start: 0.7052 (t0) cc_final: 0.6767 (t0) REVERT: F 534 GLU cc_start: 0.7690 (tp30) cc_final: 0.6964 (tp30) REVERT: F 538 LYS cc_start: 0.8497 (pttm) cc_final: 0.7951 (pttm) REVERT: F 545 LEU cc_start: 0.8719 (mm) cc_final: 0.8511 (mt) REVERT: F 607 GLU cc_start: 0.7977 (tt0) cc_final: 0.7744 (tt0) REVERT: F 616 MET cc_start: 0.8045 (ttp) cc_final: 0.7761 (ttp) REVERT: F 620 ILE cc_start: 0.7599 (tp) cc_final: 0.6659 (pt) REVERT: F 646 PHE cc_start: 0.5398 (m-80) cc_final: 0.5057 (m-80) REVERT: F 673 ILE cc_start: 0.7537 (mm) cc_final: 0.7324 (mm) REVERT: F 694 GLU cc_start: 0.6977 (tp30) cc_final: 0.6678 (tp30) REVERT: F 746 GLU cc_start: 0.8583 (pm20) cc_final: 0.7937 (pp20) REVERT: F 958 TRP cc_start: 0.8293 (m-10) cc_final: 0.8030 (m-10) REVERT: F 961 ASN cc_start: 0.8173 (m-40) cc_final: 0.7755 (m110) REVERT: G 15 ARG cc_start: 0.7516 (ptp-110) cc_final: 0.7254 (ptp-110) REVERT: G 71 GLU cc_start: 0.7156 (pm20) cc_final: 0.6374 (pm20) REVERT: G 72 TRP cc_start: 0.6752 (m100) cc_final: 0.6498 (m100) REVERT: G 75 MET cc_start: 0.7827 (tpt) cc_final: 0.7391 (tpt) REVERT: G 209 GLU cc_start: 0.8029 (pp20) cc_final: 0.7566 (tm-30) REVERT: H 65 ASN cc_start: 0.5195 (p0) cc_final: 0.4623 (p0) REVERT: H 70 LEU cc_start: 0.7486 (mt) cc_final: 0.6864 (mt) REVERT: H 206 MET cc_start: 0.5848 (tpt) cc_final: 0.5458 (tpt) REVERT: H 219 LYS cc_start: 0.8400 (tptp) cc_final: 0.8196 (tptt) REVERT: H 221 GLU cc_start: 0.6455 (pp20) cc_final: 0.6252 (pp20) outliers start: 11 outliers final: 2 residues processed: 869 average time/residue: 0.2373 time to fit residues: 329.4918 Evaluate side-chains 803 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 800 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 65 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 446 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 299 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 ASN ** E 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 609 HIS ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN ** F 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.209386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.167599 restraints weight = 81512.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.172690 restraints weight = 53032.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.176656 restraints weight = 37857.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.179280 restraints weight = 28757.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.181266 restraints weight = 23125.978| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 38368 Z= 0.157 Angle : 0.672 9.286 51708 Z= 0.361 Chirality : 0.046 0.240 5500 Planarity : 0.004 0.096 6636 Dihedral : 5.906 82.754 4984 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.71 % Favored : 90.09 % Rotamer: Outliers : 0.22 % Allowed : 5.24 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.12), residues: 4512 helix: -0.63 (0.11), residues: 2266 sheet: -0.84 (0.29), residues: 309 loop : -2.52 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 517 TYR 0.048 0.002 TYR B 455 PHE 0.046 0.002 PHE A 659 TRP 0.054 0.002 TRP E 919 HIS 0.015 0.001 HIS F 852 Details of bonding type rmsd covalent geometry : bond 0.00320 (38368) covalent geometry : angle 0.67250 (51708) hydrogen bonds : bond 0.04525 ( 1637) hydrogen bonds : angle 5.71447 ( 4638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 860 time to evaluate : 1.282 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 28 GLU cc_start: 0.8606 (pm20) cc_final: 0.8274 (pm20) REVERT: A 29 CYS cc_start: 0.8887 (m) cc_final: 0.8419 (t) REVERT: A 60 TRP cc_start: 0.7171 (p-90) cc_final: 0.6817 (p-90) REVERT: A 105 LYS cc_start: 0.7905 (mmtm) cc_final: 0.7496 (mmmm) REVERT: A 109 GLN cc_start: 0.7949 (tt0) cc_final: 0.7721 (tt0) REVERT: A 118 HIS cc_start: 0.6794 (m90) cc_final: 0.6201 (m90) REVERT: A 120 LYS cc_start: 0.8511 (mttt) cc_final: 0.8212 (mttt) REVERT: A 124 MET cc_start: 0.8378 (tpp) cc_final: 0.7076 (tpp) REVERT: A 125 ASN cc_start: 0.8767 (m110) cc_final: 0.8339 (p0) REVERT: A 128 HIS cc_start: 0.7630 (m-70) cc_final: 0.7069 (m-70) REVERT: A 137 LEU cc_start: 0.8716 (tp) cc_final: 0.8395 (tp) REVERT: A 144 LYS cc_start: 0.8454 (ptpp) cc_final: 0.8237 (pttp) REVERT: A 223 TYR cc_start: 0.7564 (m-80) cc_final: 0.7237 (m-80) REVERT: A 396 MET cc_start: 0.6749 (ptp) cc_final: 0.6158 (ptp) REVERT: A 421 MET cc_start: 0.4469 (mpp) cc_final: 0.4232 (mpp) REVERT: A 562 THR cc_start: 0.4286 (m) cc_final: 0.4059 (m) REVERT: A 583 VAL cc_start: 0.8793 (t) cc_final: 0.8542 (t) REVERT: A 594 PHE cc_start: 0.7603 (t80) cc_final: 0.7219 (t80) REVERT: A 609 HIS cc_start: 0.8604 (m-70) cc_final: 0.8349 (m-70) REVERT: A 616 MET cc_start: 0.8100 (tpt) cc_final: 0.7708 (tmm) REVERT: A 686 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 694 GLU cc_start: 0.6790 (mp0) cc_final: 0.6568 (mp0) REVERT: A 704 MET cc_start: 0.5500 (ttt) cc_final: 0.5151 (ttt) REVERT: A 711 GLN cc_start: 0.8262 (mp10) cc_final: 0.7880 (mm-40) REVERT: B 31 LYS cc_start: 0.8677 (tmmt) cc_final: 0.8425 (tmtt) REVERT: B 32 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 36 SER cc_start: 0.8103 (m) cc_final: 0.7520 (m) REVERT: B 118 HIS cc_start: 0.7850 (m-70) cc_final: 0.7416 (m-70) REVERT: B 119 ASP cc_start: 0.8599 (m-30) cc_final: 0.8058 (m-30) REVERT: B 122 LEU cc_start: 0.8938 (mt) cc_final: 0.8608 (pp) REVERT: B 179 LYS cc_start: 0.7270 (mppt) cc_final: 0.6901 (mmtt) REVERT: B 188 ASP cc_start: 0.8107 (t0) cc_final: 0.7885 (t0) REVERT: B 190 TYR cc_start: 0.8033 (m-10) cc_final: 0.7639 (m-10) REVERT: B 193 TYR cc_start: 0.7065 (t80) cc_final: 0.6503 (t80) REVERT: B 197 TYR cc_start: 0.7530 (p90) cc_final: 0.7228 (p90) REVERT: B 228 LEU cc_start: 0.8153 (mt) cc_final: 0.7631 (mt) REVERT: B 258 LEU cc_start: 0.8627 (mt) cc_final: 0.8319 (mt) REVERT: B 421 MET cc_start: 0.6115 (mtm) cc_final: 0.5663 (mtm) REVERT: B 435 ASP cc_start: 0.8369 (m-30) cc_final: 0.8080 (m-30) REVERT: B 437 LYS cc_start: 0.8702 (mmtp) cc_final: 0.8444 (mmmm) REVERT: B 441 PHE cc_start: 0.8515 (m-10) cc_final: 0.8295 (m-80) REVERT: B 442 LEU cc_start: 0.8738 (mt) cc_final: 0.8455 (mt) REVERT: B 478 ARG cc_start: 0.7973 (ptp90) cc_final: 0.7568 (ptt-90) REVERT: B 480 ARG cc_start: 0.8200 (mmt180) cc_final: 0.7504 (mmm-85) REVERT: B 481 ILE cc_start: 0.8707 (mm) cc_final: 0.8344 (mm) REVERT: B 482 TYR cc_start: 0.7249 (t80) cc_final: 0.6889 (t80) REVERT: B 522 PHE cc_start: 0.7638 (t80) cc_final: 0.7432 (t80) REVERT: B 523 ASN cc_start: 0.8044 (m-40) cc_final: 0.7773 (m-40) REVERT: B 524 ILE cc_start: 0.8133 (pt) cc_final: 0.7530 (mm) REVERT: B 560 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 587 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7781 (mtt180) REVERT: B 593 ARG cc_start: 0.7974 (ptt180) cc_final: 0.7717 (ptt180) REVERT: B 597 GLU cc_start: 0.8214 (tt0) cc_final: 0.7837 (tt0) REVERT: B 614 ASN cc_start: 0.7651 (m-40) cc_final: 0.7130 (m-40) REVERT: B 618 LEU cc_start: 0.8004 (mm) cc_final: 0.7779 (mm) REVERT: B 652 PHE cc_start: 0.6756 (t80) cc_final: 0.6345 (t80) REVERT: B 757 TRP cc_start: 0.6327 (m-10) cc_final: 0.5995 (m-10) REVERT: D 176 ARG cc_start: 0.4341 (ttp80) cc_final: 0.1450 (mmm-85) REVERT: E 92 TYR cc_start: 0.7489 (t80) cc_final: 0.6971 (t80) REVERT: E 124 MET cc_start: 0.7805 (pmm) cc_final: 0.6680 (ppp) REVERT: E 125 ASN cc_start: 0.8394 (t0) cc_final: 0.8184 (t0) REVERT: E 158 VAL cc_start: 0.8194 (t) cc_final: 0.7914 (p) REVERT: E 165 ARG cc_start: 0.7867 (mmt90) cc_final: 0.7626 (mtt-85) REVERT: E 307 GLU cc_start: 0.7364 (tt0) cc_final: 0.6856 (tt0) REVERT: E 375 LYS cc_start: 0.8813 (tmmt) cc_final: 0.8304 (tmtt) REVERT: E 379 GLU cc_start: 0.8651 (pt0) cc_final: 0.8129 (mp0) REVERT: E 419 ASP cc_start: 0.8133 (p0) cc_final: 0.7779 (m-30) REVERT: E 421 MET cc_start: 0.7977 (mmt) cc_final: 0.7411 (mmt) REVERT: E 437 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7854 (mmtm) REVERT: E 448 TRP cc_start: 0.8194 (m-90) cc_final: 0.7623 (m-90) REVERT: E 492 PHE cc_start: 0.7626 (m-80) cc_final: 0.7310 (m-80) REVERT: E 527 LEU cc_start: 0.8678 (tp) cc_final: 0.8338 (tp) REVERT: E 543 GLU cc_start: 0.6578 (pm20) cc_final: 0.6194 (pm20) REVERT: E 564 LYS cc_start: 0.8265 (tptm) cc_final: 0.7690 (mttp) REVERT: E 568 GLU cc_start: 0.8520 (mp0) cc_final: 0.8258 (mm-30) REVERT: E 590 ASP cc_start: 0.7852 (t0) cc_final: 0.7621 (t0) REVERT: E 607 GLU cc_start: 0.7823 (pm20) cc_final: 0.7494 (pm20) REVERT: E 634 LEU cc_start: 0.8126 (mm) cc_final: 0.7758 (tt) REVERT: E 636 PHE cc_start: 0.8137 (t80) cc_final: 0.7618 (t80) REVERT: E 645 PHE cc_start: 0.7890 (t80) cc_final: 0.6970 (t80) REVERT: E 651 ASP cc_start: 0.8202 (m-30) cc_final: 0.7955 (m-30) REVERT: E 674 ASP cc_start: 0.7566 (m-30) cc_final: 0.7289 (m-30) REVERT: E 693 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: E 705 ASN cc_start: 0.8284 (p0) cc_final: 0.7997 (p0) REVERT: E 712 PHE cc_start: 0.7496 (m-10) cc_final: 0.7047 (m-10) REVERT: E 722 PHE cc_start: 0.8105 (t80) cc_final: 0.7863 (t80) REVERT: E 744 PHE cc_start: 0.8217 (t80) cc_final: 0.7918 (t80) REVERT: E 832 GLN cc_start: 0.8215 (pm20) cc_final: 0.7933 (pm20) REVERT: E 913 MET cc_start: 0.7447 (mmm) cc_final: 0.6674 (mmm) REVERT: E 974 LYS cc_start: 0.9201 (tppt) cc_final: 0.8754 (tppt) REVERT: F 25 ASN cc_start: 0.8919 (p0) cc_final: 0.8630 (p0) REVERT: F 98 MET cc_start: 0.8506 (mmp) cc_final: 0.8261 (mmp) REVERT: F 105 LYS cc_start: 0.7527 (tptt) cc_final: 0.7115 (tptt) REVERT: F 120 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8728 (mmtt) REVERT: F 201 SER cc_start: 0.8074 (p) cc_final: 0.7715 (m) REVERT: F 242 LYS cc_start: 0.8116 (ptmm) cc_final: 0.7673 (ptmt) REVERT: F 277 SER cc_start: 0.8485 (t) cc_final: 0.7809 (p) REVERT: F 284 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7387 (tm-30) REVERT: F 290 MET cc_start: 0.8548 (mmp) cc_final: 0.8250 (mmp) REVERT: F 329 ASP cc_start: 0.8095 (m-30) cc_final: 0.7785 (m-30) REVERT: F 336 TYR cc_start: 0.7612 (m-80) cc_final: 0.7204 (m-80) REVERT: F 422 LYS cc_start: 0.8728 (tmmt) cc_final: 0.8223 (tptt) REVERT: F 426 GLU cc_start: 0.7555 (pm20) cc_final: 0.7293 (pm20) REVERT: F 437 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8421 (mmmt) REVERT: F 471 TYR cc_start: 0.6549 (t80) cc_final: 0.5939 (t80) REVERT: F 487 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7125 (tm-30) REVERT: F 491 GLN cc_start: 0.6933 (tt0) cc_final: 0.6169 (tt0) REVERT: F 516 GLU cc_start: 0.8006 (tp30) cc_final: 0.7708 (tp30) REVERT: F 518 GLU cc_start: 0.8094 (tp30) cc_final: 0.7634 (tp30) REVERT: F 519 MET cc_start: 0.7562 (mmm) cc_final: 0.7255 (mmm) REVERT: F 534 GLU cc_start: 0.7767 (tp30) cc_final: 0.6562 (tp30) REVERT: F 535 PHE cc_start: 0.7429 (t80) cc_final: 0.7184 (t80) REVERT: F 538 LYS cc_start: 0.8515 (pttm) cc_final: 0.7534 (pttt) REVERT: F 545 LEU cc_start: 0.8770 (mm) cc_final: 0.8535 (mp) REVERT: F 576 PHE cc_start: 0.5658 (m-10) cc_final: 0.4684 (m-10) REVERT: F 607 GLU cc_start: 0.7983 (tt0) cc_final: 0.7753 (tt0) REVERT: F 620 ILE cc_start: 0.7445 (tp) cc_final: 0.7176 (tt) REVERT: F 648 GLU cc_start: 0.7189 (mp0) cc_final: 0.6884 (mp0) REVERT: F 694 GLU cc_start: 0.7144 (tp30) cc_final: 0.6779 (tp30) REVERT: F 746 GLU cc_start: 0.8109 (pm20) cc_final: 0.7714 (pp20) REVERT: F 834 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7878 (mp10) REVERT: F 940 TYR cc_start: 0.7859 (t80) cc_final: 0.7638 (t80) REVERT: F 943 PHE cc_start: 0.7497 (m-80) cc_final: 0.6960 (m-80) REVERT: F 958 TRP cc_start: 0.8507 (m-10) cc_final: 0.8177 (m-10) REVERT: F 961 ASN cc_start: 0.8309 (m-40) cc_final: 0.7961 (m110) REVERT: G 195 PHE cc_start: 0.7603 (m-80) cc_final: 0.7332 (m-80) REVERT: G 206 MET cc_start: 0.7239 (mtm) cc_final: 0.6563 (mtm) REVERT: G 209 GLU cc_start: 0.7796 (pp20) cc_final: 0.7484 (tm-30) REVERT: H 65 ASN cc_start: 0.5184 (p0) cc_final: 0.4490 (p0) REVERT: H 70 LEU cc_start: 0.7375 (mt) cc_final: 0.6901 (mt) REVERT: H 192 TYR cc_start: 0.7716 (m-80) cc_final: 0.7347 (m-80) REVERT: H 206 MET cc_start: 0.6108 (tpt) cc_final: 0.5572 (tpt) REVERT: H 219 LYS cc_start: 0.8465 (tptp) cc_final: 0.8186 (tptt) outliers start: 9 outliers final: 1 residues processed: 866 average time/residue: 0.2250 time to fit residues: 312.0844 Evaluate side-chains 801 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 799 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 16 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 445 optimal weight: 4.9990 chunk 164 optimal weight: 0.0770 chunk 217 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN E 67 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 609 HIS ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 GLN ** F 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.207730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.165063 restraints weight = 82258.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.170292 restraints weight = 54192.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.174040 restraints weight = 38557.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.176736 restraints weight = 29367.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.178699 restraints weight = 23646.024| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38368 Z= 0.165 Angle : 0.668 10.512 51708 Z= 0.358 Chirality : 0.046 0.268 5500 Planarity : 0.004 0.098 6636 Dihedral : 5.856 82.831 4984 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.64 % Favored : 90.16 % Rotamer: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.12), residues: 4512 helix: -0.57 (0.11), residues: 2271 sheet: -0.95 (0.29), residues: 297 loop : -2.49 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 502 TYR 0.028 0.002 TYR B 134 PHE 0.057 0.002 PHE A 659 TRP 0.041 0.002 TRP B 601 HIS 0.012 0.001 HIS F 852 Details of bonding type rmsd covalent geometry : bond 0.00333 (38368) covalent geometry : angle 0.66754 (51708) hydrogen bonds : bond 0.04412 ( 1637) hydrogen bonds : angle 5.62551 ( 4638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 876 time to evaluate : 1.403 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: symmetry clash revert: symmetry clash REVERT: A 29 CYS cc_start: 0.8943 (m) cc_final: 0.8414 (t) REVERT: A 60 TRP cc_start: 0.7255 (p-90) cc_final: 0.6902 (p-90) REVERT: A 105 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7561 (mmmm) REVERT: A 109 GLN cc_start: 0.7930 (tt0) cc_final: 0.7680 (tt0) REVERT: A 120 LYS cc_start: 0.8551 (mttt) cc_final: 0.8257 (mttt) REVERT: A 124 MET cc_start: 0.8454 (tpp) cc_final: 0.7849 (tpp) REVERT: A 125 ASN cc_start: 0.8849 (m110) cc_final: 0.8617 (m110) REVERT: A 128 HIS cc_start: 0.7703 (m-70) cc_final: 0.7045 (m-70) REVERT: A 144 LYS cc_start: 0.8462 (ptpp) cc_final: 0.8126 (pttt) REVERT: A 176 LYS cc_start: 0.8214 (mttt) cc_final: 0.7933 (mmmt) REVERT: A 190 TYR cc_start: 0.7043 (m-80) cc_final: 0.6510 (m-80) REVERT: A 197 TYR cc_start: 0.7997 (m-10) cc_final: 0.7774 (m-10) REVERT: A 286 TYR cc_start: 0.6508 (m-10) cc_final: 0.6137 (m-10) REVERT: A 329 ASP cc_start: 0.7893 (t0) cc_final: 0.7670 (t0) REVERT: A 393 VAL cc_start: 0.6748 (t) cc_final: 0.6419 (p) REVERT: A 396 MET cc_start: 0.6936 (ptp) cc_final: 0.6291 (ptp) REVERT: A 421 MET cc_start: 0.4537 (mpp) cc_final: 0.4299 (mpp) REVERT: A 562 THR cc_start: 0.4389 (m) cc_final: 0.4135 (m) REVERT: A 583 VAL cc_start: 0.8830 (t) cc_final: 0.8491 (t) REVERT: A 587 ARG cc_start: 0.8790 (mtp180) cc_final: 0.8586 (mtp180) REVERT: A 588 LEU cc_start: 0.8298 (mt) cc_final: 0.7795 (mt) REVERT: A 594 PHE cc_start: 0.7724 (t80) cc_final: 0.7220 (t80) REVERT: A 609 HIS cc_start: 0.8654 (m-70) cc_final: 0.8311 (m-70) REVERT: A 616 MET cc_start: 0.8051 (tpt) cc_final: 0.7801 (tmm) REVERT: A 671 CYS cc_start: 0.8306 (p) cc_final: 0.7621 (t) REVERT: A 686 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 694 GLU cc_start: 0.6881 (mp0) cc_final: 0.6637 (mp0) REVERT: A 704 MET cc_start: 0.5343 (ttt) cc_final: 0.5015 (ttt) REVERT: A 711 GLN cc_start: 0.8256 (mp10) cc_final: 0.7819 (mm-40) REVERT: A 936 MET cc_start: 0.2482 (mmp) cc_final: 0.0280 (ttm) REVERT: B 28 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8126 (pt0) REVERT: B 31 LYS cc_start: 0.8683 (tmmt) cc_final: 0.8482 (ptmm) REVERT: B 32 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 36 SER cc_start: 0.8161 (m) cc_final: 0.7507 (m) REVERT: B 118 HIS cc_start: 0.7952 (m-70) cc_final: 0.7587 (m-70) REVERT: B 137 LEU cc_start: 0.8056 (tt) cc_final: 0.7794 (pp) REVERT: B 179 LYS cc_start: 0.7342 (mppt) cc_final: 0.6993 (mmtt) REVERT: B 183 VAL cc_start: 0.8062 (t) cc_final: 0.7859 (m) REVERT: B 190 TYR cc_start: 0.8018 (m-10) cc_final: 0.7682 (m-10) REVERT: B 193 TYR cc_start: 0.7136 (t80) cc_final: 0.6614 (t80) REVERT: B 197 TYR cc_start: 0.7576 (p90) cc_final: 0.7235 (p90) REVERT: B 228 LEU cc_start: 0.8175 (mt) cc_final: 0.7618 (mt) REVERT: B 229 LEU cc_start: 0.8686 (mt) cc_final: 0.8346 (pp) REVERT: B 258 LEU cc_start: 0.8671 (mt) cc_final: 0.8358 (mt) REVERT: B 327 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8175 (mmtp) REVERT: B 385 PHE cc_start: 0.8467 (t80) cc_final: 0.8258 (t80) REVERT: B 421 MET cc_start: 0.6235 (mtm) cc_final: 0.5642 (mtm) REVERT: B 435 ASP cc_start: 0.8407 (m-30) cc_final: 0.8103 (m-30) REVERT: B 437 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8421 (mmmm) REVERT: B 441 PHE cc_start: 0.8583 (m-10) cc_final: 0.8339 (m-80) REVERT: B 478 ARG cc_start: 0.7979 (ptp90) cc_final: 0.7655 (ptt180) REVERT: B 480 ARG cc_start: 0.8144 (mmt180) cc_final: 0.7618 (mmm-85) REVERT: B 481 ILE cc_start: 0.8703 (mm) cc_final: 0.8394 (mm) REVERT: B 482 TYR cc_start: 0.7321 (t80) cc_final: 0.6848 (t80) REVERT: B 522 PHE cc_start: 0.7702 (t80) cc_final: 0.7233 (t80) REVERT: B 524 ILE cc_start: 0.8194 (pt) cc_final: 0.7590 (mm) REVERT: B 531 MET cc_start: 0.3974 (ppp) cc_final: 0.3668 (ppp) REVERT: B 557 LYS cc_start: 0.9152 (mmtm) cc_final: 0.8802 (mmtp) REVERT: B 587 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7588 (mtt180) REVERT: B 593 ARG cc_start: 0.7971 (ptt180) cc_final: 0.7523 (ptt180) REVERT: B 614 ASN cc_start: 0.7688 (m-40) cc_final: 0.7207 (m-40) REVERT: B 757 TRP cc_start: 0.6495 (m-10) cc_final: 0.6081 (m-10) REVERT: E 45 PHE cc_start: 0.7450 (m-80) cc_final: 0.7198 (m-80) REVERT: E 92 TYR cc_start: 0.7581 (t80) cc_final: 0.7002 (t80) REVERT: E 118 HIS cc_start: 0.7982 (m90) cc_final: 0.7607 (m90) REVERT: E 124 MET cc_start: 0.7813 (pmm) cc_final: 0.6966 (ppp) REVERT: E 125 ASN cc_start: 0.8516 (t0) cc_final: 0.8194 (t0) REVERT: E 158 VAL cc_start: 0.8242 (t) cc_final: 0.7927 (p) REVERT: E 195 GLN cc_start: 0.6288 (OUTLIER) cc_final: 0.5895 (tp40) REVERT: E 197 TYR cc_start: 0.7665 (m-80) cc_final: 0.7164 (m-80) REVERT: E 270 ASP cc_start: 0.7663 (t0) cc_final: 0.7358 (t0) REVERT: E 307 GLU cc_start: 0.7096 (tt0) cc_final: 0.6555 (tt0) REVERT: E 375 LYS cc_start: 0.8809 (tmmt) cc_final: 0.8235 (tmtt) REVERT: E 379 GLU cc_start: 0.8644 (pt0) cc_final: 0.8137 (mp0) REVERT: E 419 ASP cc_start: 0.8167 (p0) cc_final: 0.7827 (m-30) REVERT: E 421 MET cc_start: 0.8035 (mmt) cc_final: 0.7319 (mmt) REVERT: E 448 TRP cc_start: 0.8238 (m-90) cc_final: 0.7726 (m-90) REVERT: E 451 SER cc_start: 0.8699 (p) cc_final: 0.8390 (p) REVERT: E 453 ASP cc_start: 0.8302 (m-30) cc_final: 0.8029 (m-30) REVERT: E 476 ILE cc_start: 0.7461 (mm) cc_final: 0.7125 (mm) REVERT: E 478 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7778 (ttp-110) REVERT: E 487 GLN cc_start: 0.6844 (pt0) cc_final: 0.6640 (tt0) REVERT: E 492 PHE cc_start: 0.7704 (m-80) cc_final: 0.7351 (m-80) REVERT: E 527 LEU cc_start: 0.8769 (tp) cc_final: 0.8361 (tp) REVERT: E 550 PHE cc_start: 0.6632 (p90) cc_final: 0.6401 (p90) REVERT: E 557 LYS cc_start: 0.7886 (mmmm) cc_final: 0.7647 (mppt) REVERT: E 564 LYS cc_start: 0.8200 (tptm) cc_final: 0.7591 (mttp) REVERT: E 568 GLU cc_start: 0.8529 (mp0) cc_final: 0.8144 (mp0) REVERT: E 590 ASP cc_start: 0.7827 (t0) cc_final: 0.7614 (t0) REVERT: E 607 GLU cc_start: 0.7809 (pm20) cc_final: 0.7484 (pm20) REVERT: E 636 PHE cc_start: 0.8111 (t80) cc_final: 0.7683 (t80) REVERT: E 645 PHE cc_start: 0.7962 (t80) cc_final: 0.7061 (t80) REVERT: E 651 ASP cc_start: 0.8162 (m-30) cc_final: 0.7959 (m-30) REVERT: E 663 ASP cc_start: 0.8220 (m-30) cc_final: 0.7895 (m-30) REVERT: E 666 ASN cc_start: 0.7860 (t0) cc_final: 0.7555 (t0) REVERT: E 674 ASP cc_start: 0.7643 (m-30) cc_final: 0.7363 (m-30) REVERT: E 691 ILE cc_start: 0.8423 (mm) cc_final: 0.7912 (mm) REVERT: E 695 ILE cc_start: 0.8120 (pt) cc_final: 0.7743 (pt) REVERT: E 705 ASN cc_start: 0.8207 (p0) cc_final: 0.7912 (p0) REVERT: E 706 VAL cc_start: 0.8157 (t) cc_final: 0.7856 (p) REVERT: E 707 VAL cc_start: 0.8527 (m) cc_final: 0.7922 (t) REVERT: E 712 PHE cc_start: 0.7679 (m-10) cc_final: 0.7473 (m-10) REVERT: E 722 PHE cc_start: 0.8217 (t80) cc_final: 0.7769 (t80) REVERT: E 744 PHE cc_start: 0.8326 (t80) cc_final: 0.7895 (t80) REVERT: E 775 ILE cc_start: 0.8352 (mt) cc_final: 0.8134 (mt) REVERT: E 832 GLN cc_start: 0.8241 (pm20) cc_final: 0.7957 (pm20) REVERT: E 837 PHE cc_start: 0.8526 (t80) cc_final: 0.8321 (t80) REVERT: E 913 MET cc_start: 0.7508 (mmm) cc_final: 0.6752 (mmm) REVERT: E 966 LEU cc_start: 0.7821 (tp) cc_final: 0.7526 (tp) REVERT: E 974 LYS cc_start: 0.9212 (tppt) cc_final: 0.8770 (tppt) REVERT: F 25 ASN cc_start: 0.8930 (p0) cc_final: 0.8634 (p0) REVERT: F 73 SER cc_start: 0.8485 (p) cc_final: 0.8273 (t) REVERT: F 98 MET cc_start: 0.8549 (mmp) cc_final: 0.8332 (mmp) REVERT: F 105 LYS cc_start: 0.7523 (tptt) cc_final: 0.7114 (tptt) REVERT: F 201 SER cc_start: 0.8057 (p) cc_final: 0.7702 (m) REVERT: F 228 LEU cc_start: 0.8167 (tp) cc_final: 0.7896 (tp) REVERT: F 242 LYS cc_start: 0.8194 (ptmm) cc_final: 0.7627 (ptmm) REVERT: F 291 ASP cc_start: 0.8281 (m-30) cc_final: 0.8034 (m-30) REVERT: F 313 TYR cc_start: 0.7052 (t80) cc_final: 0.6658 (t80) REVERT: F 329 ASP cc_start: 0.8161 (m-30) cc_final: 0.7767 (m-30) REVERT: F 336 TYR cc_start: 0.7675 (m-80) cc_final: 0.7261 (m-80) REVERT: F 376 LYS cc_start: 0.8223 (tptp) cc_final: 0.7133 (tptp) REVERT: F 419 ASP cc_start: 0.8061 (p0) cc_final: 0.7848 (p0) REVERT: F 421 MET cc_start: 0.8718 (ptt) cc_final: 0.8258 (ptp) REVERT: F 422 LYS cc_start: 0.8706 (tmmt) cc_final: 0.8312 (tptt) REVERT: F 442 LEU cc_start: 0.8681 (mt) cc_final: 0.8473 (mt) REVERT: F 483 GLN cc_start: 0.8846 (mt0) cc_final: 0.8296 (mt0) REVERT: F 487 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7147 (tm-30) REVERT: F 491 GLN cc_start: 0.7060 (tt0) cc_final: 0.6309 (tt0) REVERT: F 516 GLU cc_start: 0.8112 (tp30) cc_final: 0.7728 (tp30) REVERT: F 518 GLU cc_start: 0.8082 (tp30) cc_final: 0.7634 (tp30) REVERT: F 519 MET cc_start: 0.7667 (mmm) cc_final: 0.7375 (mmm) REVERT: F 534 GLU cc_start: 0.7841 (tp30) cc_final: 0.7447 (tp30) REVERT: F 543 GLU cc_start: 0.8468 (pp20) cc_final: 0.8170 (pp20) REVERT: F 545 LEU cc_start: 0.8795 (mm) cc_final: 0.8438 (mp) REVERT: F 555 THR cc_start: 0.7845 (m) cc_final: 0.7599 (p) REVERT: F 576 PHE cc_start: 0.5673 (m-10) cc_final: 0.4299 (m-80) REVERT: F 607 GLU cc_start: 0.7957 (tt0) cc_final: 0.7727 (tt0) REVERT: F 616 MET cc_start: 0.8110 (ttp) cc_final: 0.7786 (ttp) REVERT: F 620 ILE cc_start: 0.7495 (tp) cc_final: 0.6407 (pt) REVERT: F 674 ASP cc_start: 0.7860 (m-30) cc_final: 0.7572 (p0) REVERT: F 694 GLU cc_start: 0.7157 (tp30) cc_final: 0.6840 (tp30) REVERT: F 833 LYS cc_start: 0.8493 (pttt) cc_final: 0.8291 (pttt) REVERT: F 942 PHE cc_start: 0.8164 (t80) cc_final: 0.7691 (t80) REVERT: F 943 PHE cc_start: 0.7509 (m-80) cc_final: 0.6692 (m-80) REVERT: F 958 TRP cc_start: 0.8600 (m-10) cc_final: 0.8294 (m-10) REVERT: F 961 ASN cc_start: 0.8356 (m-40) cc_final: 0.8011 (m-40) REVERT: G 15 ARG cc_start: 0.7787 (ptp-110) cc_final: 0.7551 (ptp-110) REVERT: G 61 LEU cc_start: 0.8104 (mp) cc_final: 0.7779 (mp) REVERT: G 71 GLU cc_start: 0.6502 (pm20) cc_final: 0.5616 (pm20) REVERT: G 195 PHE cc_start: 0.7668 (m-80) cc_final: 0.7398 (m-80) REVERT: G 201 SER cc_start: 0.6915 (p) cc_final: 0.6489 (p) REVERT: G 206 MET cc_start: 0.7294 (mtm) cc_final: 0.6737 (mtm) REVERT: G 209 GLU cc_start: 0.7736 (pp20) cc_final: 0.7162 (tm-30) REVERT: G 210 ASN cc_start: 0.8431 (m110) cc_final: 0.8134 (m-40) REVERT: G 219 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7983 (mtmm) REVERT: H 31 SER cc_start: 0.8008 (t) cc_final: 0.7783 (p) REVERT: H 65 ASN cc_start: 0.5444 (p0) cc_final: 0.4704 (p0) REVERT: H 70 LEU cc_start: 0.7344 (mt) cc_final: 0.7006 (mt) REVERT: H 192 TYR cc_start: 0.7713 (m-80) cc_final: 0.7319 (m-80) REVERT: H 206 MET cc_start: 0.6164 (tpt) cc_final: 0.5430 (tpt) REVERT: H 219 LYS cc_start: 0.8415 (tptp) cc_final: 0.7958 (tptt) outliers start: 6 outliers final: 1 residues processed: 878 average time/residue: 0.2608 time to fit residues: 364.8065 Evaluate side-chains 824 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 822 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 84 optimal weight: 7.9990 chunk 342 optimal weight: 0.9980 chunk 448 optimal weight: 0.6980 chunk 311 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 388 optimal weight: 0.5980 chunk 266 optimal weight: 0.8980 chunk 391 optimal weight: 0.9990 chunk 401 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 609 HIS E 797 ASN ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 ASN F 681 GLN F 711 GLN ** F 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 881 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.208475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.165999 restraints weight = 81786.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.171197 restraints weight = 53519.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.174923 restraints weight = 38134.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.177595 restraints weight = 29113.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.179548 restraints weight = 23469.491| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38368 Z= 0.146 Angle : 0.659 11.394 51708 Z= 0.350 Chirality : 0.045 0.282 5500 Planarity : 0.005 0.159 6636 Dihedral : 5.739 83.518 4984 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.20 % Favored : 90.56 % Rotamer: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.12), residues: 4512 helix: -0.45 (0.11), residues: 2269 sheet: -1.06 (0.29), residues: 299 loop : -2.45 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 819 TYR 0.027 0.001 TYR B 134 PHE 0.053 0.002 PHE A 659 TRP 0.061 0.002 TRP E 919 HIS 0.022 0.001 HIS F 852 Details of bonding type rmsd covalent geometry : bond 0.00304 (38368) covalent geometry : angle 0.65935 (51708) hydrogen bonds : bond 0.04197 ( 1637) hydrogen bonds : angle 5.47598 ( 4638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 862 time to evaluate : 1.528 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: A 28 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: A 29 CYS cc_start: 0.8940 (m) cc_final: 0.8439 (t) REVERT: A 60 TRP cc_start: 0.7238 (p-90) cc_final: 0.6881 (p-90) REVERT: A 105 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7601 (mmmm) REVERT: A 109 GLN cc_start: 0.7907 (tt0) cc_final: 0.7687 (tt0) REVERT: A 120 LYS cc_start: 0.8530 (mttt) cc_final: 0.8215 (mttt) REVERT: A 124 MET cc_start: 0.8431 (tpp) cc_final: 0.7726 (tpp) REVERT: A 128 HIS cc_start: 0.7659 (m-70) cc_final: 0.7013 (m-70) REVERT: A 144 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8154 (pttt) REVERT: A 190 TYR cc_start: 0.7049 (m-80) cc_final: 0.6504 (m-80) REVERT: A 197 TYR cc_start: 0.8041 (m-10) cc_final: 0.7809 (m-10) REVERT: A 223 TYR cc_start: 0.7754 (m-80) cc_final: 0.7404 (m-80) REVERT: A 329 ASP cc_start: 0.7905 (t0) cc_final: 0.7624 (t0) REVERT: A 393 VAL cc_start: 0.6828 (t) cc_final: 0.6508 (p) REVERT: A 396 MET cc_start: 0.6926 (ptp) cc_final: 0.6266 (ptp) REVERT: A 421 MET cc_start: 0.4494 (mpp) cc_final: 0.4246 (mpp) REVERT: A 482 TYR cc_start: 0.3681 (t80) cc_final: 0.3306 (t80) REVERT: A 583 VAL cc_start: 0.8769 (t) cc_final: 0.8449 (t) REVERT: A 586 LEU cc_start: 0.8956 (pp) cc_final: 0.8315 (pp) REVERT: A 587 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8588 (mtp180) REVERT: A 588 LEU cc_start: 0.8267 (mt) cc_final: 0.7765 (mt) REVERT: A 589 TYR cc_start: 0.7954 (m-80) cc_final: 0.7227 (m-80) REVERT: A 594 PHE cc_start: 0.7641 (t80) cc_final: 0.7270 (t80) REVERT: A 609 HIS cc_start: 0.8622 (m-70) cc_final: 0.8294 (m-70) REVERT: A 613 ARG cc_start: 0.8305 (mmp80) cc_final: 0.7902 (mmp80) REVERT: A 616 MET cc_start: 0.7945 (tpt) cc_final: 0.7713 (tmm) REVERT: A 671 CYS cc_start: 0.8251 (p) cc_final: 0.7550 (t) REVERT: A 686 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7932 (mm-30) REVERT: A 694 GLU cc_start: 0.6905 (mp0) cc_final: 0.6635 (mp0) REVERT: A 704 MET cc_start: 0.5335 (ttt) cc_final: 0.5004 (ttt) REVERT: A 711 GLN cc_start: 0.8278 (mp10) cc_final: 0.7816 (mm-40) REVERT: A 936 MET cc_start: 0.2805 (mmp) cc_final: 0.0727 (ttm) REVERT: B 28 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8128 (pt0) REVERT: B 32 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 36 SER cc_start: 0.8125 (m) cc_final: 0.7602 (m) REVERT: B 118 HIS cc_start: 0.7919 (m-70) cc_final: 0.7550 (m-70) REVERT: B 135 ASP cc_start: 0.8123 (m-30) cc_final: 0.7897 (m-30) REVERT: B 136 ASN cc_start: 0.8418 (p0) cc_final: 0.8212 (p0) REVERT: B 137 LEU cc_start: 0.8143 (tt) cc_final: 0.7902 (tt) REVERT: B 147 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7503 (mmtm) REVERT: B 179 LYS cc_start: 0.7303 (mppt) cc_final: 0.6958 (mmtt) REVERT: B 187 GLU cc_start: 0.7607 (pp20) cc_final: 0.7398 (pp20) REVERT: B 190 TYR cc_start: 0.8066 (m-10) cc_final: 0.7724 (m-10) REVERT: B 191 LEU cc_start: 0.8530 (mt) cc_final: 0.8308 (mt) REVERT: B 197 TYR cc_start: 0.7616 (p90) cc_final: 0.7209 (p90) REVERT: B 228 LEU cc_start: 0.8227 (mt) cc_final: 0.7663 (mt) REVERT: B 229 LEU cc_start: 0.8683 (mt) cc_final: 0.8366 (pp) REVERT: B 258 LEU cc_start: 0.8668 (mt) cc_final: 0.8316 (mt) REVERT: B 327 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8319 (mmtp) REVERT: B 385 PHE cc_start: 0.8437 (t80) cc_final: 0.8236 (t80) REVERT: B 421 MET cc_start: 0.6246 (mtm) cc_final: 0.5699 (mtm) REVERT: B 435 ASP cc_start: 0.8384 (m-30) cc_final: 0.8036 (m-30) REVERT: B 437 LYS cc_start: 0.8695 (mmtp) cc_final: 0.8326 (mmmm) REVERT: B 441 PHE cc_start: 0.8547 (m-10) cc_final: 0.8265 (m-80) REVERT: B 442 LEU cc_start: 0.8670 (mt) cc_final: 0.8239 (mt) REVERT: B 472 TYR cc_start: 0.7461 (t80) cc_final: 0.7045 (t80) REVERT: B 478 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7624 (ptt180) REVERT: B 480 ARG cc_start: 0.8103 (mmt180) cc_final: 0.7613 (mmm-85) REVERT: B 481 ILE cc_start: 0.8715 (mm) cc_final: 0.8385 (mm) REVERT: B 482 TYR cc_start: 0.7300 (t80) cc_final: 0.6834 (t80) REVERT: B 522 PHE cc_start: 0.7721 (t80) cc_final: 0.7237 (t80) REVERT: B 524 ILE cc_start: 0.8181 (pt) cc_final: 0.7544 (mm) REVERT: B 531 MET cc_start: 0.4004 (ppp) cc_final: 0.3446 (ppp) REVERT: B 557 LYS cc_start: 0.9153 (mmtm) cc_final: 0.8844 (mmmm) REVERT: B 560 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7379 (tm-30) REVERT: B 569 MET cc_start: 0.6609 (tmm) cc_final: 0.6246 (tmm) REVERT: B 587 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7654 (mtt180) REVERT: B 593 ARG cc_start: 0.7939 (ptt180) cc_final: 0.7486 (ptt180) REVERT: B 614 ASN cc_start: 0.7705 (m-40) cc_final: 0.7289 (m-40) REVERT: B 757 TRP cc_start: 0.6483 (m-10) cc_final: 0.6174 (m-10) REVERT: E 92 TYR cc_start: 0.7483 (t80) cc_final: 0.6967 (t80) REVERT: E 118 HIS cc_start: 0.7854 (m90) cc_final: 0.7582 (m90) REVERT: E 158 VAL cc_start: 0.8216 (t) cc_final: 0.7886 (p) REVERT: E 197 TYR cc_start: 0.7666 (m-80) cc_final: 0.7158 (m-80) REVERT: E 307 GLU cc_start: 0.7203 (tt0) cc_final: 0.6621 (tt0) REVERT: E 309 ILE cc_start: 0.8386 (pt) cc_final: 0.8135 (mp) REVERT: E 341 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 343 ASN cc_start: 0.8825 (p0) cc_final: 0.8527 (p0) REVERT: E 373 LEU cc_start: 0.7612 (tp) cc_final: 0.7291 (tp) REVERT: E 378 TYR cc_start: 0.7753 (m-10) cc_final: 0.7403 (m-80) REVERT: E 419 ASP cc_start: 0.8128 (p0) cc_final: 0.7768 (m-30) REVERT: E 421 MET cc_start: 0.8038 (mmt) cc_final: 0.7270 (mmt) REVERT: E 422 LYS cc_start: 0.8658 (tppt) cc_final: 0.8266 (tppt) REVERT: E 448 TRP cc_start: 0.8176 (m-90) cc_final: 0.7691 (m-90) REVERT: E 451 SER cc_start: 0.8684 (p) cc_final: 0.8360 (p) REVERT: E 453 ASP cc_start: 0.8254 (m-30) cc_final: 0.7981 (m-30) REVERT: E 476 ILE cc_start: 0.7504 (mm) cc_final: 0.7097 (mm) REVERT: E 487 GLN cc_start: 0.6839 (pt0) cc_final: 0.6566 (tt0) REVERT: E 508 THR cc_start: 0.7793 (p) cc_final: 0.6229 (p) REVERT: E 527 LEU cc_start: 0.8733 (tp) cc_final: 0.8323 (tp) REVERT: E 564 LYS cc_start: 0.8172 (tptm) cc_final: 0.7720 (mttp) REVERT: E 568 GLU cc_start: 0.8461 (mp0) cc_final: 0.8150 (mp0) REVERT: E 569 MET cc_start: 0.8870 (mmm) cc_final: 0.8435 (mmm) REVERT: E 590 ASP cc_start: 0.7821 (t0) cc_final: 0.7594 (t0) REVERT: E 607 GLU cc_start: 0.7816 (pm20) cc_final: 0.7434 (pm20) REVERT: E 609 HIS cc_start: 0.7863 (m90) cc_final: 0.7562 (m90) REVERT: E 634 LEU cc_start: 0.8192 (mm) cc_final: 0.7845 (tt) REVERT: E 636 PHE cc_start: 0.8170 (t80) cc_final: 0.7726 (t80) REVERT: E 645 PHE cc_start: 0.7938 (t80) cc_final: 0.7135 (t80) REVERT: E 662 ASP cc_start: 0.8529 (p0) cc_final: 0.8137 (p0) REVERT: E 666 ASN cc_start: 0.7910 (t0) cc_final: 0.7542 (t0) REVERT: E 669 ARG cc_start: 0.7963 (ttt90) cc_final: 0.7607 (ttt90) REVERT: E 674 ASP cc_start: 0.7521 (m-30) cc_final: 0.7238 (m-30) REVERT: E 691 ILE cc_start: 0.8461 (mm) cc_final: 0.7911 (mm) REVERT: E 693 GLU cc_start: 0.8244 (pm20) cc_final: 0.7970 (pm20) REVERT: E 695 ILE cc_start: 0.8020 (pt) cc_final: 0.7721 (pt) REVERT: E 706 VAL cc_start: 0.8142 (t) cc_final: 0.7801 (p) REVERT: E 707 VAL cc_start: 0.8487 (m) cc_final: 0.7742 (t) REVERT: E 712 PHE cc_start: 0.7437 (m-10) cc_final: 0.7199 (m-10) REVERT: E 722 PHE cc_start: 0.8199 (t80) cc_final: 0.7812 (t80) REVERT: E 744 PHE cc_start: 0.8241 (t80) cc_final: 0.7761 (t80) REVERT: E 832 GLN cc_start: 0.8223 (pm20) cc_final: 0.7938 (pm20) REVERT: E 913 MET cc_start: 0.7355 (mmm) cc_final: 0.6543 (mmm) REVERT: E 966 LEU cc_start: 0.7829 (tp) cc_final: 0.7529 (tp) REVERT: E 974 LYS cc_start: 0.9195 (tppt) cc_final: 0.8845 (tppt) REVERT: F 25 ASN cc_start: 0.8875 (p0) cc_final: 0.8620 (p0) REVERT: F 201 SER cc_start: 0.7994 (p) cc_final: 0.7603 (m) REVERT: F 227 MET cc_start: 0.8206 (tmm) cc_final: 0.7966 (tmm) REVERT: F 242 LYS cc_start: 0.8254 (ptmm) cc_final: 0.7699 (ptmm) REVERT: F 284 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7161 (tm-30) REVERT: F 290 MET cc_start: 0.8545 (mmp) cc_final: 0.8312 (mmp) REVERT: F 329 ASP cc_start: 0.8107 (m-30) cc_final: 0.7750 (m-30) REVERT: F 336 TYR cc_start: 0.7656 (m-80) cc_final: 0.7236 (m-80) REVERT: F 357 MET cc_start: 0.7874 (pmm) cc_final: 0.7665 (tpt) REVERT: F 376 LYS cc_start: 0.8404 (tptp) cc_final: 0.8116 (tptt) REVERT: F 419 ASP cc_start: 0.8094 (p0) cc_final: 0.7677 (p0) REVERT: F 422 LYS cc_start: 0.8689 (tmmt) cc_final: 0.8414 (tmmt) REVERT: F 471 TYR cc_start: 0.6527 (t80) cc_final: 0.6099 (t80) REVERT: F 483 GLN cc_start: 0.8781 (mt0) cc_final: 0.8254 (mt0) REVERT: F 487 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7275 (tm-30) REVERT: F 491 GLN cc_start: 0.7132 (tt0) cc_final: 0.6375 (tt0) REVERT: F 516 GLU cc_start: 0.8095 (tp30) cc_final: 0.7708 (tp30) REVERT: F 518 GLU cc_start: 0.8038 (tp30) cc_final: 0.7618 (tp30) REVERT: F 519 MET cc_start: 0.7701 (mmm) cc_final: 0.7425 (mmm) REVERT: F 531 MET cc_start: 0.6360 (mmp) cc_final: 0.5910 (mmp) REVERT: F 534 GLU cc_start: 0.7814 (tp30) cc_final: 0.7365 (tp30) REVERT: F 538 LYS cc_start: 0.8494 (pttm) cc_final: 0.8108 (pttt) REVERT: F 540 LYS cc_start: 0.7932 (mmtm) cc_final: 0.7717 (mmtm) REVERT: F 543 GLU cc_start: 0.8433 (pp20) cc_final: 0.8193 (pp20) REVERT: F 545 LEU cc_start: 0.8804 (mm) cc_final: 0.8573 (mp) REVERT: F 555 THR cc_start: 0.7812 (m) cc_final: 0.7527 (p) REVERT: F 576 PHE cc_start: 0.5622 (m-10) cc_final: 0.4282 (m-80) REVERT: F 616 MET cc_start: 0.8064 (ttp) cc_final: 0.7774 (ttp) REVERT: F 620 ILE cc_start: 0.7420 (tp) cc_final: 0.6285 (pt) REVERT: F 627 ARG cc_start: 0.7099 (ttt180) cc_final: 0.6794 (ttt180) REVERT: F 674 ASP cc_start: 0.7881 (m-30) cc_final: 0.7527 (p0) REVERT: F 694 GLU cc_start: 0.7192 (tp30) cc_final: 0.6827 (tp30) REVERT: F 731 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7710 (mm-30) REVERT: F 833 LYS cc_start: 0.8483 (pttt) cc_final: 0.8260 (pttt) REVERT: F 913 MET cc_start: 0.8050 (pmm) cc_final: 0.7577 (pmm) REVERT: F 940 TYR cc_start: 0.7953 (t80) cc_final: 0.7704 (t80) REVERT: F 942 PHE cc_start: 0.8166 (t80) cc_final: 0.7655 (t80) REVERT: F 943 PHE cc_start: 0.7543 (m-80) cc_final: 0.6704 (m-80) REVERT: F 987 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7536 (mmp80) REVERT: G 29 THR cc_start: 0.8001 (p) cc_final: 0.7638 (t) REVERT: G 61 LEU cc_start: 0.8121 (mp) cc_final: 0.7776 (mp) REVERT: G 71 GLU cc_start: 0.6607 (pm20) cc_final: 0.5784 (pm20) REVERT: G 72 TRP cc_start: 0.6405 (m100) cc_final: 0.5805 (m100) REVERT: G 194 GLN cc_start: 0.6919 (tp40) cc_final: 0.5911 (mm-40) REVERT: G 195 PHE cc_start: 0.7750 (m-80) cc_final: 0.6855 (m-80) REVERT: G 201 SER cc_start: 0.6997 (p) cc_final: 0.6500 (p) REVERT: G 206 MET cc_start: 0.7319 (mtm) cc_final: 0.6661 (mtm) REVERT: G 219 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7968 (mtmm) REVERT: H 65 ASN cc_start: 0.5457 (p0) cc_final: 0.4683 (p0) REVERT: H 197 ASN cc_start: 0.6346 (t0) cc_final: 0.6145 (t0) REVERT: H 206 MET cc_start: 0.6171 (tpt) cc_final: 0.5379 (tpt) REVERT: H 219 LYS cc_start: 0.8384 (tptp) cc_final: 0.7947 (tptt) outliers start: 4 outliers final: 1 residues processed: 864 average time/residue: 0.2524 time to fit residues: 347.4803 Evaluate side-chains 794 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 792 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 100 optimal weight: 0.7980 chunk 442 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 269 optimal weight: 0.9990 chunk 350 optimal weight: 0.5980 chunk 368 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 chunk 343 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN D 60 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN ** F 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.207719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.163648 restraints weight = 82032.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.168827 restraints weight = 53762.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.172451 restraints weight = 38584.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.175027 restraints weight = 29857.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.176820 restraints weight = 24406.757| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 38368 Z= 0.141 Angle : 0.660 12.545 51708 Z= 0.349 Chirality : 0.045 0.267 5500 Planarity : 0.005 0.119 6636 Dihedral : 5.688 84.357 4984 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.35 % Favored : 90.40 % Rotamer: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.12), residues: 4512 helix: -0.41 (0.11), residues: 2268 sheet: -1.03 (0.29), residues: 303 loop : -2.39 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 502 TYR 0.024 0.001 TYR B 455 PHE 0.051 0.002 PHE A 659 TRP 0.047 0.002 TRP B 601 HIS 0.008 0.001 HIS E 852 Details of bonding type rmsd covalent geometry : bond 0.00295 (38368) covalent geometry : angle 0.65992 (51708) hydrogen bonds : bond 0.04118 ( 1637) hydrogen bonds : angle 5.39137 ( 4638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 855 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 CYS cc_start: 0.9019 (m) cc_final: 0.8343 (t) REVERT: A 60 TRP cc_start: 0.7237 (p-90) cc_final: 0.6883 (p-90) REVERT: A 105 LYS cc_start: 0.7964 (mmtm) cc_final: 0.7545 (mmmm) REVERT: A 109 GLN cc_start: 0.7904 (tt0) cc_final: 0.7568 (tt0) REVERT: A 120 LYS cc_start: 0.8546 (mttt) cc_final: 0.8209 (mttp) REVERT: A 124 MET cc_start: 0.8376 (tpp) cc_final: 0.7739 (tpp) REVERT: A 125 ASN cc_start: 0.8947 (m-40) cc_final: 0.8709 (m110) REVERT: A 128 HIS cc_start: 0.7681 (m-70) cc_final: 0.6977 (m-70) REVERT: A 190 TYR cc_start: 0.7023 (m-80) cc_final: 0.6500 (m-80) REVERT: A 197 TYR cc_start: 0.8003 (m-10) cc_final: 0.7799 (m-10) REVERT: A 313 TYR cc_start: 0.6705 (t80) cc_final: 0.6302 (t80) REVERT: A 329 ASP cc_start: 0.7867 (t0) cc_final: 0.7553 (t0) REVERT: A 393 VAL cc_start: 0.6855 (t) cc_final: 0.6530 (p) REVERT: A 396 MET cc_start: 0.6945 (ptp) cc_final: 0.6276 (ptp) REVERT: A 421 MET cc_start: 0.4432 (mpp) cc_final: 0.4174 (mpp) REVERT: A 477 ASN cc_start: 0.8377 (m110) cc_final: 0.8144 (m110) REVERT: A 482 TYR cc_start: 0.3633 (t80) cc_final: 0.3281 (t80) REVERT: A 583 VAL cc_start: 0.8764 (t) cc_final: 0.8402 (t) REVERT: A 586 LEU cc_start: 0.8955 (pp) cc_final: 0.8273 (pp) REVERT: A 588 LEU cc_start: 0.8274 (mt) cc_final: 0.7704 (mt) REVERT: A 589 TYR cc_start: 0.7900 (m-80) cc_final: 0.7227 (m-80) REVERT: A 594 PHE cc_start: 0.7680 (t80) cc_final: 0.7221 (t80) REVERT: A 609 HIS cc_start: 0.8526 (m-70) cc_final: 0.8217 (m-70) REVERT: A 671 CYS cc_start: 0.8240 (p) cc_final: 0.7541 (t) REVERT: A 686 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 694 GLU cc_start: 0.6905 (mp0) cc_final: 0.6584 (mp0) REVERT: A 698 GLN cc_start: 0.7159 (tp-100) cc_final: 0.6713 (tp-100) REVERT: A 704 MET cc_start: 0.5320 (ttt) cc_final: 0.4968 (ttt) REVERT: A 711 GLN cc_start: 0.8274 (mp10) cc_final: 0.7822 (mm-40) REVERT: A 936 MET cc_start: 0.2543 (mmp) cc_final: 0.0517 (ttm) REVERT: B 28 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8174 (pt0) REVERT: B 31 LYS cc_start: 0.8574 (ptmm) cc_final: 0.8318 (ptmm) REVERT: B 32 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 36 SER cc_start: 0.8033 (m) cc_final: 0.7517 (m) REVERT: B 118 HIS cc_start: 0.7885 (m-70) cc_final: 0.7483 (m-70) REVERT: B 137 LEU cc_start: 0.8222 (tt) cc_final: 0.7923 (tt) REVERT: B 179 LYS cc_start: 0.7288 (mppt) cc_final: 0.6989 (mmtt) REVERT: B 197 TYR cc_start: 0.7580 (p90) cc_final: 0.7200 (p90) REVERT: B 227 MET cc_start: 0.7697 (tmm) cc_final: 0.7433 (tmm) REVERT: B 228 LEU cc_start: 0.8194 (mt) cc_final: 0.7604 (mt) REVERT: B 229 LEU cc_start: 0.8668 (mt) cc_final: 0.8365 (pp) REVERT: B 258 LEU cc_start: 0.8664 (mt) cc_final: 0.8378 (mt) REVERT: B 327 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8340 (mmtp) REVERT: B 350 LYS cc_start: 0.7586 (tppt) cc_final: 0.7303 (tppt) REVERT: B 385 PHE cc_start: 0.8397 (t80) cc_final: 0.8178 (t80) REVERT: B 421 MET cc_start: 0.6199 (mtm) cc_final: 0.5655 (mtm) REVERT: B 435 ASP cc_start: 0.8408 (m-30) cc_final: 0.8051 (m-30) REVERT: B 437 LYS cc_start: 0.8695 (mmtp) cc_final: 0.8330 (mmmm) REVERT: B 441 PHE cc_start: 0.8556 (m-10) cc_final: 0.8185 (m-80) REVERT: B 442 LEU cc_start: 0.8686 (mt) cc_final: 0.8221 (mt) REVERT: B 472 TYR cc_start: 0.7258 (t80) cc_final: 0.6864 (t80) REVERT: B 478 ARG cc_start: 0.8169 (ptt180) cc_final: 0.7808 (ptt180) REVERT: B 480 ARG cc_start: 0.7942 (mmt180) cc_final: 0.7475 (mmm-85) REVERT: B 481 ILE cc_start: 0.8705 (mm) cc_final: 0.8367 (mm) REVERT: B 482 TYR cc_start: 0.7249 (t80) cc_final: 0.6790 (t80) REVERT: B 522 PHE cc_start: 0.7580 (t80) cc_final: 0.7207 (t80) REVERT: B 524 ILE cc_start: 0.8101 (pt) cc_final: 0.7470 (mm) REVERT: B 531 MET cc_start: 0.3513 (ppp) cc_final: 0.2646 (ppp) REVERT: B 560 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 569 MET cc_start: 0.6758 (tmm) cc_final: 0.6151 (tmm) REVERT: B 587 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7579 (mtt180) REVERT: B 593 ARG cc_start: 0.7892 (ptt180) cc_final: 0.7453 (ptt180) REVERT: B 600 LEU cc_start: 0.8011 (tp) cc_final: 0.7722 (tp) REVERT: B 614 ASN cc_start: 0.7666 (m-40) cc_final: 0.7237 (m-40) REVERT: B 757 TRP cc_start: 0.6462 (m-10) cc_final: 0.6062 (m-10) REVERT: D 1 MET cc_start: 0.5235 (mmp) cc_final: 0.4961 (mmp) REVERT: E 92 TYR cc_start: 0.7514 (t80) cc_final: 0.6936 (t80) REVERT: E 118 HIS cc_start: 0.7814 (m90) cc_final: 0.7570 (m90) REVERT: E 156 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7942 (mm-30) REVERT: E 158 VAL cc_start: 0.8172 (t) cc_final: 0.7874 (p) REVERT: E 227 MET cc_start: 0.8067 (tpt) cc_final: 0.7806 (tpt) REVERT: E 307 GLU cc_start: 0.7180 (tt0) cc_final: 0.6551 (tt0) REVERT: E 329 ASP cc_start: 0.7874 (p0) cc_final: 0.7520 (p0) REVERT: E 341 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8041 (tm-30) REVERT: E 343 ASN cc_start: 0.8922 (p0) cc_final: 0.8642 (p0) REVERT: E 373 LEU cc_start: 0.7694 (tp) cc_final: 0.7266 (tp) REVERT: E 378 TYR cc_start: 0.7744 (m-10) cc_final: 0.7431 (m-80) REVERT: E 393 VAL cc_start: 0.8284 (m) cc_final: 0.7987 (p) REVERT: E 419 ASP cc_start: 0.8068 (p0) cc_final: 0.7698 (m-30) REVERT: E 421 MET cc_start: 0.7925 (mmt) cc_final: 0.7161 (mmt) REVERT: E 422 LYS cc_start: 0.8660 (tppt) cc_final: 0.8258 (tppt) REVERT: E 451 SER cc_start: 0.8630 (p) cc_final: 0.8301 (p) REVERT: E 453 ASP cc_start: 0.8189 (m-30) cc_final: 0.7986 (m-30) REVERT: E 469 CYS cc_start: 0.8001 (m) cc_final: 0.7783 (m) REVERT: E 487 GLN cc_start: 0.6942 (pt0) cc_final: 0.6686 (tt0) REVERT: E 492 PHE cc_start: 0.7688 (m-80) cc_final: 0.7161 (m-80) REVERT: E 527 LEU cc_start: 0.8731 (tp) cc_final: 0.8307 (tp) REVERT: E 544 PHE cc_start: 0.7095 (t80) cc_final: 0.6827 (t80) REVERT: E 564 LYS cc_start: 0.8246 (tptm) cc_final: 0.7624 (mttp) REVERT: E 568 GLU cc_start: 0.8515 (mp0) cc_final: 0.8076 (mp0) REVERT: E 578 MET cc_start: 0.8468 (mtm) cc_final: 0.8105 (ttm) REVERT: E 607 GLU cc_start: 0.7825 (pm20) cc_final: 0.7366 (pm20) REVERT: E 609 HIS cc_start: 0.7888 (m90) cc_final: 0.7543 (m90) REVERT: E 634 LEU cc_start: 0.8245 (mm) cc_final: 0.7891 (tt) REVERT: E 636 PHE cc_start: 0.8202 (t80) cc_final: 0.7743 (t80) REVERT: E 645 PHE cc_start: 0.7953 (t80) cc_final: 0.7089 (t80) REVERT: E 651 ASP cc_start: 0.8126 (m-30) cc_final: 0.7920 (m-30) REVERT: E 666 ASN cc_start: 0.7867 (t0) cc_final: 0.7465 (t0) REVERT: E 669 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7492 (ttt90) REVERT: E 674 ASP cc_start: 0.7437 (m-30) cc_final: 0.7143 (m-30) REVERT: E 691 ILE cc_start: 0.8429 (mm) cc_final: 0.7851 (mm) REVERT: E 695 ILE cc_start: 0.8039 (pt) cc_final: 0.7717 (pt) REVERT: E 705 ASN cc_start: 0.8121 (p0) cc_final: 0.7652 (p0) REVERT: E 706 VAL cc_start: 0.8090 (t) cc_final: 0.7635 (p) REVERT: E 707 VAL cc_start: 0.8457 (m) cc_final: 0.7680 (t) REVERT: E 712 PHE cc_start: 0.7625 (m-10) cc_final: 0.7316 (m-10) REVERT: E 722 PHE cc_start: 0.8190 (t80) cc_final: 0.7716 (t80) REVERT: E 832 GLN cc_start: 0.8251 (pm20) cc_final: 0.7948 (pm20) REVERT: E 913 MET cc_start: 0.7548 (mmm) cc_final: 0.6727 (mmm) REVERT: E 919 TRP cc_start: 0.7960 (m-90) cc_final: 0.7280 (m100) REVERT: E 966 LEU cc_start: 0.7824 (tp) cc_final: 0.7533 (tp) REVERT: E 974 LYS cc_start: 0.9204 (tppt) cc_final: 0.8848 (tppt) REVERT: F 25 ASN cc_start: 0.8888 (p0) cc_final: 0.8605 (p0) REVERT: F 201 SER cc_start: 0.7964 (p) cc_final: 0.7385 (p) REVERT: F 242 LYS cc_start: 0.8287 (ptmm) cc_final: 0.7803 (ptmm) REVERT: F 284 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7368 (tm-30) REVERT: F 291 ASP cc_start: 0.8359 (m-30) cc_final: 0.8083 (m-30) REVERT: F 329 ASP cc_start: 0.8022 (m-30) cc_final: 0.7684 (m-30) REVERT: F 336 TYR cc_start: 0.7657 (m-80) cc_final: 0.7238 (m-80) REVERT: F 376 LYS cc_start: 0.8251 (tptp) cc_final: 0.7896 (tptt) REVERT: F 422 LYS cc_start: 0.8716 (tmmt) cc_final: 0.8336 (tptt) REVERT: F 442 LEU cc_start: 0.8666 (mt) cc_final: 0.8438 (mt) REVERT: F 452 TYR cc_start: 0.7121 (t80) cc_final: 0.6741 (t80) REVERT: F 471 TYR cc_start: 0.6562 (t80) cc_final: 0.6033 (t80) REVERT: F 483 GLN cc_start: 0.8705 (mt0) cc_final: 0.8172 (mt0) REVERT: F 487 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7441 (tm-30) REVERT: F 514 ARG cc_start: 0.8179 (tmm-80) cc_final: 0.7896 (ttp80) REVERT: F 516 GLU cc_start: 0.7964 (tp30) cc_final: 0.7542 (tp30) REVERT: F 518 GLU cc_start: 0.7941 (tp30) cc_final: 0.7408 (tp30) REVERT: F 519 MET cc_start: 0.7576 (mmm) cc_final: 0.7055 (mmm) REVERT: F 534 GLU cc_start: 0.7709 (tp30) cc_final: 0.7298 (tp30) REVERT: F 538 LYS cc_start: 0.8438 (pttm) cc_final: 0.7846 (pttm) REVERT: F 540 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7713 (mmtm) REVERT: F 545 LEU cc_start: 0.8807 (mm) cc_final: 0.8506 (mp) REVERT: F 555 THR cc_start: 0.7744 (m) cc_final: 0.7487 (p) REVERT: F 576 PHE cc_start: 0.5713 (m-10) cc_final: 0.4942 (m-10) REVERT: F 620 ILE cc_start: 0.7386 (tp) cc_final: 0.6265 (pt) REVERT: F 694 GLU cc_start: 0.7111 (tp30) cc_final: 0.6775 (tp30) REVERT: F 724 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8188 (ptpp) REVERT: F 758 LEU cc_start: 0.8612 (mt) cc_final: 0.8371 (mt) REVERT: F 833 LYS cc_start: 0.8537 (pttt) cc_final: 0.8134 (pttt) REVERT: F 834 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8104 (mm110) REVERT: F 913 MET cc_start: 0.7999 (pmm) cc_final: 0.7599 (pmm) REVERT: F 940 TYR cc_start: 0.8011 (t80) cc_final: 0.7730 (t80) REVERT: F 942 PHE cc_start: 0.8180 (t80) cc_final: 0.7694 (t80) REVERT: F 943 PHE cc_start: 0.7569 (m-80) cc_final: 0.6769 (m-80) REVERT: G 15 ARG cc_start: 0.7715 (ptp-110) cc_final: 0.7466 (ptp-110) REVERT: G 29 THR cc_start: 0.8010 (p) cc_final: 0.7566 (p) REVERT: G 61 LEU cc_start: 0.8143 (mp) cc_final: 0.7779 (mp) REVERT: G 71 GLU cc_start: 0.6359 (pm20) cc_final: 0.5425 (pm20) REVERT: G 72 TRP cc_start: 0.6390 (m100) cc_final: 0.5628 (m100) REVERT: G 194 GLN cc_start: 0.6911 (tp40) cc_final: 0.5941 (mm-40) REVERT: G 195 PHE cc_start: 0.7789 (m-80) cc_final: 0.6930 (m-80) REVERT: G 201 SER cc_start: 0.6979 (p) cc_final: 0.6453 (p) REVERT: G 206 MET cc_start: 0.7117 (mtm) cc_final: 0.6591 (mtm) REVERT: G 219 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7956 (mtmm) REVERT: H 65 ASN cc_start: 0.5363 (p0) cc_final: 0.4572 (p0) REVERT: H 206 MET cc_start: 0.6032 (tpt) cc_final: 0.5443 (tpt) outliers start: 2 outliers final: 1 residues processed: 855 average time/residue: 0.2554 time to fit residues: 348.5167 Evaluate side-chains 807 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 806 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 138 optimal weight: 1.9990 chunk 324 optimal weight: 8.9990 chunk 251 optimal weight: 0.5980 chunk 306 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 chunk 351 optimal weight: 0.0370 chunk 304 optimal weight: 0.0030 chunk 204 optimal weight: 5.9990 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 786 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 521 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.209171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.164874 restraints weight = 81414.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.170047 restraints weight = 53700.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.173698 restraints weight = 38810.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176124 restraints weight = 30077.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 77)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.178137 restraints weight = 24844.290| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38368 Z= 0.127 Angle : 0.657 13.286 51708 Z= 0.345 Chirality : 0.044 0.328 5500 Planarity : 0.004 0.100 6636 Dihedral : 5.605 85.936 4984 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.95 % Favored : 90.80 % Rotamer: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.12), residues: 4512 helix: -0.34 (0.11), residues: 2263 sheet: -0.93 (0.28), residues: 322 loop : -2.36 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 233 TYR 0.026 0.001 TYR B 455 PHE 0.042 0.002 PHE A 659 TRP 0.047 0.002 TRP B 601 HIS 0.007 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00268 (38368) covalent geometry : angle 0.65741 (51708) hydrogen bonds : bond 0.03916 ( 1637) hydrogen bonds : angle 5.22370 ( 4638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 857 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 CYS cc_start: 0.8957 (m) cc_final: 0.8398 (t) REVERT: A 60 TRP cc_start: 0.7212 (p-90) cc_final: 0.6859 (p-90) REVERT: A 98 MET cc_start: 0.7317 (mmp) cc_final: 0.7090 (mmp) REVERT: A 105 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7523 (mmmm) REVERT: A 109 GLN cc_start: 0.7941 (tt0) cc_final: 0.7621 (tt0) REVERT: A 120 LYS cc_start: 0.8508 (mttt) cc_final: 0.8223 (mttp) REVERT: A 124 MET cc_start: 0.8371 (tpp) cc_final: 0.7739 (tpp) REVERT: A 125 ASN cc_start: 0.8929 (m-40) cc_final: 0.8639 (m110) REVERT: A 128 HIS cc_start: 0.7517 (m-70) cc_final: 0.6983 (m-70) REVERT: A 190 TYR cc_start: 0.7049 (m-80) cc_final: 0.6475 (m-80) REVERT: A 197 TYR cc_start: 0.8047 (m-10) cc_final: 0.7818 (m-10) REVERT: A 313 TYR cc_start: 0.6727 (t80) cc_final: 0.6421 (t80) REVERT: A 393 VAL cc_start: 0.6840 (t) cc_final: 0.6512 (p) REVERT: A 396 MET cc_start: 0.6870 (ptp) cc_final: 0.6243 (ptp) REVERT: A 421 MET cc_start: 0.4449 (mpp) cc_final: 0.4187 (mpp) REVERT: A 477 ASN cc_start: 0.8297 (m110) cc_final: 0.8042 (m110) REVERT: A 482 TYR cc_start: 0.3646 (t80) cc_final: 0.3334 (t80) REVERT: A 586 LEU cc_start: 0.8934 (pp) cc_final: 0.8275 (pp) REVERT: A 588 LEU cc_start: 0.8256 (mt) cc_final: 0.7946 (mt) REVERT: A 589 TYR cc_start: 0.7927 (m-80) cc_final: 0.7285 (m-80) REVERT: A 594 PHE cc_start: 0.7532 (t80) cc_final: 0.7257 (t80) REVERT: A 609 HIS cc_start: 0.8551 (m-70) cc_final: 0.8258 (m-70) REVERT: A 613 ARG cc_start: 0.8210 (mmp80) cc_final: 0.7796 (mmp80) REVERT: A 622 LYS cc_start: 0.7982 (pptt) cc_final: 0.7263 (pttt) REVERT: A 671 CYS cc_start: 0.8170 (p) cc_final: 0.7492 (t) REVERT: A 686 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7760 (mm-30) REVERT: A 694 GLU cc_start: 0.6848 (mp0) cc_final: 0.6523 (mp0) REVERT: A 698 GLN cc_start: 0.7090 (tp-100) cc_final: 0.6635 (tp-100) REVERT: A 704 MET cc_start: 0.5290 (ttt) cc_final: 0.4962 (ttt) REVERT: A 711 GLN cc_start: 0.8317 (mp10) cc_final: 0.7852 (mm-40) REVERT: A 913 MET cc_start: -0.5661 (mmp) cc_final: -0.5871 (mmt) REVERT: A 936 MET cc_start: 0.2528 (mmp) cc_final: 0.0584 (ttm) REVERT: B 28 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8166 (pt0) REVERT: B 31 LYS cc_start: 0.8520 (ptmm) cc_final: 0.8296 (ptmm) REVERT: B 32 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 36 SER cc_start: 0.8033 (m) cc_final: 0.7517 (m) REVERT: B 118 HIS cc_start: 0.7946 (m-70) cc_final: 0.7614 (m-70) REVERT: B 179 LYS cc_start: 0.7302 (mppt) cc_final: 0.6990 (mmtt) REVERT: B 188 ASP cc_start: 0.8110 (t0) cc_final: 0.7875 (t0) REVERT: B 190 TYR cc_start: 0.7888 (m-10) cc_final: 0.7402 (m-10) REVERT: B 197 TYR cc_start: 0.7646 (p90) cc_final: 0.7191 (p90) REVERT: B 227 MET cc_start: 0.7719 (tmm) cc_final: 0.7446 (tmm) REVERT: B 228 LEU cc_start: 0.8231 (mt) cc_final: 0.7602 (mt) REVERT: B 229 LEU cc_start: 0.8661 (mt) cc_final: 0.8311 (pp) REVERT: B 258 LEU cc_start: 0.8638 (mt) cc_final: 0.8289 (mt) REVERT: B 327 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8149 (mmtp) REVERT: B 350 LYS cc_start: 0.7495 (tppt) cc_final: 0.7216 (tppt) REVERT: B 385 PHE cc_start: 0.8357 (t80) cc_final: 0.8114 (t80) REVERT: B 412 LEU cc_start: 0.8525 (tp) cc_final: 0.8224 (tt) REVERT: B 421 MET cc_start: 0.6169 (mtm) cc_final: 0.5464 (mtm) REVERT: B 435 ASP cc_start: 0.8438 (m-30) cc_final: 0.8123 (m-30) REVERT: B 437 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8353 (mmmm) REVERT: B 441 PHE cc_start: 0.8461 (m-10) cc_final: 0.8149 (m-80) REVERT: B 442 LEU cc_start: 0.8650 (mt) cc_final: 0.8177 (mt) REVERT: B 472 TYR cc_start: 0.7282 (t80) cc_final: 0.6946 (t80) REVERT: B 478 ARG cc_start: 0.8131 (ptt180) cc_final: 0.7801 (ptt180) REVERT: B 480 ARG cc_start: 0.7962 (mmt180) cc_final: 0.7481 (mmm-85) REVERT: B 481 ILE cc_start: 0.8722 (mm) cc_final: 0.8352 (mm) REVERT: B 486 THR cc_start: 0.7004 (m) cc_final: 0.6712 (m) REVERT: B 522 PHE cc_start: 0.7543 (t80) cc_final: 0.7297 (t80) REVERT: B 524 ILE cc_start: 0.8214 (pt) cc_final: 0.7548 (mm) REVERT: B 531 MET cc_start: 0.3654 (ppp) cc_final: 0.3447 (ppp) REVERT: B 569 MET cc_start: 0.6835 (tmm) cc_final: 0.6161 (tmm) REVERT: B 587 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7553 (mtt180) REVERT: B 593 ARG cc_start: 0.7907 (ptt180) cc_final: 0.7501 (ptt180) REVERT: B 614 ASN cc_start: 0.7715 (m-40) cc_final: 0.7362 (m-40) REVERT: B 757 TRP cc_start: 0.6496 (m-10) cc_final: 0.6168 (m-10) REVERT: C 206 MET cc_start: 0.4432 (pmm) cc_final: 0.3801 (pmm) REVERT: D 1 MET cc_start: 0.5191 (mmp) cc_final: 0.4889 (mmp) REVERT: E 92 TYR cc_start: 0.7524 (t80) cc_final: 0.6971 (t80) REVERT: E 118 HIS cc_start: 0.7712 (m90) cc_final: 0.7424 (m90) REVERT: E 120 LYS cc_start: 0.9071 (mttp) cc_final: 0.8870 (mttp) REVERT: E 158 VAL cc_start: 0.8105 (t) cc_final: 0.7823 (p) REVERT: E 227 MET cc_start: 0.8091 (tpt) cc_final: 0.7825 (tpt) REVERT: E 307 GLU cc_start: 0.7264 (tt0) cc_final: 0.6654 (tt0) REVERT: E 329 ASP cc_start: 0.7849 (p0) cc_final: 0.7457 (p0) REVERT: E 341 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7997 (tm-30) REVERT: E 373 LEU cc_start: 0.7649 (tp) cc_final: 0.7181 (tp) REVERT: E 378 TYR cc_start: 0.7795 (m-10) cc_final: 0.7466 (m-80) REVERT: E 393 VAL cc_start: 0.8315 (m) cc_final: 0.8000 (p) REVERT: E 396 MET cc_start: 0.6955 (tmm) cc_final: 0.6730 (tmm) REVERT: E 419 ASP cc_start: 0.7997 (p0) cc_final: 0.7614 (m-30) REVERT: E 421 MET cc_start: 0.7985 (mmt) cc_final: 0.7202 (mmt) REVERT: E 422 LYS cc_start: 0.8652 (tppt) cc_final: 0.8249 (tppt) REVERT: E 453 ASP cc_start: 0.8182 (m-30) cc_final: 0.7912 (m-30) REVERT: E 475 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7325 (mm-40) REVERT: E 527 LEU cc_start: 0.8620 (tp) cc_final: 0.8250 (tp) REVERT: E 544 PHE cc_start: 0.7086 (t80) cc_final: 0.6860 (t80) REVERT: E 564 LYS cc_start: 0.8246 (tptm) cc_final: 0.7668 (mttp) REVERT: E 568 GLU cc_start: 0.8504 (mp0) cc_final: 0.8155 (mp0) REVERT: E 607 GLU cc_start: 0.7876 (pm20) cc_final: 0.7390 (pm20) REVERT: E 609 HIS cc_start: 0.7905 (m90) cc_final: 0.7476 (m90) REVERT: E 634 LEU cc_start: 0.8229 (mm) cc_final: 0.7860 (tt) REVERT: E 636 PHE cc_start: 0.8207 (t80) cc_final: 0.7775 (t80) REVERT: E 645 PHE cc_start: 0.7972 (t80) cc_final: 0.7177 (t80) REVERT: E 651 ASP cc_start: 0.8129 (m-30) cc_final: 0.7914 (m-30) REVERT: E 662 ASP cc_start: 0.8368 (p0) cc_final: 0.7926 (p0) REVERT: E 666 ASN cc_start: 0.7869 (t0) cc_final: 0.7490 (t0) REVERT: E 669 ARG cc_start: 0.7969 (ttt90) cc_final: 0.7567 (ttt90) REVERT: E 674 ASP cc_start: 0.7357 (m-30) cc_final: 0.7067 (m-30) REVERT: E 691 ILE cc_start: 0.8409 (mm) cc_final: 0.7756 (mm) REVERT: E 707 VAL cc_start: 0.8372 (m) cc_final: 0.7793 (t) REVERT: E 712 PHE cc_start: 0.7457 (m-10) cc_final: 0.7122 (m-10) REVERT: E 722 PHE cc_start: 0.8213 (t80) cc_final: 0.7809 (t80) REVERT: E 832 GLN cc_start: 0.8238 (pm20) cc_final: 0.7936 (pm20) REVERT: E 913 MET cc_start: 0.7581 (mmm) cc_final: 0.6740 (mmm) REVERT: E 966 LEU cc_start: 0.7763 (tp) cc_final: 0.7484 (tp) REVERT: E 974 LYS cc_start: 0.9216 (tppt) cc_final: 0.8876 (tppt) REVERT: F 25 ASN cc_start: 0.8882 (p0) cc_final: 0.8618 (p0) REVERT: F 98 MET cc_start: 0.8519 (mmp) cc_final: 0.8247 (mmp) REVERT: F 201 SER cc_start: 0.7938 (p) cc_final: 0.7439 (p) REVERT: F 227 MET cc_start: 0.8096 (tmm) cc_final: 0.7874 (tmm) REVERT: F 242 LYS cc_start: 0.8264 (ptmm) cc_final: 0.7785 (ptmm) REVERT: F 290 MET cc_start: 0.8542 (mmp) cc_final: 0.8310 (mmp) REVERT: F 315 LYS cc_start: 0.7618 (mmtm) cc_final: 0.7271 (mmtm) REVERT: F 329 ASP cc_start: 0.7958 (m-30) cc_final: 0.7698 (m-30) REVERT: F 336 TYR cc_start: 0.7670 (m-80) cc_final: 0.7264 (m-80) REVERT: F 376 LYS cc_start: 0.8397 (tptp) cc_final: 0.8074 (tptt) REVERT: F 417 LYS cc_start: 0.7549 (pttm) cc_final: 0.7284 (pttm) REVERT: F 422 LYS cc_start: 0.8688 (tmmt) cc_final: 0.8209 (tptt) REVERT: F 471 TYR cc_start: 0.6488 (t80) cc_final: 0.5962 (t80) REVERT: F 483 GLN cc_start: 0.8713 (mt0) cc_final: 0.8188 (mt0) REVERT: F 487 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7418 (tm-30) REVERT: F 516 GLU cc_start: 0.7922 (tp30) cc_final: 0.7571 (tp30) REVERT: F 518 GLU cc_start: 0.7985 (tp30) cc_final: 0.7491 (tp30) REVERT: F 519 MET cc_start: 0.7567 (mmm) cc_final: 0.7105 (mmm) REVERT: F 534 GLU cc_start: 0.7754 (tp30) cc_final: 0.7163 (tp30) REVERT: F 538 LYS cc_start: 0.8388 (pttm) cc_final: 0.7815 (pttm) REVERT: F 545 LEU cc_start: 0.8840 (mm) cc_final: 0.8501 (mp) REVERT: F 555 THR cc_start: 0.7724 (m) cc_final: 0.7485 (p) REVERT: F 576 PHE cc_start: 0.5690 (m-10) cc_final: 0.4976 (m-10) REVERT: F 620 ILE cc_start: 0.7370 (tp) cc_final: 0.7131 (tt) REVERT: F 674 ASP cc_start: 0.7845 (m-30) cc_final: 0.7643 (p0) REVERT: F 677 ARG cc_start: 0.6494 (ttp80) cc_final: 0.6102 (ttp80) REVERT: F 683 LYS cc_start: 0.8448 (mttp) cc_final: 0.8178 (mttp) REVERT: F 694 GLU cc_start: 0.6994 (tp30) cc_final: 0.6739 (tp30) REVERT: F 724 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8190 (ptpp) REVERT: F 758 LEU cc_start: 0.8641 (mt) cc_final: 0.8383 (mt) REVERT: F 767 LEU cc_start: 0.7498 (mp) cc_final: 0.6899 (mt) REVERT: F 833 LYS cc_start: 0.8529 (pttt) cc_final: 0.8163 (pttt) REVERT: F 834 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8126 (mm110) REVERT: F 913 MET cc_start: 0.8052 (pmm) cc_final: 0.7560 (pmm) REVERT: F 937 ASP cc_start: 0.7787 (t0) cc_final: 0.7489 (t0) REVERT: F 940 TYR cc_start: 0.7998 (t80) cc_final: 0.7781 (t80) REVERT: F 942 PHE cc_start: 0.8197 (t80) cc_final: 0.7771 (t80) REVERT: F 943 PHE cc_start: 0.7569 (m-80) cc_final: 0.6798 (m-80) REVERT: G 15 ARG cc_start: 0.7704 (ptp-110) cc_final: 0.7493 (ptp-110) REVERT: G 29 THR cc_start: 0.7978 (p) cc_final: 0.7625 (t) REVERT: G 61 LEU cc_start: 0.7970 (mp) cc_final: 0.7567 (mp) REVERT: G 71 GLU cc_start: 0.6421 (pm20) cc_final: 0.5685 (pm20) REVERT: G 72 TRP cc_start: 0.6348 (m100) cc_final: 0.5486 (m100) REVERT: G 194 GLN cc_start: 0.6844 (tp40) cc_final: 0.5944 (mm-40) REVERT: G 195 PHE cc_start: 0.7829 (m-80) cc_final: 0.6909 (m-80) REVERT: G 201 SER cc_start: 0.6981 (p) cc_final: 0.6489 (p) REVERT: G 206 MET cc_start: 0.7094 (mtm) cc_final: 0.6546 (mtm) REVERT: G 219 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7932 (mtmm) REVERT: H 65 ASN cc_start: 0.5188 (p0) cc_final: 0.4442 (p0) REVERT: H 197 ASN cc_start: 0.6139 (t0) cc_final: 0.5699 (t0) REVERT: H 206 MET cc_start: 0.5951 (tpt) cc_final: 0.5587 (tpt) REVERT: H 219 LYS cc_start: 0.8290 (tptp) cc_final: 0.8084 (tptt) outliers start: 1 outliers final: 0 residues processed: 857 average time/residue: 0.2337 time to fit residues: 320.2696 Evaluate side-chains 805 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 805 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 chunk 449 optimal weight: 4.9990 chunk 15 optimal weight: 0.0010 chunk 366 optimal weight: 2.9990 chunk 210 optimal weight: 30.0000 chunk 265 optimal weight: 0.0770 chunk 239 optimal weight: 0.0570 chunk 345 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 overall best weight: 0.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 HIS ** E 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.210512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.167139 restraints weight = 81024.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.172391 restraints weight = 53090.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.176058 restraints weight = 38097.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.178590 restraints weight = 29337.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.180551 restraints weight = 24009.505| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38368 Z= 0.125 Angle : 0.653 13.831 51708 Z= 0.344 Chirality : 0.045 0.289 5500 Planarity : 0.004 0.103 6636 Dihedral : 5.521 87.213 4984 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.75 % Favored : 90.98 % Rotamer: Outliers : 0.05 % Allowed : 1.48 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.12), residues: 4512 helix: -0.31 (0.11), residues: 2276 sheet: -0.98 (0.28), residues: 322 loop : -2.33 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 233 TYR 0.045 0.001 TYR E 455 PHE 0.055 0.001 PHE A 659 TRP 0.047 0.002 TRP B 601 HIS 0.006 0.001 HIS E 852 Details of bonding type rmsd covalent geometry : bond 0.00264 (38368) covalent geometry : angle 0.65259 (51708) hydrogen bonds : bond 0.03814 ( 1637) hydrogen bonds : angle 5.14403 ( 4638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 847 time to evaluate : 1.423 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 29 CYS cc_start: 0.8943 (m) cc_final: 0.8445 (t) REVERT: A 60 TRP cc_start: 0.7249 (p-90) cc_final: 0.6884 (p-90) REVERT: A 98 MET cc_start: 0.7317 (mmp) cc_final: 0.7083 (mmp) REVERT: A 105 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7515 (mmmm) REVERT: A 109 GLN cc_start: 0.7943 (tt0) cc_final: 0.7609 (tt0) REVERT: A 120 LYS cc_start: 0.8534 (mttt) cc_final: 0.8233 (mttp) REVERT: A 124 MET cc_start: 0.8333 (tpp) cc_final: 0.7752 (tpp) REVERT: A 125 ASN cc_start: 0.8912 (m-40) cc_final: 0.8587 (m110) REVERT: A 128 HIS cc_start: 0.7482 (m-70) cc_final: 0.7002 (m-70) REVERT: A 190 TYR cc_start: 0.7005 (m-80) cc_final: 0.6503 (m-80) REVERT: A 233 ARG cc_start: 0.6994 (tmm160) cc_final: 0.6500 (tmm160) REVERT: A 313 TYR cc_start: 0.6741 (t80) cc_final: 0.6454 (t80) REVERT: A 329 ASP cc_start: 0.7694 (t0) cc_final: 0.7369 (t0) REVERT: A 393 VAL cc_start: 0.6844 (t) cc_final: 0.6517 (p) REVERT: A 396 MET cc_start: 0.6898 (ptp) cc_final: 0.6363 (ptp) REVERT: A 421 MET cc_start: 0.4394 (mpp) cc_final: 0.4139 (mpp) REVERT: A 477 ASN cc_start: 0.8268 (m110) cc_final: 0.7989 (m110) REVERT: A 482 TYR cc_start: 0.3702 (t80) cc_final: 0.3345 (t80) REVERT: A 586 LEU cc_start: 0.8942 (pp) cc_final: 0.8300 (pp) REVERT: A 588 LEU cc_start: 0.8273 (mt) cc_final: 0.7751 (mt) REVERT: A 589 TYR cc_start: 0.7937 (m-80) cc_final: 0.7289 (m-80) REVERT: A 594 PHE cc_start: 0.7621 (t80) cc_final: 0.7178 (t80) REVERT: A 609 HIS cc_start: 0.8546 (m-70) cc_final: 0.8289 (m-70) REVERT: A 613 ARG cc_start: 0.8154 (mmp80) cc_final: 0.7618 (ttp-170) REVERT: A 622 LYS cc_start: 0.7957 (pptt) cc_final: 0.7229 (pttt) REVERT: A 671 CYS cc_start: 0.8105 (p) cc_final: 0.7407 (t) REVERT: A 686 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 694 GLU cc_start: 0.6762 (mp0) cc_final: 0.6445 (mp0) REVERT: A 698 GLN cc_start: 0.7073 (tp-100) cc_final: 0.6640 (tp-100) REVERT: A 704 MET cc_start: 0.5205 (ttt) cc_final: 0.4896 (ttt) REVERT: A 711 GLN cc_start: 0.8264 (mp10) cc_final: 0.7796 (mm-40) REVERT: A 936 MET cc_start: 0.2492 (mmp) cc_final: 0.0574 (ttm) REVERT: B 32 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 36 SER cc_start: 0.8054 (m) cc_final: 0.7509 (m) REVERT: B 118 HIS cc_start: 0.7833 (m-70) cc_final: 0.7630 (m-70) REVERT: B 179 LYS cc_start: 0.7263 (mppt) cc_final: 0.7004 (mmtt) REVERT: B 188 ASP cc_start: 0.8170 (t0) cc_final: 0.7847 (t0) REVERT: B 190 TYR cc_start: 0.8053 (m-10) cc_final: 0.7650 (m-10) REVERT: B 197 TYR cc_start: 0.7669 (p90) cc_final: 0.7184 (p90) REVERT: B 227 MET cc_start: 0.7736 (tmm) cc_final: 0.7486 (tmm) REVERT: B 228 LEU cc_start: 0.8245 (mt) cc_final: 0.7609 (mt) REVERT: B 229 LEU cc_start: 0.8670 (mt) cc_final: 0.8334 (pp) REVERT: B 258 LEU cc_start: 0.8576 (mt) cc_final: 0.8269 (mt) REVERT: B 260 TYR cc_start: 0.6654 (t80) cc_final: 0.6063 (t80) REVERT: B 327 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8313 (mmtp) REVERT: B 350 LYS cc_start: 0.7487 (tppt) cc_final: 0.7173 (tppt) REVERT: B 385 PHE cc_start: 0.8378 (t80) cc_final: 0.8130 (t80) REVERT: B 412 LEU cc_start: 0.8528 (tp) cc_final: 0.8208 (tt) REVERT: B 421 MET cc_start: 0.6163 (mtm) cc_final: 0.5445 (mtm) REVERT: B 435 ASP cc_start: 0.8429 (m-30) cc_final: 0.8136 (m-30) REVERT: B 437 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8340 (mmmm) REVERT: B 441 PHE cc_start: 0.8425 (m-10) cc_final: 0.8109 (m-80) REVERT: B 442 LEU cc_start: 0.8627 (mt) cc_final: 0.8156 (mt) REVERT: B 472 TYR cc_start: 0.7237 (t80) cc_final: 0.6872 (t80) REVERT: B 478 ARG cc_start: 0.8149 (ptt180) cc_final: 0.7831 (ptt180) REVERT: B 480 ARG cc_start: 0.7982 (mmt180) cc_final: 0.7532 (mmm-85) REVERT: B 481 ILE cc_start: 0.8775 (mm) cc_final: 0.8422 (mm) REVERT: B 524 ILE cc_start: 0.8229 (pt) cc_final: 0.7580 (mm) REVERT: B 531 MET cc_start: 0.3840 (ppp) cc_final: 0.2847 (ppp) REVERT: B 569 MET cc_start: 0.6864 (tmm) cc_final: 0.6141 (tmm) REVERT: B 593 ARG cc_start: 0.7844 (ptt180) cc_final: 0.7419 (ptt180) REVERT: B 600 LEU cc_start: 0.7840 (tp) cc_final: 0.7597 (tp) REVERT: B 614 ASN cc_start: 0.7725 (m-40) cc_final: 0.7377 (m-40) REVERT: B 757 TRP cc_start: 0.6470 (m-10) cc_final: 0.6162 (m-10) REVERT: C 206 MET cc_start: 0.4184 (pmm) cc_final: 0.3757 (pmm) REVERT: E 118 HIS cc_start: 0.7743 (m90) cc_final: 0.7415 (m90) REVERT: E 120 LYS cc_start: 0.9105 (mttp) cc_final: 0.8894 (mttp) REVERT: E 158 VAL cc_start: 0.8013 (t) cc_final: 0.7718 (p) REVERT: E 307 GLU cc_start: 0.7280 (tt0) cc_final: 0.6701 (tt0) REVERT: E 343 ASN cc_start: 0.8821 (p0) cc_final: 0.8530 (p0) REVERT: E 373 LEU cc_start: 0.7707 (tp) cc_final: 0.7218 (tp) REVERT: E 378 TYR cc_start: 0.7833 (m-10) cc_final: 0.7536 (m-80) REVERT: E 379 GLU cc_start: 0.8521 (pt0) cc_final: 0.8182 (pt0) REVERT: E 393 VAL cc_start: 0.8279 (m) cc_final: 0.8016 (p) REVERT: E 396 MET cc_start: 0.6982 (tmm) cc_final: 0.6733 (tmm) REVERT: E 419 ASP cc_start: 0.7979 (p0) cc_final: 0.7568 (m-30) REVERT: E 421 MET cc_start: 0.7958 (mmt) cc_final: 0.7247 (mmt) REVERT: E 422 LYS cc_start: 0.8635 (tppt) cc_final: 0.8205 (tppt) REVERT: E 448 TRP cc_start: 0.7958 (m-90) cc_final: 0.7515 (m-90) REVERT: E 475 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7324 (mm-40) REVERT: E 527 LEU cc_start: 0.8482 (tp) cc_final: 0.8106 (tp) REVERT: E 531 MET cc_start: 0.7051 (tpt) cc_final: 0.6834 (mmm) REVERT: E 541 ILE cc_start: 0.6457 (mt) cc_final: 0.5979 (tt) REVERT: E 564 LYS cc_start: 0.8277 (tptm) cc_final: 0.7731 (mttp) REVERT: E 568 GLU cc_start: 0.8475 (mp0) cc_final: 0.8160 (mp0) REVERT: E 607 GLU cc_start: 0.7824 (pm20) cc_final: 0.7390 (pm20) REVERT: E 609 HIS cc_start: 0.7889 (m90) cc_final: 0.7504 (m90) REVERT: E 634 LEU cc_start: 0.8257 (mm) cc_final: 0.7811 (tt) REVERT: E 636 PHE cc_start: 0.8179 (t80) cc_final: 0.7809 (t80) REVERT: E 645 PHE cc_start: 0.7946 (t80) cc_final: 0.7116 (t80) REVERT: E 651 ASP cc_start: 0.8097 (m-30) cc_final: 0.7878 (m-30) REVERT: E 662 ASP cc_start: 0.8319 (p0) cc_final: 0.7876 (p0) REVERT: E 666 ASN cc_start: 0.7844 (t0) cc_final: 0.7467 (t0) REVERT: E 669 ARG cc_start: 0.7898 (ttt90) cc_final: 0.7419 (ttt90) REVERT: E 674 ASP cc_start: 0.7373 (m-30) cc_final: 0.7010 (m-30) REVERT: E 688 LEU cc_start: 0.8227 (tp) cc_final: 0.7966 (tp) REVERT: E 691 ILE cc_start: 0.8459 (mm) cc_final: 0.7811 (mm) REVERT: E 705 ASN cc_start: 0.8172 (p0) cc_final: 0.7908 (p0) REVERT: E 712 PHE cc_start: 0.7484 (m-10) cc_final: 0.7145 (m-10) REVERT: E 722 PHE cc_start: 0.8219 (t80) cc_final: 0.7707 (t80) REVERT: E 832 GLN cc_start: 0.8247 (pm20) cc_final: 0.7950 (pm20) REVERT: E 897 ILE cc_start: 0.8125 (mt) cc_final: 0.7880 (mt) REVERT: E 913 MET cc_start: 0.7562 (mmm) cc_final: 0.6712 (mmm) REVERT: E 919 TRP cc_start: 0.7873 (m-90) cc_final: 0.7279 (m100) REVERT: E 966 LEU cc_start: 0.7763 (tp) cc_final: 0.7490 (tp) REVERT: E 974 LYS cc_start: 0.9228 (tppt) cc_final: 0.8836 (tppt) REVERT: F 25 ASN cc_start: 0.8879 (p0) cc_final: 0.8616 (p0) REVERT: F 66 TYR cc_start: 0.8145 (m-80) cc_final: 0.7902 (m-80) REVERT: F 98 MET cc_start: 0.8509 (mmp) cc_final: 0.8274 (mmp) REVERT: F 100 PHE cc_start: 0.7788 (t80) cc_final: 0.6822 (t80) REVERT: F 201 SER cc_start: 0.7988 (p) cc_final: 0.7431 (p) REVERT: F 227 MET cc_start: 0.8093 (tmm) cc_final: 0.7055 (tmm) REVERT: F 228 LEU cc_start: 0.7904 (tp) cc_final: 0.7489 (mp) REVERT: F 242 LYS cc_start: 0.8268 (ptmm) cc_final: 0.7791 (ptmm) REVERT: F 290 MET cc_start: 0.8507 (mmp) cc_final: 0.8278 (mmp) REVERT: F 311 TYR cc_start: 0.6986 (t80) cc_final: 0.6783 (t80) REVERT: F 315 LYS cc_start: 0.7554 (mmtm) cc_final: 0.7223 (mmtm) REVERT: F 329 ASP cc_start: 0.8077 (m-30) cc_final: 0.7608 (m-30) REVERT: F 336 TYR cc_start: 0.7649 (m-80) cc_final: 0.7218 (m-80) REVERT: F 341 GLU cc_start: 0.7670 (tt0) cc_final: 0.7443 (tt0) REVERT: F 422 LYS cc_start: 0.8710 (tmmt) cc_final: 0.8199 (tptt) REVERT: F 436 TYR cc_start: 0.8318 (t80) cc_final: 0.7932 (t80) REVERT: F 452 TYR cc_start: 0.7204 (t80) cc_final: 0.6732 (t80) REVERT: F 471 TYR cc_start: 0.6530 (t80) cc_final: 0.5782 (t80) REVERT: F 483 GLN cc_start: 0.8706 (mt0) cc_final: 0.8186 (mt0) REVERT: F 487 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7471 (tm-30) REVERT: F 514 ARG cc_start: 0.8278 (tmm-80) cc_final: 0.7856 (ttp80) REVERT: F 516 GLU cc_start: 0.7987 (tp30) cc_final: 0.7579 (tp30) REVERT: F 518 GLU cc_start: 0.8025 (tp30) cc_final: 0.7508 (tp30) REVERT: F 519 MET cc_start: 0.7540 (mmm) cc_final: 0.7207 (mmm) REVERT: F 531 MET cc_start: 0.6196 (mmp) cc_final: 0.5131 (mmp) REVERT: F 534 GLU cc_start: 0.7793 (tp30) cc_final: 0.7371 (tp30) REVERT: F 538 LYS cc_start: 0.8426 (pttm) cc_final: 0.8000 (pttt) REVERT: F 545 LEU cc_start: 0.8821 (mm) cc_final: 0.8370 (mp) REVERT: F 560 GLU cc_start: 0.6946 (tp30) cc_final: 0.6725 (tp30) REVERT: F 576 PHE cc_start: 0.5705 (m-10) cc_final: 0.4996 (m-10) REVERT: F 593 ARG cc_start: 0.6864 (ptm160) cc_final: 0.6621 (ptm160) REVERT: F 620 ILE cc_start: 0.7398 (tp) cc_final: 0.7168 (tt) REVERT: F 677 ARG cc_start: 0.6404 (ttp80) cc_final: 0.6046 (ttp80) REVERT: F 694 GLU cc_start: 0.7084 (tp30) cc_final: 0.6788 (tp30) REVERT: F 724 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8301 (ptpt) REVERT: F 746 GLU cc_start: 0.8090 (pp20) cc_final: 0.7425 (pp20) REVERT: F 758 LEU cc_start: 0.8646 (mt) cc_final: 0.8361 (mt) REVERT: F 767 LEU cc_start: 0.7711 (mp) cc_final: 0.7183 (mt) REVERT: F 833 LYS cc_start: 0.8517 (pttt) cc_final: 0.8148 (pttt) REVERT: F 834 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8108 (mm110) REVERT: F 852 HIS cc_start: 0.7709 (p-80) cc_final: 0.7086 (p-80) REVERT: F 913 MET cc_start: 0.8028 (pmm) cc_final: 0.7664 (pmm) REVERT: F 942 PHE cc_start: 0.8235 (t80) cc_final: 0.7854 (t80) REVERT: F 943 PHE cc_start: 0.7629 (m-80) cc_final: 0.6894 (m-80) REVERT: F 998 GLU cc_start: 0.8082 (tp30) cc_final: 0.7678 (tp30) REVERT: G 29 THR cc_start: 0.8058 (p) cc_final: 0.7741 (t) REVERT: G 61 LEU cc_start: 0.7979 (mp) cc_final: 0.7631 (mp) REVERT: G 71 GLU cc_start: 0.6449 (pm20) cc_final: 0.5769 (pm20) REVERT: G 72 TRP cc_start: 0.6306 (m100) cc_final: 0.5446 (m100) REVERT: G 194 GLN cc_start: 0.7086 (tp40) cc_final: 0.6226 (mm-40) REVERT: G 195 PHE cc_start: 0.7892 (m-80) cc_final: 0.6931 (m-80) REVERT: G 201 SER cc_start: 0.7058 (p) cc_final: 0.6544 (p) REVERT: G 206 MET cc_start: 0.7066 (mtm) cc_final: 0.6546 (mtm) REVERT: G 219 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7975 (mtmm) REVERT: H 13 PHE cc_start: 0.5804 (m-80) cc_final: 0.5199 (m-80) REVERT: H 65 ASN cc_start: 0.5217 (p0) cc_final: 0.4474 (p0) REVERT: H 171 TYR cc_start: 0.7535 (t80) cc_final: 0.7250 (t80) REVERT: H 197 ASN cc_start: 0.6009 (t0) cc_final: 0.5587 (t0) REVERT: H 206 MET cc_start: 0.6056 (tpt) cc_final: 0.5521 (tpt) REVERT: H 219 LYS cc_start: 0.8357 (tptp) cc_final: 0.8114 (tptt) outliers start: 2 outliers final: 0 residues processed: 848 average time/residue: 0.2346 time to fit residues: 319.1898 Evaluate side-chains 799 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 799 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 241 optimal weight: 0.7980 chunk 320 optimal weight: 0.9990 chunk 277 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 359 optimal weight: 0.0970 chunk 422 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 392 optimal weight: 0.8980 chunk 301 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 606 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 HIS ** E 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.210199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.166122 restraints weight = 81821.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.171291 restraints weight = 53530.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.175026 restraints weight = 38535.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.177657 restraints weight = 29721.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.179359 restraints weight = 24330.904| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38368 Z= 0.132 Angle : 0.674 16.526 51708 Z= 0.354 Chirality : 0.045 0.317 5500 Planarity : 0.004 0.100 6636 Dihedral : 5.500 88.121 4984 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.13 % Favored : 90.60 % Rotamer: Outliers : 0.07 % Allowed : 0.87 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.12), residues: 4512 helix: -0.31 (0.11), residues: 2281 sheet: -1.01 (0.28), residues: 320 loop : -2.28 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 233 TYR 0.039 0.001 TYR B 482 PHE 0.070 0.001 PHE A 659 TRP 0.049 0.002 TRP B 601 HIS 0.007 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00282 (38368) covalent geometry : angle 0.67441 (51708) hydrogen bonds : bond 0.03901 ( 1637) hydrogen bonds : angle 5.18190 ( 4638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 847 time to evaluate : 1.489 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 29 CYS cc_start: 0.9014 (m) cc_final: 0.8550 (m) REVERT: A 32 GLU cc_start: 0.8916 (tt0) cc_final: 0.8716 (pt0) REVERT: A 60 TRP cc_start: 0.7284 (p-90) cc_final: 0.6915 (p-90) REVERT: A 98 MET cc_start: 0.7299 (mmp) cc_final: 0.7056 (mmp) REVERT: A 105 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7527 (mmmm) REVERT: A 109 GLN cc_start: 0.7909 (tt0) cc_final: 0.7579 (tt0) REVERT: A 120 LYS cc_start: 0.8533 (mttt) cc_final: 0.8221 (mttp) REVERT: A 124 MET cc_start: 0.8348 (tpp) cc_final: 0.7730 (tpp) REVERT: A 125 ASN cc_start: 0.8922 (m-40) cc_final: 0.8598 (m110) REVERT: A 128 HIS cc_start: 0.7526 (m-70) cc_final: 0.7058 (m-70) REVERT: A 144 LYS cc_start: 0.8671 (pttt) cc_final: 0.8458 (pttt) REVERT: A 190 TYR cc_start: 0.7023 (m-80) cc_final: 0.6533 (m-80) REVERT: A 223 TYR cc_start: 0.7606 (m-80) cc_final: 0.6921 (m-80) REVERT: A 233 ARG cc_start: 0.7099 (tmm160) cc_final: 0.6606 (tmm160) REVERT: A 313 TYR cc_start: 0.6666 (t80) cc_final: 0.6369 (t80) REVERT: A 326 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7568 (mtp180) REVERT: A 393 VAL cc_start: 0.6828 (t) cc_final: 0.6540 (p) REVERT: A 396 MET cc_start: 0.6961 (ptp) cc_final: 0.6297 (ptp) REVERT: A 421 MET cc_start: 0.4446 (mpp) cc_final: 0.4170 (mpp) REVERT: A 477 ASN cc_start: 0.8282 (m110) cc_final: 0.8025 (m110) REVERT: A 482 TYR cc_start: 0.3689 (t80) cc_final: 0.3357 (t80) REVERT: A 540 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6671 (ttpt) REVERT: A 586 LEU cc_start: 0.8944 (pp) cc_final: 0.8289 (pp) REVERT: A 588 LEU cc_start: 0.8266 (mt) cc_final: 0.7755 (mt) REVERT: A 589 TYR cc_start: 0.7908 (m-80) cc_final: 0.7243 (m-80) REVERT: A 594 PHE cc_start: 0.7541 (t80) cc_final: 0.7128 (t80) REVERT: A 622 LYS cc_start: 0.7911 (pptt) cc_final: 0.7229 (pttt) REVERT: A 671 CYS cc_start: 0.8114 (p) cc_final: 0.7402 (t) REVERT: A 686 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 688 LEU cc_start: 0.9032 (tp) cc_final: 0.8762 (tp) REVERT: A 694 GLU cc_start: 0.6780 (mp0) cc_final: 0.6479 (mp0) REVERT: A 698 GLN cc_start: 0.7098 (tp-100) cc_final: 0.6672 (tp-100) REVERT: A 704 MET cc_start: 0.5256 (ttt) cc_final: 0.4956 (ttt) REVERT: A 711 GLN cc_start: 0.8259 (mp10) cc_final: 0.7787 (mm-40) REVERT: A 913 MET cc_start: -0.5448 (mmp) cc_final: -0.5781 (mmp) REVERT: A 936 MET cc_start: 0.2324 (mmp) cc_final: 0.0418 (ttm) REVERT: A 976 MET cc_start: 0.5105 (mpp) cc_final: 0.4767 (mpp) REVERT: B 28 GLU cc_start: 0.8567 (pt0) cc_final: 0.8181 (pt0) REVERT: B 31 LYS cc_start: 0.8539 (tmmt) cc_final: 0.8319 (ptmm) REVERT: B 32 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7648 (mm-30) REVERT: B 36 SER cc_start: 0.8077 (m) cc_final: 0.7589 (m) REVERT: B 95 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7752 (mmtt) REVERT: B 118 HIS cc_start: 0.7865 (m-70) cc_final: 0.7623 (m-70) REVERT: B 179 LYS cc_start: 0.7291 (mppt) cc_final: 0.7009 (mmtt) REVERT: B 188 ASP cc_start: 0.8184 (t0) cc_final: 0.7949 (t0) REVERT: B 190 TYR cc_start: 0.8074 (m-10) cc_final: 0.7672 (m-10) REVERT: B 197 TYR cc_start: 0.7629 (p90) cc_final: 0.7165 (p90) REVERT: B 227 MET cc_start: 0.7745 (tmm) cc_final: 0.7489 (tmm) REVERT: B 228 LEU cc_start: 0.8229 (mt) cc_final: 0.7586 (mt) REVERT: B 229 LEU cc_start: 0.8657 (mt) cc_final: 0.8316 (pp) REVERT: B 258 LEU cc_start: 0.8632 (mt) cc_final: 0.8317 (mt) REVERT: B 260 TYR cc_start: 0.6674 (t80) cc_final: 0.6175 (t80) REVERT: B 327 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8230 (mmtp) REVERT: B 350 LYS cc_start: 0.7450 (tppt) cc_final: 0.7149 (tppt) REVERT: B 385 PHE cc_start: 0.8378 (t80) cc_final: 0.8134 (t80) REVERT: B 412 LEU cc_start: 0.8557 (tp) cc_final: 0.8226 (tt) REVERT: B 421 MET cc_start: 0.6175 (mtm) cc_final: 0.5477 (mtm) REVERT: B 435 ASP cc_start: 0.8428 (m-30) cc_final: 0.8172 (m-30) REVERT: B 437 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8334 (mmmm) REVERT: B 441 PHE cc_start: 0.8451 (m-10) cc_final: 0.8133 (m-80) REVERT: B 442 LEU cc_start: 0.8637 (mt) cc_final: 0.8163 (mt) REVERT: B 472 TYR cc_start: 0.7231 (t80) cc_final: 0.6886 (t80) REVERT: B 478 ARG cc_start: 0.8125 (ptt180) cc_final: 0.7827 (ptt180) REVERT: B 481 ILE cc_start: 0.8741 (mm) cc_final: 0.8390 (mm) REVERT: B 524 ILE cc_start: 0.8190 (pt) cc_final: 0.7623 (mm) REVERT: B 593 ARG cc_start: 0.7801 (ptt180) cc_final: 0.7402 (ptt180) REVERT: B 600 LEU cc_start: 0.7787 (tp) cc_final: 0.7560 (tp) REVERT: B 614 ASN cc_start: 0.7744 (m-40) cc_final: 0.7411 (m-40) REVERT: C 206 MET cc_start: 0.4310 (pmm) cc_final: 0.3813 (pmm) REVERT: E 92 TYR cc_start: 0.7554 (t80) cc_final: 0.7072 (t80) REVERT: E 118 HIS cc_start: 0.7777 (m90) cc_final: 0.7428 (m90) REVERT: E 120 LYS cc_start: 0.9113 (mttp) cc_final: 0.8903 (mttp) REVERT: E 158 VAL cc_start: 0.8032 (t) cc_final: 0.7738 (p) REVERT: E 254 GLU cc_start: 0.6507 (pm20) cc_final: 0.6265 (pt0) REVERT: E 307 GLU cc_start: 0.7267 (tt0) cc_final: 0.6704 (tt0) REVERT: E 328 ILE cc_start: 0.6980 (pt) cc_final: 0.6751 (pt) REVERT: E 373 LEU cc_start: 0.7761 (tp) cc_final: 0.7243 (tp) REVERT: E 378 TYR cc_start: 0.7853 (m-10) cc_final: 0.7522 (m-80) REVERT: E 379 GLU cc_start: 0.8529 (pt0) cc_final: 0.8227 (pt0) REVERT: E 393 VAL cc_start: 0.8310 (m) cc_final: 0.8057 (p) REVERT: E 396 MET cc_start: 0.7002 (tmm) cc_final: 0.6739 (tmm) REVERT: E 419 ASP cc_start: 0.7943 (p0) cc_final: 0.7555 (m-30) REVERT: E 421 MET cc_start: 0.7936 (mmt) cc_final: 0.7254 (mmt) REVERT: E 422 LYS cc_start: 0.8633 (tppt) cc_final: 0.8230 (tppt) REVERT: E 448 TRP cc_start: 0.8066 (m-90) cc_final: 0.7584 (m-90) REVERT: E 475 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7305 (mm-40) REVERT: E 527 LEU cc_start: 0.8444 (tp) cc_final: 0.8070 (tp) REVERT: E 531 MET cc_start: 0.7239 (tpt) cc_final: 0.7008 (mmm) REVERT: E 544 PHE cc_start: 0.7138 (t80) cc_final: 0.6895 (t80) REVERT: E 564 LYS cc_start: 0.8357 (tptm) cc_final: 0.7757 (mttp) REVERT: E 568 GLU cc_start: 0.8526 (mp0) cc_final: 0.8125 (mp0) REVERT: E 607 GLU cc_start: 0.7847 (pm20) cc_final: 0.7402 (pm20) REVERT: E 609 HIS cc_start: 0.7918 (m90) cc_final: 0.7521 (m90) REVERT: E 629 ARG cc_start: 0.7332 (ttt180) cc_final: 0.7003 (ttt-90) REVERT: E 634 LEU cc_start: 0.8152 (mm) cc_final: 0.7909 (tp) REVERT: E 645 PHE cc_start: 0.7950 (t80) cc_final: 0.7116 (t80) REVERT: E 651 ASP cc_start: 0.8071 (m-30) cc_final: 0.7866 (m-30) REVERT: E 662 ASP cc_start: 0.8358 (p0) cc_final: 0.7913 (p0) REVERT: E 666 ASN cc_start: 0.7826 (t0) cc_final: 0.7497 (t0) REVERT: E 669 ARG cc_start: 0.7900 (ttt90) cc_final: 0.7441 (ttt90) REVERT: E 674 ASP cc_start: 0.7418 (m-30) cc_final: 0.7082 (m-30) REVERT: E 691 ILE cc_start: 0.8426 (mm) cc_final: 0.7814 (mm) REVERT: E 705 ASN cc_start: 0.8181 (p0) cc_final: 0.7968 (p0) REVERT: E 706 VAL cc_start: 0.8209 (t) cc_final: 0.7732 (p) REVERT: E 712 PHE cc_start: 0.7491 (m-10) cc_final: 0.7172 (m-10) REVERT: E 722 PHE cc_start: 0.8193 (t80) cc_final: 0.7729 (t80) REVERT: E 913 MET cc_start: 0.7606 (mmm) cc_final: 0.6759 (mmm) REVERT: E 919 TRP cc_start: 0.7867 (m-90) cc_final: 0.7327 (m100) REVERT: E 966 LEU cc_start: 0.7773 (tp) cc_final: 0.7506 (tp) REVERT: E 974 LYS cc_start: 0.9251 (tppt) cc_final: 0.8852 (tppt) REVERT: F 25 ASN cc_start: 0.8874 (p0) cc_final: 0.8613 (p0) REVERT: F 66 TYR cc_start: 0.8148 (m-80) cc_final: 0.7872 (m-80) REVERT: F 98 MET cc_start: 0.8497 (mmp) cc_final: 0.8265 (mmp) REVERT: F 100 PHE cc_start: 0.7798 (t80) cc_final: 0.6862 (t80) REVERT: F 201 SER cc_start: 0.7976 (p) cc_final: 0.7393 (p) REVERT: F 227 MET cc_start: 0.8027 (tmm) cc_final: 0.7033 (tmm) REVERT: F 228 LEU cc_start: 0.7916 (tp) cc_final: 0.7516 (mp) REVERT: F 242 LYS cc_start: 0.8272 (ptmm) cc_final: 0.7815 (ptmm) REVERT: F 290 MET cc_start: 0.8539 (mmp) cc_final: 0.8317 (mmp) REVERT: F 315 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7316 (mmtm) REVERT: F 329 ASP cc_start: 0.8056 (m-30) cc_final: 0.7568 (m-30) REVERT: F 336 TYR cc_start: 0.7610 (m-80) cc_final: 0.7170 (m-80) REVERT: F 376 LYS cc_start: 0.8270 (tptt) cc_final: 0.8023 (tptt) REVERT: F 422 LYS cc_start: 0.8651 (tmmt) cc_final: 0.8273 (tptt) REVERT: F 436 TYR cc_start: 0.8282 (t80) cc_final: 0.7774 (t80) REVERT: F 442 LEU cc_start: 0.8746 (mt) cc_final: 0.8518 (mt) REVERT: F 483 GLN cc_start: 0.8692 (mt0) cc_final: 0.8152 (mt0) REVERT: F 487 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7359 (tp40) REVERT: F 516 GLU cc_start: 0.7966 (tp30) cc_final: 0.7567 (tp30) REVERT: F 518 GLU cc_start: 0.8009 (tp30) cc_final: 0.7526 (tp30) REVERT: F 519 MET cc_start: 0.7486 (mmm) cc_final: 0.7199 (mmm) REVERT: F 521 ASN cc_start: 0.7341 (t0) cc_final: 0.7103 (t0) REVERT: F 531 MET cc_start: 0.6227 (mmp) cc_final: 0.5820 (mmp) REVERT: F 534 GLU cc_start: 0.7791 (tp30) cc_final: 0.7563 (tp30) REVERT: F 538 LYS cc_start: 0.8408 (pttm) cc_final: 0.7998 (pttt) REVERT: F 545 LEU cc_start: 0.8848 (mm) cc_final: 0.8435 (mp) REVERT: F 559 PHE cc_start: 0.7295 (t80) cc_final: 0.6978 (t80) REVERT: F 560 GLU cc_start: 0.6976 (tp30) cc_final: 0.6698 (tp30) REVERT: F 576 PHE cc_start: 0.5798 (m-10) cc_final: 0.5076 (m-10) REVERT: F 616 MET cc_start: 0.7997 (ttp) cc_final: 0.7673 (ptp) REVERT: F 620 ILE cc_start: 0.7718 (tp) cc_final: 0.7446 (tt) REVERT: F 694 GLU cc_start: 0.7104 (tp30) cc_final: 0.6779 (tp30) REVERT: F 724 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8342 (ptpt) REVERT: F 746 GLU cc_start: 0.8066 (pp20) cc_final: 0.7408 (pp20) REVERT: F 758 LEU cc_start: 0.8658 (mt) cc_final: 0.8361 (mt) REVERT: F 767 LEU cc_start: 0.7724 (mp) cc_final: 0.7158 (mt) REVERT: F 815 PHE cc_start: 0.7820 (t80) cc_final: 0.7019 (t80) REVERT: F 913 MET cc_start: 0.8071 (pmm) cc_final: 0.7819 (pmm) REVERT: F 940 TYR cc_start: 0.8016 (t80) cc_final: 0.7786 (t80) REVERT: F 941 ASP cc_start: 0.8043 (m-30) cc_final: 0.7777 (m-30) REVERT: F 942 PHE cc_start: 0.8211 (t80) cc_final: 0.7845 (t80) REVERT: F 943 PHE cc_start: 0.7624 (m-80) cc_final: 0.6920 (m-80) REVERT: G 15 ARG cc_start: 0.7674 (ptp-110) cc_final: 0.7436 (ptp-110) REVERT: G 61 LEU cc_start: 0.7998 (mp) cc_final: 0.7652 (mp) REVERT: G 71 GLU cc_start: 0.6399 (pm20) cc_final: 0.5763 (pm20) REVERT: G 72 TRP cc_start: 0.6271 (m100) cc_final: 0.5355 (m100) REVERT: G 194 GLN cc_start: 0.7021 (tp40) cc_final: 0.6202 (mm-40) REVERT: G 195 PHE cc_start: 0.7914 (m-80) cc_final: 0.6997 (m-80) REVERT: G 201 SER cc_start: 0.7064 (p) cc_final: 0.6557 (p) REVERT: G 206 MET cc_start: 0.7084 (mtm) cc_final: 0.6628 (mtm) REVERT: G 217 GLU cc_start: 0.7459 (tp30) cc_final: 0.6986 (tp30) REVERT: G 219 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7972 (mtmm) REVERT: H 13 PHE cc_start: 0.5895 (m-80) cc_final: 0.5342 (m-80) REVERT: H 65 ASN cc_start: 0.5152 (p0) cc_final: 0.4459 (p0) REVERT: H 197 ASN cc_start: 0.6030 (t0) cc_final: 0.5611 (t0) REVERT: H 206 MET cc_start: 0.6215 (tpt) cc_final: 0.5628 (tpt) REVERT: H 219 LYS cc_start: 0.8349 (tptp) cc_final: 0.8133 (tptt) outliers start: 3 outliers final: 1 residues processed: 849 average time/residue: 0.2471 time to fit residues: 335.8798 Evaluate side-chains 809 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 808 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 47 optimal weight: 0.0970 chunk 306 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 432 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 370 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN E 606 HIS ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN ** F 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.204072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.160006 restraints weight = 80129.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.165037 restraints weight = 52353.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.168582 restraints weight = 37701.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.171051 restraints weight = 29250.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.172916 restraints weight = 24109.092| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 38368 Z= 0.205 Angle : 0.732 14.244 51708 Z= 0.393 Chirality : 0.047 0.452 5500 Planarity : 0.005 0.130 6636 Dihedral : 5.785 85.645 4984 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.97 % Favored : 89.78 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.12), residues: 4512 helix: -0.51 (0.11), residues: 2282 sheet: -1.03 (0.29), residues: 300 loop : -2.30 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 233 TYR 0.041 0.002 TYR B 482 PHE 0.054 0.002 PHE A 659 TRP 0.058 0.003 TRP B 601 HIS 0.012 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00416 (38368) covalent geometry : angle 0.73241 (51708) hydrogen bonds : bond 0.04555 ( 1637) hydrogen bonds : angle 5.56534 ( 4638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 855 time to evaluate : 1.482 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 29 CYS cc_start: 0.9067 (m) cc_final: 0.8512 (t) REVERT: A 32 GLU cc_start: 0.8883 (tt0) cc_final: 0.8569 (pt0) REVERT: A 38 ARG cc_start: 0.8082 (tpt170) cc_final: 0.7652 (tpt170) REVERT: A 56 TYR cc_start: 0.6562 (t80) cc_final: 0.6086 (t80) REVERT: A 60 TRP cc_start: 0.7427 (p-90) cc_final: 0.7003 (p-90) REVERT: A 98 MET cc_start: 0.7374 (mmp) cc_final: 0.7111 (mmp) REVERT: A 105 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7832 (mmtm) REVERT: A 120 LYS cc_start: 0.8623 (mttt) cc_final: 0.8363 (mttp) REVERT: A 124 MET cc_start: 0.8399 (tpp) cc_final: 0.7820 (tpp) REVERT: A 125 ASN cc_start: 0.8922 (m-40) cc_final: 0.8720 (m-40) REVERT: A 144 LYS cc_start: 0.8643 (pttt) cc_final: 0.8385 (pttt) REVERT: A 176 LYS cc_start: 0.8497 (mmtm) cc_final: 0.8139 (mmtm) REVERT: A 190 TYR cc_start: 0.7167 (m-80) cc_final: 0.6686 (m-80) REVERT: A 233 ARG cc_start: 0.7227 (tmm160) cc_final: 0.6735 (tmm160) REVERT: A 238 ASP cc_start: 0.7719 (p0) cc_final: 0.7009 (m-30) REVERT: A 284 GLU cc_start: 0.7948 (tp30) cc_final: 0.7693 (tp30) REVERT: A 313 TYR cc_start: 0.6732 (t80) cc_final: 0.6378 (t80) REVERT: A 326 ARG cc_start: 0.8004 (mtm110) cc_final: 0.7362 (mtm110) REVERT: A 329 ASP cc_start: 0.7995 (t0) cc_final: 0.7101 (t0) REVERT: A 393 VAL cc_start: 0.7011 (t) cc_final: 0.6734 (p) REVERT: A 421 MET cc_start: 0.4546 (mpp) cc_final: 0.4303 (mpp) REVERT: A 476 ILE cc_start: 0.7731 (tt) cc_final: 0.7333 (mt) REVERT: A 482 TYR cc_start: 0.3961 (t80) cc_final: 0.3665 (t80) REVERT: A 540 LYS cc_start: 0.7278 (ttpt) cc_final: 0.6835 (ttpt) REVERT: A 586 LEU cc_start: 0.8993 (pp) cc_final: 0.8375 (pp) REVERT: A 589 TYR cc_start: 0.7907 (m-80) cc_final: 0.7261 (m-80) REVERT: A 594 PHE cc_start: 0.7582 (t80) cc_final: 0.7088 (t80) REVERT: A 616 MET cc_start: 0.7642 (ptt) cc_final: 0.7317 (tpt) REVERT: A 622 LYS cc_start: 0.8054 (pptt) cc_final: 0.7378 (pttt) REVERT: A 685 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 686 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 694 GLU cc_start: 0.6869 (mp0) cc_final: 0.6573 (mp0) REVERT: A 698 GLN cc_start: 0.7344 (tp-100) cc_final: 0.6904 (tp-100) REVERT: A 704 MET cc_start: 0.5302 (ttt) cc_final: 0.4990 (ttt) REVERT: A 711 GLN cc_start: 0.8293 (mp10) cc_final: 0.7809 (mm-40) REVERT: A 913 MET cc_start: -0.5278 (mmp) cc_final: -0.5592 (mmp) REVERT: A 936 MET cc_start: 0.2510 (mmp) cc_final: 0.0571 (ttm) REVERT: A 976 MET cc_start: 0.5178 (mpp) cc_final: 0.4871 (mpp) REVERT: B 28 GLU cc_start: 0.8701 (pt0) cc_final: 0.8298 (pt0) REVERT: B 32 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8188 (mm-30) REVERT: B 95 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7915 (mmtt) REVERT: B 118 HIS cc_start: 0.7987 (m-70) cc_final: 0.7738 (m-70) REVERT: B 135 ASP cc_start: 0.8118 (m-30) cc_final: 0.7744 (m-30) REVERT: B 179 LYS cc_start: 0.7358 (mppt) cc_final: 0.7074 (mmtt) REVERT: B 183 VAL cc_start: 0.7917 (t) cc_final: 0.7693 (m) REVERT: B 190 TYR cc_start: 0.8128 (m-10) cc_final: 0.7721 (m-10) REVERT: B 197 TYR cc_start: 0.7624 (p90) cc_final: 0.7184 (p90) REVERT: B 228 LEU cc_start: 0.8240 (mt) cc_final: 0.7627 (mt) REVERT: B 229 LEU cc_start: 0.8689 (mt) cc_final: 0.8430 (pp) REVERT: B 258 LEU cc_start: 0.8747 (mt) cc_final: 0.8458 (mt) REVERT: B 260 TYR cc_start: 0.6914 (t80) cc_final: 0.6487 (t80) REVERT: B 327 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8377 (mmtp) REVERT: B 336 TYR cc_start: 0.6706 (m-80) cc_final: 0.6364 (m-10) REVERT: B 350 LYS cc_start: 0.7549 (tppt) cc_final: 0.7245 (tppt) REVERT: B 385 PHE cc_start: 0.8415 (t80) cc_final: 0.8203 (t80) REVERT: B 412 LEU cc_start: 0.8648 (tp) cc_final: 0.8242 (tt) REVERT: B 421 MET cc_start: 0.6256 (mtm) cc_final: 0.5483 (mtm) REVERT: B 435 ASP cc_start: 0.8442 (m-30) cc_final: 0.8205 (m-30) REVERT: B 437 LYS cc_start: 0.8707 (mmtp) cc_final: 0.8296 (mmmm) REVERT: B 441 PHE cc_start: 0.8602 (m-10) cc_final: 0.8261 (m-80) REVERT: B 442 LEU cc_start: 0.8726 (mt) cc_final: 0.8271 (mt) REVERT: B 472 TYR cc_start: 0.7321 (t80) cc_final: 0.6894 (t80) REVERT: B 476 ILE cc_start: 0.8713 (mm) cc_final: 0.8475 (mm) REVERT: B 481 ILE cc_start: 0.8766 (mm) cc_final: 0.8437 (mm) REVERT: B 482 TYR cc_start: 0.7153 (t80) cc_final: 0.6647 (t80) REVERT: B 492 PHE cc_start: 0.7978 (m-80) cc_final: 0.7677 (m-80) REVERT: B 531 MET cc_start: 0.3588 (ppp) cc_final: 0.2635 (ppp) REVERT: B 569 MET cc_start: 0.7038 (tmm) cc_final: 0.6187 (tmm) REVERT: B 593 ARG cc_start: 0.7914 (ptt180) cc_final: 0.7661 (ptt180) REVERT: B 597 GLU cc_start: 0.8199 (tt0) cc_final: 0.7915 (tt0) REVERT: C 206 MET cc_start: 0.4439 (pmm) cc_final: 0.3960 (pmm) REVERT: E 70 LEU cc_start: 0.7053 (mp) cc_final: 0.6658 (mt) REVERT: E 92 TYR cc_start: 0.7593 (t80) cc_final: 0.7070 (t80) REVERT: E 118 HIS cc_start: 0.7965 (m90) cc_final: 0.7547 (m90) REVERT: E 144 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8233 (pttm) REVERT: E 164 SER cc_start: 0.8289 (p) cc_final: 0.8084 (p) REVERT: E 193 TYR cc_start: 0.7761 (t80) cc_final: 0.7502 (t80) REVERT: E 307 GLU cc_start: 0.7261 (tt0) cc_final: 0.6657 (tt0) REVERT: E 379 GLU cc_start: 0.8552 (pt0) cc_final: 0.8236 (pt0) REVERT: E 393 VAL cc_start: 0.8343 (m) cc_final: 0.8075 (p) REVERT: E 396 MET cc_start: 0.7079 (tmm) cc_final: 0.6736 (tmm) REVERT: E 419 ASP cc_start: 0.8126 (p0) cc_final: 0.7794 (m-30) REVERT: E 421 MET cc_start: 0.8014 (mmt) cc_final: 0.7251 (mmt) REVERT: E 422 LYS cc_start: 0.8676 (tppt) cc_final: 0.8242 (tppt) REVERT: E 437 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7787 (mmtt) REVERT: E 448 TRP cc_start: 0.8124 (m-90) cc_final: 0.7696 (m-90) REVERT: E 472 TYR cc_start: 0.7405 (t80) cc_final: 0.7125 (t80) REVERT: E 527 LEU cc_start: 0.8652 (tp) cc_final: 0.8404 (tp) REVERT: E 564 LYS cc_start: 0.8337 (tptm) cc_final: 0.7724 (mttp) REVERT: E 568 GLU cc_start: 0.8507 (mp0) cc_final: 0.7963 (mp0) REVERT: E 607 GLU cc_start: 0.7871 (pm20) cc_final: 0.7491 (pm20) REVERT: E 609 HIS cc_start: 0.8106 (m90) cc_final: 0.7681 (m90) REVERT: E 629 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7220 (ttt-90) REVERT: E 634 LEU cc_start: 0.8236 (mm) cc_final: 0.7734 (tt) REVERT: E 645 PHE cc_start: 0.7989 (t80) cc_final: 0.7162 (t80) REVERT: E 651 ASP cc_start: 0.8149 (m-30) cc_final: 0.7884 (m-30) REVERT: E 662 ASP cc_start: 0.8481 (p0) cc_final: 0.8066 (p0) REVERT: E 663 ASP cc_start: 0.8434 (m-30) cc_final: 0.8222 (m-30) REVERT: E 666 ASN cc_start: 0.7943 (t0) cc_final: 0.7594 (t0) REVERT: E 669 ARG cc_start: 0.8047 (ttt90) cc_final: 0.7656 (ttt90) REVERT: E 674 ASP cc_start: 0.7510 (m-30) cc_final: 0.7214 (m-30) REVERT: E 691 ILE cc_start: 0.8442 (mm) cc_final: 0.7819 (mm) REVERT: E 695 ILE cc_start: 0.8143 (pt) cc_final: 0.7863 (pt) REVERT: E 705 ASN cc_start: 0.8304 (p0) cc_final: 0.8006 (p0) REVERT: E 706 VAL cc_start: 0.8399 (t) cc_final: 0.7981 (p) REVERT: E 712 PHE cc_start: 0.7486 (m-10) cc_final: 0.7148 (m-10) REVERT: E 722 PHE cc_start: 0.8350 (t80) cc_final: 0.7705 (t80) REVERT: E 742 PHE cc_start: 0.7370 (t80) cc_final: 0.7095 (t80) REVERT: E 815 PHE cc_start: 0.6877 (t80) cc_final: 0.6656 (t80) REVERT: E 837 PHE cc_start: 0.8620 (t80) cc_final: 0.8402 (t80) REVERT: E 913 MET cc_start: 0.7705 (mmm) cc_final: 0.6992 (mmm) REVERT: E 914 SER cc_start: 0.8624 (p) cc_final: 0.8344 (t) REVERT: E 919 TRP cc_start: 0.7976 (m-90) cc_final: 0.7484 (m100) REVERT: E 966 LEU cc_start: 0.7848 (tp) cc_final: 0.7552 (tp) REVERT: E 974 LYS cc_start: 0.9244 (tppt) cc_final: 0.8829 (tppt) REVERT: F 25 ASN cc_start: 0.8902 (p0) cc_final: 0.8661 (p0) REVERT: F 100 PHE cc_start: 0.7928 (t80) cc_final: 0.7670 (t80) REVERT: F 201 SER cc_start: 0.8004 (p) cc_final: 0.7386 (p) REVERT: F 227 MET cc_start: 0.8123 (tmm) cc_final: 0.7901 (tmm) REVERT: F 242 LYS cc_start: 0.8499 (ptmm) cc_final: 0.8089 (ptmm) REVERT: F 290 MET cc_start: 0.8556 (mmp) cc_final: 0.8252 (mmp) REVERT: F 291 ASP cc_start: 0.8300 (m-30) cc_final: 0.7927 (m-30) REVERT: F 315 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7552 (mmtm) REVERT: F 329 ASP cc_start: 0.8066 (m-30) cc_final: 0.7628 (m-30) REVERT: F 336 TYR cc_start: 0.7676 (m-80) cc_final: 0.7233 (m-80) REVERT: F 357 MET cc_start: 0.8108 (pmm) cc_final: 0.7805 (pmm) REVERT: F 358 GLU cc_start: 0.8240 (tm-30) cc_final: 0.8034 (tm-30) REVERT: F 376 LYS cc_start: 0.8350 (tptt) cc_final: 0.6765 (tptp) REVERT: F 380 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.7780 (mtt-85) REVERT: F 442 LEU cc_start: 0.8769 (mt) cc_final: 0.8503 (mt) REVERT: F 483 GLN cc_start: 0.8770 (mt0) cc_final: 0.8218 (mt0) REVERT: F 487 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7615 (tm-30) REVERT: F 516 GLU cc_start: 0.8023 (tp30) cc_final: 0.7677 (tp30) REVERT: F 518 GLU cc_start: 0.8072 (tp30) cc_final: 0.7523 (tp30) REVERT: F 519 MET cc_start: 0.7544 (mmm) cc_final: 0.7268 (mmm) REVERT: F 531 MET cc_start: 0.6293 (mmp) cc_final: 0.5895 (mmp) REVERT: F 533 PHE cc_start: 0.5570 (m-80) cc_final: 0.5315 (m-80) REVERT: F 534 GLU cc_start: 0.7839 (tp30) cc_final: 0.7382 (tm-30) REVERT: F 537 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8099 (mmtm) REVERT: F 538 LYS cc_start: 0.8428 (pttm) cc_final: 0.6792 (pttt) REVERT: F 545 LEU cc_start: 0.8891 (mm) cc_final: 0.8418 (mp) REVERT: F 555 THR cc_start: 0.7776 (m) cc_final: 0.7453 (p) REVERT: F 620 ILE cc_start: 0.7851 (tp) cc_final: 0.7590 (tt) REVERT: F 677 ARG cc_start: 0.6678 (ttp80) cc_final: 0.6440 (ttp80) REVERT: F 694 GLU cc_start: 0.7160 (tp30) cc_final: 0.6736 (tp30) REVERT: F 724 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8199 (ptpt) REVERT: F 746 GLU cc_start: 0.8191 (pp20) cc_final: 0.7640 (pp20) REVERT: F 758 LEU cc_start: 0.8735 (mt) cc_final: 0.8436 (mt) REVERT: F 767 LEU cc_start: 0.7954 (mp) cc_final: 0.7388 (mt) REVERT: F 815 PHE cc_start: 0.7934 (t80) cc_final: 0.7505 (t80) REVERT: F 833 LYS cc_start: 0.8581 (pttt) cc_final: 0.7901 (mmtm) REVERT: F 834 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8314 (mp10) REVERT: F 913 MET cc_start: 0.8058 (pmm) cc_final: 0.7604 (pmm) REVERT: F 940 TYR cc_start: 0.8121 (t80) cc_final: 0.7794 (t80) REVERT: F 942 PHE cc_start: 0.8239 (t80) cc_final: 0.7963 (t80) REVERT: F 943 PHE cc_start: 0.7741 (m-80) cc_final: 0.6978 (m-80) REVERT: G 15 ARG cc_start: 0.7777 (ptp-110) cc_final: 0.7557 (ptp-110) REVERT: G 61 LEU cc_start: 0.8171 (mp) cc_final: 0.7787 (mp) REVERT: G 194 GLN cc_start: 0.7322 (tp40) cc_final: 0.6736 (mm-40) REVERT: G 195 PHE cc_start: 0.8088 (m-80) cc_final: 0.7279 (m-80) REVERT: G 201 SER cc_start: 0.7207 (p) cc_final: 0.6448 (p) REVERT: G 206 MET cc_start: 0.7302 (mtm) cc_final: 0.6907 (mtm) REVERT: G 219 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8022 (mtmm) REVERT: H 13 PHE cc_start: 0.6053 (m-80) cc_final: 0.5444 (m-80) REVERT: H 65 ASN cc_start: 0.5077 (p0) cc_final: 0.4348 (p0) REVERT: H 171 TYR cc_start: 0.7631 (t80) cc_final: 0.7257 (t80) REVERT: H 197 ASN cc_start: 0.6273 (t0) cc_final: 0.5902 (t0) REVERT: H 206 MET cc_start: 0.6459 (tpt) cc_final: 0.5811 (tpt) outliers start: 2 outliers final: 1 residues processed: 857 average time/residue: 0.2573 time to fit residues: 352.3909 Evaluate side-chains 810 residues out of total 4124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 809 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 315 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 317 optimal weight: 0.8980 chunk 427 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 133 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 195 GLN ** E 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 961 ASN ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.207698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.163537 restraints weight = 80903.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.168636 restraints weight = 52726.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.172323 restraints weight = 37945.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.174886 restraints weight = 29270.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.176835 restraints weight = 23930.090| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38368 Z= 0.148 Angle : 0.693 15.650 51708 Z= 0.365 Chirality : 0.046 0.379 5500 Planarity : 0.005 0.099 6636 Dihedral : 5.630 85.499 4984 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.74 % Rotamer: Outliers : 0.02 % Allowed : 0.46 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.12), residues: 4512 helix: -0.44 (0.11), residues: 2290 sheet: -1.18 (0.28), residues: 320 loop : -2.29 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 233 TYR 0.036 0.001 TYR B 482 PHE 0.048 0.002 PHE A 659 TRP 0.054 0.002 TRP B 601 HIS 0.011 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00310 (38368) covalent geometry : angle 0.69296 (51708) hydrogen bonds : bond 0.04109 ( 1637) hydrogen bonds : angle 5.30358 ( 4638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9094.09 seconds wall clock time: 157 minutes 16.72 seconds (9436.72 seconds total)