Starting phenix.real_space_refine on Fri Nov 21 03:42:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygn_39257/11_2025/8ygn_39257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygn_39257/11_2025/8ygn_39257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygn_39257/11_2025/8ygn_39257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygn_39257/11_2025/8ygn_39257.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygn_39257/11_2025/8ygn_39257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygn_39257/11_2025/8ygn_39257.cif" } resolution = 4.27 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 14987 2.51 5 N 3749 2.21 5 O 4421 1.98 5 H 20406 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43648 Number of models: 1 Model: "" Number of chains: 6 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: "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: "A" Number of atoms: 16194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 16194 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "B" Number of atoms: 16194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 16194 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "E" Number of atoms: 4470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4470 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain: "F" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4394 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Time building chain proxies: 7.72, per 1000 atoms: 0.18 Number of scatterers: 43648 At special positions: 0 Unit cell: (107.07, 136.12, 181.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 4421 8.00 N 3749 7.00 C 14987 6.00 H 20406 1.00 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: 4.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 10 sheets defined 61.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.676A pdb=" N ALA C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 39 Processing helix chain 'A' and resid 47 through 52 removed outlier: 4.078A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 80 through 95 removed outlier: 4.039A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.621A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.940A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.933A pdb=" N ASN A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 removed outlier: 3.609A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP A 194 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 222 through 237 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.133A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.973A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.200A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 removed outlier: 4.235A pdb=" N PHE A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.820A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 374 through 392 removed outlier: 3.908A pdb=" N PHE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.550A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.765A pdb=" N TYR A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 463 removed outlier: 3.533A pdb=" N SER A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 452 " --> pdb=" O TRP A 448 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 495 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 529 removed outlier: 4.095A pdb=" N PHE A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.814A pdb=" N TYR A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 544 removed outlier: 4.214A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 removed outlier: 3.654A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.562A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.792A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.889A pdb=" N LEU A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 648 through 659 removed outlier: 4.433A pdb=" N ASN A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.515A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.717A pdb=" N GLU A 685 " --> pdb=" O GLN A 681 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.589A pdb=" N THR A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 741 removed outlier: 3.506A pdb=" N LEU A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 761 removed outlier: 3.729A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.522A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.586A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 808 " --> pdb=" O TYR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 831 through 840 removed outlier: 3.501A pdb=" N LEU A 838 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.569A pdb=" N LEU A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.708A pdb=" N ILE A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 removed outlier: 4.207A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.873A pdb=" N PHE A 943 " --> pdb=" O GLN A 939 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 962 Processing helix chain 'A' and resid 963 through 970 removed outlier: 3.576A pdb=" N LYS A 969 " --> pdb=" O LYS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 991 removed outlier: 3.513A pdb=" N VAL A 983 " --> pdb=" O HIS A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1004 removed outlier: 3.605A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A1002 " --> pdb=" O GLU A 998 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A1004 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 39 removed outlier: 3.578A pdb=" N CYS B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.589A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 Processing helix chain 'B' and resid 80 through 108 removed outlier: 3.909A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 7.077A pdb=" N GLU B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N MET B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.800A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.550A pdb=" N ALA B 161 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 197 removed outlier: 6.155A pdb=" N ASP B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.566A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.709A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.618A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 removed outlier: 3.873A pdb=" N ILE B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 4.174A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 334 removed outlier: 4.048A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.684A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 374 through 392 removed outlier: 3.562A pdb=" N LYS B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.705A pdb=" N LEU B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 463 removed outlier: 3.614A pdb=" N SER B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 452 " --> pdb=" O TRP B 448 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 459 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 468 through 495 removed outlier: 3.958A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 480 " --> pdb=" O ILE B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.538A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 3.569A pdb=" N ASP B 526 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 528 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.592A pdb=" N LYS B 538 " --> pdb=" O GLU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.653A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 545 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 570 removed outlier: 3.751A pdb=" N THR B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 556 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 564 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 595 removed outlier: 3.676A pdb=" N VAL B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 604 Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.587A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU B 624 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.704A pdb=" N ARG B 657 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.643A pdb=" N LEU B 667 " --> pdb=" O ASP B 663 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER B 670 " --> pdb=" O ASN B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 682 through 701 removed outlier: 3.754A pdb=" N GLU B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 removed outlier: 3.672A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 713 " --> pdb=" O TYR B 709 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 726 Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.714A pdb=" N LEU B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.793A pdb=" N TYR B 755 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 784 removed outlier: 3.543A pdb=" N ILE B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.841A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 removed outlier: 3.835A pdb=" N GLU B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 842 Processing helix chain 'B' and resid 846 through 856 Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.723A pdb=" N ILE B 871 " --> pdb=" O ASN B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 902 removed outlier: 3.718A pdb=" N VAL B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.949A pdb=" N THR B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP B 919 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B 920 " --> pdb=" O PHE B 916 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.949A pdb=" N MET B 930 " --> pdb=" O ASN B 927 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.697A pdb=" N PHE B 943 " --> pdb=" O GLN B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 949 removed outlier: 3.783A pdb=" N PHE B 949 " --> pdb=" O PRO B 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 949' Processing helix chain 'B' and resid 957 through 962 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 990 Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.529A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 47 through 54 removed outlier: 3.918A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 72 removed outlier: 3.556A pdb=" N GLU E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 109 removed outlier: 3.648A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 7.164A pdb=" N GLU E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N MET E 98 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA E 99 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.862A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.707A pdb=" N VAL E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 160' Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.700A pdb=" N TYR E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.522A pdb=" N THR E 206 " --> pdb=" O ASN E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 237 removed outlier: 3.594A pdb=" N ASN E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 264 removed outlier: 3.510A pdb=" N ILE E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR E 260 " --> pdb=" O GLU E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'F' and resid 27 through 39 Processing helix chain 'F' and resid 47 through 54 removed outlier: 3.845A pdb=" N SER F 51 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 72 removed outlier: 3.619A pdb=" N LEU F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 109 removed outlier: 3.676A pdb=" N LEU F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) Proline residue: F 88 - end of helix removed outlier: 7.365A pdb=" N GLU F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N MET F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 124 removed outlier: 3.837A pdb=" N ASP F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 154 through 160 removed outlier: 3.985A pdb=" N VAL F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'F' and resid 197 through 211 removed outlier: 3.766A pdb=" N SER F 201 " --> pdb=" O TYR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 237 Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 254 through 264 removed outlier: 3.798A pdb=" N LYS F 264 " --> pdb=" O TYR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 274 No H-bonds generated for 'chain 'F' and resid 272 through 274' Processing helix chain 'F' and resid 281 through 296 Processing sheet with id=AA1, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.814A pdb=" N SER D 189 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 232 " --> pdb=" O PHE A 907 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 199 through 200 removed outlier: 3.737A pdb=" N GLU D 221 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.709A pdb=" N SER C 189 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.526A pdb=" N SER C 33 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 218 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.975A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 168 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A 43 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ILE A 216 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 45 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.776A pdb=" N VAL A 346 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.587A pdb=" N LEU B 167 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 214 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 45 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.260A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE E 213 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE E 246 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE E 215 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.015A pdb=" N SER F 150 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS F 169 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE F 152 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU F 42 " --> pdb=" O HIS F 128 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE F 130 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N PHE F 44 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 245 " --> pdb=" O ILE F 269 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 3006 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: 11.09 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20382 1.03 - 1.23: 189 1.23 - 1.43: 10222 1.43 - 1.63: 13239 1.63 - 1.82: 146 Bond restraints: 44178 Sorted by residual: bond pdb=" C ILE B 862 " pdb=" O ILE B 862 " ideal model delta sigma weight residual 1.237 1.178 0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" N ASN B 861 " pdb=" CA ASN B 861 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.25e-02 6.40e+03 1.47e+01 bond pdb=" N ILE B 862 " pdb=" CA ILE B 862 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.05e+01 bond pdb=" CA SER B 296 " pdb=" CB SER B 296 " ideal model delta sigma weight residual 1.528 1.491 0.036 1.33e-02 5.65e+03 7.43e+00 bond pdb=" N GLN B 297 " pdb=" CA GLN B 297 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.33e-02 5.65e+03 6.99e+00 ... (remaining 44173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.97: 78489 10.97 - 21.95: 4 21.95 - 32.92: 0 32.92 - 43.89: 3 43.89 - 54.86: 6 Bond angle restraints: 78502 Sorted by residual: angle pdb=" C SER A 851 " pdb=" N HIS A 852 " pdb=" H HIS A 852 " ideal model delta sigma weight residual 125.01 70.15 54.86 3.00e+00 1.11e-01 3.34e+02 angle pdb=" CA HIS A 852 " pdb=" N HIS A 852 " pdb=" H HIS A 852 " ideal model delta sigma weight residual 114.71 60.23 54.48 3.00e+00 1.11e-01 3.30e+02 angle pdb=" C SER A 858 " pdb=" N VAL A 859 " pdb=" H VAL A 859 " ideal model delta sigma weight residual 124.17 73.25 50.91 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C VAL A 859 " pdb=" N GLU A 860 " pdb=" H GLU A 860 " ideal model delta sigma weight residual 124.38 73.61 50.77 3.00e+00 1.11e-01 2.86e+02 angle pdb=" CA VAL A 859 " pdb=" N VAL A 859 " pdb=" H VAL A 859 " ideal model delta sigma weight residual 113.87 63.61 50.25 3.00e+00 1.11e-01 2.81e+02 ... (remaining 78497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 19058 17.94 - 35.88: 1615 35.88 - 53.82: 357 53.82 - 71.76: 77 71.76 - 89.70: 27 Dihedral angle restraints: 21134 sinusoidal: 10981 harmonic: 10153 Sorted by residual: dihedral pdb=" CA GLN A 297 " pdb=" C GLN A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta harmonic sigma weight residual 180.00 95.75 84.25 0 5.00e+00 4.00e-02 2.84e+02 dihedral pdb=" CA GLN B 297 " pdb=" C GLN B 297 " pdb=" N GLU B 298 " pdb=" CA GLU B 298 " ideal model delta harmonic sigma weight residual 180.00 -139.64 -40.36 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" CA ARG B 657 " pdb=" C ARG B 657 " pdb=" N HIS B 658 " pdb=" CA HIS B 658 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 21131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3181 0.077 - 0.154: 233 0.154 - 0.231: 6 0.231 - 0.308: 0 0.308 - 0.386: 2 Chirality restraints: 3422 Sorted by residual: chirality pdb=" CG LEU A 319 " pdb=" CB LEU A 319 " pdb=" CD1 LEU A 319 " pdb=" CD2 LEU A 319 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ILE A 302 " pdb=" N ILE A 302 " pdb=" C ILE A 302 " pdb=" CB ILE A 302 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU A 235 " pdb=" CB LEU A 235 " pdb=" CD1 LEU A 235 " pdb=" CD2 LEU A 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 3419 not shown) Planarity restraints: 6567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 861 " 0.186 2.00e-02 2.50e+03 4.17e-01 2.61e+03 pdb=" CG ASN B 861 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 861 " -0.176 2.00e-02 2.50e+03 pdb=" ND2 ASN B 861 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 861 " -0.691 2.00e-02 2.50e+03 pdb="HD22 ASN B 861 " 0.707 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 299 " -0.242 2.00e-02 2.50e+03 3.82e-01 2.19e+03 pdb=" CG ASN A 299 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 299 " 0.235 2.00e-02 2.50e+03 pdb=" ND2 ASN A 299 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 299 " 0.610 2.00e-02 2.50e+03 pdb="HD22 ASN A 299 " -0.626 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 297 " 0.257 2.00e-02 2.50e+03 3.39e-01 1.72e+03 pdb=" CD GLN A 297 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN A 297 " -0.242 2.00e-02 2.50e+03 pdb=" NE2 GLN A 297 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 297 " 0.538 2.00e-02 2.50e+03 pdb="HE22 GLN A 297 " -0.523 2.00e-02 2.50e+03 ... (remaining 6564 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1255 2.15 - 2.76: 79165 2.76 - 3.37: 118657 3.37 - 3.99: 145926 3.99 - 4.60: 230990 Nonbonded interactions: 575993 Sorted by model distance: nonbonded pdb=" H GLU A 860 " pdb=" HA GLU A 860 " model vdw 1.536 1.816 nonbonded pdb=" H HIS A 852 " pdb=" HA HIS A 852 " model vdw 1.610 1.816 nonbonded pdb=" H GLY A 49 " pdb=" O GLY A 217 " model vdw 1.618 2.450 nonbonded pdb=" HD1 HIS E 67 " pdb=" O SER E 73 " model vdw 1.622 2.450 nonbonded pdb=" OE1 GLU B 510 " pdb=" H GLU B 510 " model vdw 1.625 2.450 ... (remaining 575988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 26 through 297) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.330 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.030 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 23772 Z= 0.184 Angle : 0.727 17.053 32072 Z= 0.415 Chirality : 0.043 0.386 3422 Planarity : 0.005 0.078 4114 Dihedral : 13.761 89.695 8834 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.00 % Favored : 93.29 % Rotamer: Outliers : 0.12 % Allowed : 0.39 % Favored : 99.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.15), residues: 2801 helix: -0.63 (0.13), residues: 1387 sheet: -1.43 (0.34), residues: 205 loop : -1.54 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 657 TYR 0.027 0.002 TYR B 912 PHE 0.034 0.002 PHE B 856 TRP 0.037 0.002 TRP B 919 HIS 0.006 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00368 (23772) covalent geometry : angle 0.72741 (32072) hydrogen bonds : bond 0.29540 ( 1049) hydrogen bonds : angle 8.93857 ( 3006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 639 time to evaluate : 1.220 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.6301 (tptp) cc_final: 0.5854 (ptmt) REVERT: D 34 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6864 (tm-30) REVERT: D 206 MET cc_start: 0.5490 (tpt) cc_final: 0.5222 (tpt) REVERT: C 21 LEU cc_start: 0.6956 (tp) cc_final: 0.6585 (tp) REVERT: C 34 GLN cc_start: 0.7736 (tt0) cc_final: 0.7461 (tt0) REVERT: C 68 PHE cc_start: 0.7356 (t80) cc_final: 0.6931 (t80) REVERT: C 206 MET cc_start: 0.6773 (tpt) cc_final: 0.6217 (tpt) REVERT: A 28 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 33 ILE cc_start: 0.8611 (mt) cc_final: 0.8355 (mm) REVERT: A 35 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 39 ASN cc_start: 0.8497 (m-40) cc_final: 0.8139 (m-40) REVERT: A 179 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8149 (mmmt) REVERT: A 295 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 307 GLU cc_start: 0.7294 (tp30) cc_final: 0.6787 (tp30) REVERT: A 334 PHE cc_start: 0.8329 (m-80) cc_final: 0.7672 (m-80) REVERT: A 337 ASP cc_start: 0.7215 (m-30) cc_final: 0.6685 (m-30) REVERT: A 358 GLU cc_start: 0.8146 (tm-30) cc_final: 0.6946 (tm-30) REVERT: A 385 PHE cc_start: 0.7911 (t80) cc_final: 0.7708 (t80) REVERT: A 442 LEU cc_start: 0.8857 (mt) cc_final: 0.8599 (mt) REVERT: A 453 ASP cc_start: 0.7968 (m-30) cc_final: 0.7757 (m-30) REVERT: A 477 ASN cc_start: 0.8906 (m-40) cc_final: 0.8659 (m-40) REVERT: A 534 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 543 GLU cc_start: 0.8425 (tt0) cc_final: 0.7890 (tt0) REVERT: A 563 ASN cc_start: 0.8098 (t0) cc_final: 0.7864 (t0) REVERT: A 582 ILE cc_start: 0.9051 (tp) cc_final: 0.8825 (tp) REVERT: A 594 PHE cc_start: 0.7967 (t80) cc_final: 0.7739 (t80) REVERT: A 666 ASN cc_start: 0.8259 (m-40) cc_final: 0.7974 (m-40) REVERT: A 754 ARG cc_start: 0.8356 (mtt180) cc_final: 0.8083 (mtt180) REVERT: A 759 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 866 MET cc_start: 0.8248 (ttp) cc_final: 0.7887 (ttp) REVERT: B 134 TYR cc_start: 0.5158 (m-80) cc_final: 0.4372 (m-10) REVERT: B 197 TYR cc_start: 0.8309 (m-80) cc_final: 0.8104 (m-80) REVERT: B 268 ILE cc_start: 0.7767 (mp) cc_final: 0.7314 (mm) REVERT: B 337 ASP cc_start: 0.6856 (t0) cc_final: 0.6497 (t70) REVERT: B 357 MET cc_start: 0.8844 (mmp) cc_final: 0.8321 (mmm) REVERT: B 363 LEU cc_start: 0.8794 (mt) cc_final: 0.8328 (tp) REVERT: B 408 GLU cc_start: 0.7338 (tt0) cc_final: 0.6490 (mt-10) REVERT: B 434 ASP cc_start: 0.7329 (m-30) cc_final: 0.6914 (m-30) REVERT: B 517 ARG cc_start: 0.8482 (mtt-85) cc_final: 0.8169 (mtt-85) REVERT: B 561 LEU cc_start: 0.8502 (mt) cc_final: 0.8291 (mt) REVERT: B 569 MET cc_start: 0.7448 (tmm) cc_final: 0.6944 (tmm) REVERT: B 590 ASP cc_start: 0.7794 (m-30) cc_final: 0.7285 (m-30) REVERT: B 592 LEU cc_start: 0.8769 (mt) cc_final: 0.8486 (mt) REVERT: B 598 ASN cc_start: 0.8429 (m-40) cc_final: 0.8031 (m-40) REVERT: B 693 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7684 (tp30) REVERT: B 696 THR cc_start: 0.8577 (p) cc_final: 0.8286 (p) REVERT: B 708 PHE cc_start: 0.8398 (t80) cc_final: 0.7820 (t80) REVERT: B 741 LEU cc_start: 0.8605 (mm) cc_final: 0.8371 (mm) REVERT: B 746 GLU cc_start: 0.7994 (pm20) cc_final: 0.7744 (pm20) REVERT: B 769 LYS cc_start: 0.9279 (tptp) cc_final: 0.8996 (tppt) REVERT: B 856 PHE cc_start: 0.7627 (t80) cc_final: 0.7191 (t80) REVERT: B 866 MET cc_start: 0.8269 (mtp) cc_final: 0.7487 (mtm) REVERT: B 912 TYR cc_start: 0.7404 (m-10) cc_final: 0.7160 (m-10) REVERT: B 919 TRP cc_start: 0.7684 (m100) cc_final: 0.7283 (m100) REVERT: B 922 LEU cc_start: 0.8353 (mt) cc_final: 0.8129 (mt) REVERT: B 976 MET cc_start: 0.6519 (mtm) cc_final: 0.6023 (mtm) REVERT: E 92 TYR cc_start: 0.7549 (t80) cc_final: 0.7324 (t80) REVERT: F 186 LYS cc_start: 0.7593 (mtmm) cc_final: 0.7273 (mtmm) REVERT: F 193 TYR cc_start: 0.7822 (t80) cc_final: 0.7500 (t80) REVERT: F 195 GLN cc_start: 0.6058 (tp-100) cc_final: 0.5725 (mm-40) outliers start: 3 outliers final: 1 residues processed: 640 average time/residue: 0.4141 time to fit residues: 392.4268 Evaluate side-chains 617 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 615 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN A 89 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 475 GLN A 503 HIS A 666 ASN A 829 GLN A 861 ASN A 961 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 415 HIS B 477 ASN B 483 GLN B 548 ASN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN E 160 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.180389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139815 restraints weight = 125449.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147939 restraints weight = 60412.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152923 restraints weight = 34733.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.156021 restraints weight = 22929.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.157995 restraints weight = 17025.118| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 23772 Z= 0.365 Angle : 0.757 17.190 32072 Z= 0.447 Chirality : 0.046 0.336 3422 Planarity : 0.006 0.068 4114 Dihedral : 5.724 50.682 3097 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.03 % Favored : 91.29 % Rotamer: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.14), residues: 2801 helix: -0.99 (0.12), residues: 1493 sheet: -1.80 (0.33), residues: 213 loop : -1.97 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 870 TYR 0.027 0.002 TYR B 800 PHE 0.034 0.002 PHE B 856 TRP 0.016 0.002 TRP A 231 HIS 0.009 0.002 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00684 (23772) covalent geometry : angle 0.75741 (32072) hydrogen bonds : bond 0.07793 ( 1049) hydrogen bonds : angle 7.07117 ( 3006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 675 time to evaluate : 1.092 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.6549 (tptp) cc_final: 0.5652 (mtpt) REVERT: C 21 LEU cc_start: 0.7178 (tp) cc_final: 0.6744 (tp) REVERT: C 34 GLN cc_start: 0.7911 (tt0) cc_final: 0.7702 (tt0) REVERT: C 58 GLU cc_start: 0.5929 (pm20) cc_final: 0.5619 (pm20) REVERT: C 68 PHE cc_start: 0.7450 (t80) cc_final: 0.7227 (t80) REVERT: C 72 TRP cc_start: 0.7156 (p90) cc_final: 0.6924 (p90) REVERT: C 170 ARG cc_start: 0.7105 (mmp80) cc_final: 0.6608 (mmp80) REVERT: C 172 GLU cc_start: 0.3616 (mp0) cc_final: 0.3388 (mp0) REVERT: C 197 ASN cc_start: 0.8298 (t0) cc_final: 0.6494 (t0) REVERT: C 206 MET cc_start: 0.6929 (tpt) cc_final: 0.6315 (tpt) REVERT: A 28 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 35 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 39 ASN cc_start: 0.8452 (m-40) cc_final: 0.8053 (m-40) REVERT: A 196 ASN cc_start: 0.7970 (m-40) cc_final: 0.7744 (m-40) REVERT: A 306 ASP cc_start: 0.7977 (t70) cc_final: 0.7752 (t0) REVERT: A 307 GLU cc_start: 0.7052 (tp30) cc_final: 0.6736 (tp30) REVERT: A 337 ASP cc_start: 0.7417 (m-30) cc_final: 0.6966 (m-30) REVERT: A 358 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6925 (tm-30) REVERT: A 440 PHE cc_start: 0.7934 (t80) cc_final: 0.7682 (t80) REVERT: A 442 LEU cc_start: 0.8818 (mt) cc_final: 0.8546 (mt) REVERT: A 453 ASP cc_start: 0.8291 (m-30) cc_final: 0.7937 (m-30) REVERT: A 459 ILE cc_start: 0.8254 (tt) cc_final: 0.8046 (tt) REVERT: A 477 ASN cc_start: 0.9045 (m-40) cc_final: 0.8838 (m-40) REVERT: A 489 VAL cc_start: 0.8285 (p) cc_final: 0.8014 (t) REVERT: A 505 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8134 (mtmm) REVERT: A 521 ASN cc_start: 0.7378 (t0) cc_final: 0.7007 (t0) REVERT: A 534 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 543 GLU cc_start: 0.8400 (tt0) cc_final: 0.8068 (tt0) REVERT: A 560 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 580 SER cc_start: 0.9100 (p) cc_final: 0.8808 (m) REVERT: A 582 ILE cc_start: 0.9037 (tp) cc_final: 0.8792 (tp) REVERT: A 626 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8257 (tp30) REVERT: A 649 TYR cc_start: 0.6856 (t80) cc_final: 0.5842 (t80) REVERT: A 683 LYS cc_start: 0.8899 (mptt) cc_final: 0.8468 (mmtp) REVERT: A 693 GLU cc_start: 0.7176 (pp20) cc_final: 0.6765 (pp20) REVERT: A 747 ARG cc_start: 0.7529 (mtp-110) cc_final: 0.7148 (mtp85) REVERT: A 754 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8044 (mtt180) REVERT: A 763 LYS cc_start: 0.9084 (tptp) cc_final: 0.8830 (tptp) REVERT: A 811 PHE cc_start: 0.8633 (m-80) cc_final: 0.8231 (m-80) REVERT: A 976 MET cc_start: 0.7617 (mtp) cc_final: 0.7344 (mtp) REVERT: B 134 TYR cc_start: 0.5609 (m-80) cc_final: 0.5310 (m-10) REVERT: B 196 ASN cc_start: 0.8432 (m-40) cc_final: 0.8166 (m110) REVERT: B 197 TYR cc_start: 0.8444 (m-80) cc_final: 0.8103 (m-80) REVERT: B 226 ASN cc_start: 0.4094 (OUTLIER) cc_final: 0.3601 (m110) REVERT: B 337 ASP cc_start: 0.6648 (t0) cc_final: 0.6395 (t70) REVERT: B 445 LEU cc_start: 0.8931 (mt) cc_final: 0.8391 (tt) REVERT: B 477 ASN cc_start: 0.7997 (t160) cc_final: 0.7699 (t0) REVERT: B 517 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8321 (mtt-85) REVERT: B 519 MET cc_start: 0.6577 (mmm) cc_final: 0.6288 (mmm) REVERT: B 564 LYS cc_start: 0.8269 (mtmm) cc_final: 0.8033 (mtmm) REVERT: B 568 GLU cc_start: 0.8014 (mp0) cc_final: 0.7670 (mp0) REVERT: B 569 MET cc_start: 0.7811 (tmm) cc_final: 0.7281 (tmm) REVERT: B 580 SER cc_start: 0.8537 (m) cc_final: 0.8320 (p) REVERT: B 598 ASN cc_start: 0.8559 (m-40) cc_final: 0.8299 (m-40) REVERT: B 613 ARG cc_start: 0.7354 (ttm110) cc_final: 0.7060 (mtp180) REVERT: B 626 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 669 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8239 (ttm-80) REVERT: B 693 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7719 (tp30) REVERT: B 696 THR cc_start: 0.8454 (p) cc_final: 0.8027 (p) REVERT: B 708 PHE cc_start: 0.8410 (t80) cc_final: 0.7877 (t80) REVERT: B 746 GLU cc_start: 0.8136 (pm20) cc_final: 0.7796 (pm20) REVERT: B 769 LYS cc_start: 0.9116 (tptp) cc_final: 0.8856 (tppt) REVERT: B 866 MET cc_start: 0.8042 (mtp) cc_final: 0.6662 (ttm) REVERT: B 912 TYR cc_start: 0.7117 (m-10) cc_final: 0.6685 (m-80) REVERT: B 976 MET cc_start: 0.6656 (mtm) cc_final: 0.6132 (mtm) REVERT: E 69 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6029 (tm-30) REVERT: F 124 MET cc_start: 0.4856 (mmt) cc_final: 0.4377 (mmt) REVERT: F 186 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7364 (mtmm) REVERT: F 193 TYR cc_start: 0.7890 (t80) cc_final: 0.7544 (t80) outliers start: 1 outliers final: 0 residues processed: 676 average time/residue: 0.4162 time to fit residues: 415.8152 Evaluate side-chains 636 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 635 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 210 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN B 226 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS B 477 ASN B 483 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.178630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138782 restraints weight = 124681.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.146710 restraints weight = 59986.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151546 restraints weight = 34380.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.154506 restraints weight = 22740.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.156289 restraints weight = 16996.225| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 23772 Z= 0.287 Angle : 0.672 17.114 32072 Z= 0.389 Chirality : 0.043 0.312 3422 Planarity : 0.006 0.133 4114 Dihedral : 5.643 47.685 3097 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.71 % Favored : 90.68 % Rotamer: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.15), residues: 2801 helix: -0.89 (0.12), residues: 1499 sheet: -1.78 (0.33), residues: 207 loop : -2.16 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 760 TYR 0.025 0.002 TYR B 800 PHE 0.034 0.002 PHE A 742 TRP 0.014 0.002 TRP A 231 HIS 0.010 0.002 HIS B 978 Details of bonding type rmsd covalent geometry : bond 0.00532 (23772) covalent geometry : angle 0.67237 (32072) hydrogen bonds : bond 0.07130 ( 1049) hydrogen bonds : angle 6.51298 ( 3006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 670 time to evaluate : 1.197 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.6587 (tptp) cc_final: 0.5709 (mtpt) REVERT: D 221 GLU cc_start: 0.5857 (tm-30) cc_final: 0.5602 (tm-30) REVERT: C 21 LEU cc_start: 0.7088 (tp) cc_final: 0.6611 (tp) REVERT: C 58 GLU cc_start: 0.5775 (pm20) cc_final: 0.5450 (pm20) REVERT: C 64 LYS cc_start: 0.6905 (mtpt) cc_final: 0.6226 (mtpt) REVERT: C 68 PHE cc_start: 0.7382 (t80) cc_final: 0.7161 (t80) REVERT: C 72 TRP cc_start: 0.7202 (p90) cc_final: 0.6852 (p90) REVERT: C 75 MET cc_start: 0.1462 (tmm) cc_final: 0.0873 (tmm) REVERT: C 197 ASN cc_start: 0.8352 (t0) cc_final: 0.7778 (t0) REVERT: C 206 MET cc_start: 0.6845 (tpt) cc_final: 0.6282 (tpt) REVERT: A 28 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 35 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 39 ASN cc_start: 0.8444 (m-40) cc_final: 0.8071 (m-40) REVERT: A 196 ASN cc_start: 0.7924 (m-40) cc_final: 0.7683 (m-40) REVERT: A 306 ASP cc_start: 0.7970 (t70) cc_final: 0.7769 (t0) REVERT: A 307 GLU cc_start: 0.7037 (tp30) cc_final: 0.6684 (tp30) REVERT: A 337 ASP cc_start: 0.7365 (m-30) cc_final: 0.6995 (m-30) REVERT: A 442 LEU cc_start: 0.8827 (mt) cc_final: 0.8531 (mt) REVERT: A 453 ASP cc_start: 0.8191 (m-30) cc_final: 0.7854 (m-30) REVERT: A 477 ASN cc_start: 0.9060 (m-40) cc_final: 0.8846 (m-40) REVERT: A 489 VAL cc_start: 0.8247 (p) cc_final: 0.7968 (t) REVERT: A 521 ASN cc_start: 0.7428 (t0) cc_final: 0.7007 (t0) REVERT: A 534 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 543 GLU cc_start: 0.8457 (tt0) cc_final: 0.7989 (tt0) REVERT: A 560 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8068 (mt-10) REVERT: A 563 ASN cc_start: 0.8056 (t0) cc_final: 0.7771 (t0) REVERT: A 571 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6918 (mm-30) REVERT: A 580 SER cc_start: 0.9088 (p) cc_final: 0.8843 (m) REVERT: A 582 ILE cc_start: 0.8927 (tp) cc_final: 0.8646 (tp) REVERT: A 649 TYR cc_start: 0.6728 (t80) cc_final: 0.5744 (t80) REVERT: A 666 ASN cc_start: 0.8098 (m-40) cc_final: 0.7894 (m-40) REVERT: A 683 LYS cc_start: 0.8752 (mptt) cc_final: 0.8329 (mmtm) REVERT: A 693 GLU cc_start: 0.7298 (pp20) cc_final: 0.6928 (pp20) REVERT: A 709 TYR cc_start: 0.8064 (t80) cc_final: 0.6668 (t80) REVERT: A 711 GLN cc_start: 0.7403 (mp10) cc_final: 0.7108 (mp10) REVERT: A 737 VAL cc_start: 0.8814 (p) cc_final: 0.8554 (m) REVERT: A 741 LEU cc_start: 0.8415 (mm) cc_final: 0.8110 (mm) REVERT: A 754 ARG cc_start: 0.8369 (mtt180) cc_final: 0.7987 (mtt180) REVERT: A 822 GLU cc_start: 0.8684 (mp0) cc_final: 0.8009 (mm-30) REVERT: A 913 MET cc_start: 0.6319 (mmp) cc_final: 0.6056 (mmp) REVERT: A 939 GLN cc_start: 0.7768 (tt0) cc_final: 0.7402 (tt0) REVERT: A 976 MET cc_start: 0.7658 (mtp) cc_final: 0.7285 (mtp) REVERT: B 196 ASN cc_start: 0.8425 (m-40) cc_final: 0.8130 (m110) REVERT: B 337 ASP cc_start: 0.6635 (t0) cc_final: 0.6391 (t70) REVERT: B 410 ASN cc_start: 0.6479 (t0) cc_final: 0.5790 (t0) REVERT: B 421 MET cc_start: 0.8347 (ptp) cc_final: 0.8127 (ptp) REVERT: B 426 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 434 ASP cc_start: 0.7761 (m-30) cc_final: 0.7525 (m-30) REVERT: B 445 LEU cc_start: 0.8924 (mt) cc_final: 0.8447 (tt) REVERT: B 458 ILE cc_start: 0.8651 (pt) cc_final: 0.8430 (pt) REVERT: B 477 ASN cc_start: 0.7974 (t160) cc_final: 0.7710 (t0) REVERT: B 511 PHE cc_start: 0.7902 (t80) cc_final: 0.7693 (t80) REVERT: B 517 ARG cc_start: 0.8538 (mtt-85) cc_final: 0.8300 (mtt-85) REVERT: B 519 MET cc_start: 0.6512 (mmm) cc_final: 0.6230 (mmm) REVERT: B 569 MET cc_start: 0.7782 (tmm) cc_final: 0.7218 (tmm) REVERT: B 578 MET cc_start: 0.8450 (ptp) cc_final: 0.8152 (ptp) REVERT: B 590 ASP cc_start: 0.7933 (m-30) cc_final: 0.7428 (m-30) REVERT: B 598 ASN cc_start: 0.8525 (m-40) cc_final: 0.8319 (m-40) REVERT: B 626 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 682 GLU cc_start: 0.6805 (pm20) cc_final: 0.6512 (mp0) REVERT: B 693 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7669 (tp30) REVERT: B 696 THR cc_start: 0.8399 (p) cc_final: 0.8000 (p) REVERT: B 708 PHE cc_start: 0.8366 (t80) cc_final: 0.7806 (t80) REVERT: B 746 GLU cc_start: 0.8127 (pm20) cc_final: 0.7764 (pm20) REVERT: B 769 LYS cc_start: 0.9091 (tptp) cc_final: 0.8788 (tppt) REVERT: B 850 LYS cc_start: 0.7694 (mttm) cc_final: 0.7294 (mtpt) REVERT: B 870 ARG cc_start: 0.8493 (ttt-90) cc_final: 0.8195 (ttt-90) REVERT: B 947 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 976 MET cc_start: 0.6633 (mtm) cc_final: 0.6197 (mtm) REVERT: E 92 TYR cc_start: 0.7675 (t80) cc_final: 0.7435 (t80) REVERT: F 92 TYR cc_start: 0.6782 (t80) cc_final: 0.6418 (t80) REVERT: F 124 MET cc_start: 0.5062 (mmt) cc_final: 0.4673 (mmt) REVERT: F 186 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7314 (mtmm) REVERT: F 193 TYR cc_start: 0.7830 (t80) cc_final: 0.7496 (t80) outliers start: 1 outliers final: 0 residues processed: 670 average time/residue: 0.4094 time to fit residues: 406.9961 Evaluate side-chains 643 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 27 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 483 GLN B 563 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.179326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139743 restraints weight = 122495.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147551 restraints weight = 58883.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.152304 restraints weight = 33643.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.155193 restraints weight = 22213.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.156952 restraints weight = 16615.765| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 23772 Z= 0.277 Angle : 0.650 16.691 32072 Z= 0.377 Chirality : 0.042 0.305 3422 Planarity : 0.005 0.061 4114 Dihedral : 5.636 46.737 3097 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.43 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 2801 helix: -0.80 (0.12), residues: 1497 sheet: -1.79 (0.33), residues: 206 loop : -2.22 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 747 TYR 0.045 0.002 TYR B 912 PHE 0.030 0.002 PHE B 646 TRP 0.013 0.002 TRP A 231 HIS 0.011 0.002 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00519 (23772) covalent geometry : angle 0.65019 (32072) hydrogen bonds : bond 0.06133 ( 1049) hydrogen bonds : angle 6.28118 ( 3006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 675 time to evaluate : 1.177 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.6746 (tptp) cc_final: 0.6374 (mtpt) REVERT: D 221 GLU cc_start: 0.5995 (tm-30) cc_final: 0.5733 (tm-30) REVERT: C 21 LEU cc_start: 0.7242 (tp) cc_final: 0.6818 (tp) REVERT: C 53 LEU cc_start: 0.7554 (pt) cc_final: 0.7280 (pt) REVERT: C 58 GLU cc_start: 0.5708 (pm20) cc_final: 0.5333 (pm20) REVERT: C 75 MET cc_start: 0.1639 (tmm) cc_final: 0.1140 (tmm) REVERT: C 206 MET cc_start: 0.6896 (tpt) cc_final: 0.6320 (tpt) REVERT: C 208 LEU cc_start: 0.7961 (pt) cc_final: 0.7731 (pt) REVERT: A 28 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 35 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 39 ASN cc_start: 0.8447 (m-40) cc_final: 0.8066 (m-40) REVERT: A 41 LYS cc_start: 0.7792 (ttpp) cc_final: 0.7583 (ttpp) REVERT: A 196 ASN cc_start: 0.7909 (m-40) cc_final: 0.7672 (m-40) REVERT: A 306 ASP cc_start: 0.8031 (t70) cc_final: 0.7717 (t0) REVERT: A 307 GLU cc_start: 0.7037 (tp30) cc_final: 0.6738 (tp30) REVERT: A 337 ASP cc_start: 0.7389 (m-30) cc_final: 0.7119 (m-30) REVERT: A 442 LEU cc_start: 0.8815 (mt) cc_final: 0.8510 (mt) REVERT: A 453 ASP cc_start: 0.8125 (m-30) cc_final: 0.7805 (m-30) REVERT: A 477 ASN cc_start: 0.9047 (m-40) cc_final: 0.8831 (m-40) REVERT: A 489 VAL cc_start: 0.8238 (p) cc_final: 0.7961 (t) REVERT: A 521 ASN cc_start: 0.7394 (t0) cc_final: 0.6955 (t0) REVERT: A 538 LYS cc_start: 0.8265 (mttm) cc_final: 0.7940 (mtmm) REVERT: A 543 GLU cc_start: 0.8430 (tt0) cc_final: 0.8030 (tt0) REVERT: A 560 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 571 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6902 (mm-30) REVERT: A 580 SER cc_start: 0.9113 (p) cc_final: 0.8816 (m) REVERT: A 582 ILE cc_start: 0.8899 (tp) cc_final: 0.8619 (tp) REVERT: A 630 ASP cc_start: 0.6958 (t0) cc_final: 0.6747 (t0) REVERT: A 670 SER cc_start: 0.8465 (m) cc_final: 0.8229 (m) REVERT: A 685 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8564 (mt-10) REVERT: A 709 TYR cc_start: 0.7977 (t80) cc_final: 0.7355 (t80) REVERT: A 711 GLN cc_start: 0.7438 (mp10) cc_final: 0.7148 (mp10) REVERT: A 737 VAL cc_start: 0.8779 (p) cc_final: 0.8512 (m) REVERT: A 738 LYS cc_start: 0.8478 (tptp) cc_final: 0.8191 (tptp) REVERT: A 741 LEU cc_start: 0.8454 (mm) cc_final: 0.8086 (mm) REVERT: A 822 GLU cc_start: 0.8721 (mp0) cc_final: 0.7917 (mm-30) REVERT: A 913 MET cc_start: 0.6420 (mmp) cc_final: 0.6134 (mmp) REVERT: A 976 MET cc_start: 0.7577 (mtp) cc_final: 0.7198 (mtp) REVERT: B 196 ASN cc_start: 0.8459 (m-40) cc_final: 0.8193 (m110) REVERT: B 197 TYR cc_start: 0.8550 (m-80) cc_final: 0.8196 (m-80) REVERT: B 410 ASN cc_start: 0.6443 (t0) cc_final: 0.5894 (t0) REVERT: B 411 SER cc_start: 0.8559 (t) cc_final: 0.8242 (p) REVERT: B 421 MET cc_start: 0.8284 (ptp) cc_final: 0.8031 (ptp) REVERT: B 426 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7180 (tm-30) REVERT: B 434 ASP cc_start: 0.7794 (m-30) cc_final: 0.7503 (m-30) REVERT: B 445 LEU cc_start: 0.8958 (mt) cc_final: 0.8449 (tt) REVERT: B 477 ASN cc_start: 0.7916 (t160) cc_final: 0.7632 (t0) REVERT: B 499 THR cc_start: 0.8448 (m) cc_final: 0.7826 (t) REVERT: B 511 PHE cc_start: 0.7886 (t80) cc_final: 0.7632 (t80) REVERT: B 517 ARG cc_start: 0.8504 (mtt-85) cc_final: 0.8174 (mtt-85) REVERT: B 519 MET cc_start: 0.6549 (mmm) cc_final: 0.6294 (mmm) REVERT: B 568 GLU cc_start: 0.8509 (pt0) cc_final: 0.8126 (pt0) REVERT: B 569 MET cc_start: 0.7931 (tmm) cc_final: 0.7237 (tmm) REVERT: B 590 ASP cc_start: 0.7882 (m-30) cc_final: 0.7440 (m-30) REVERT: B 598 ASN cc_start: 0.8532 (m-40) cc_final: 0.8303 (m-40) REVERT: B 689 VAL cc_start: 0.8098 (t) cc_final: 0.7748 (p) REVERT: B 708 PHE cc_start: 0.8376 (t80) cc_final: 0.7807 (t80) REVERT: B 727 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8272 (ttmm) REVERT: B 746 GLU cc_start: 0.8101 (pm20) cc_final: 0.7719 (pm20) REVERT: B 769 LYS cc_start: 0.9115 (tptp) cc_final: 0.8783 (tppt) REVERT: B 835 ILE cc_start: 0.8213 (mt) cc_final: 0.8008 (pt) REVERT: B 850 LYS cc_start: 0.7552 (mttm) cc_final: 0.7110 (mtpt) REVERT: B 856 PHE cc_start: 0.7690 (t80) cc_final: 0.7317 (t80) REVERT: B 866 MET cc_start: 0.8230 (mtm) cc_final: 0.7774 (ttm) REVERT: B 870 ARG cc_start: 0.8474 (ttt-90) cc_final: 0.8271 (ttt-90) REVERT: B 912 TYR cc_start: 0.7194 (m-10) cc_final: 0.6951 (m-10) REVERT: B 947 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8215 (mm-30) REVERT: B 976 MET cc_start: 0.6688 (mtm) cc_final: 0.6258 (mtm) REVERT: E 69 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6106 (tm-30) REVERT: E 92 TYR cc_start: 0.7620 (t80) cc_final: 0.7379 (t80) REVERT: E 244 PHE cc_start: 0.2922 (m-10) cc_final: 0.2566 (m-80) REVERT: F 46 VAL cc_start: 0.8012 (t) cc_final: 0.7771 (p) REVERT: F 92 TYR cc_start: 0.6774 (t80) cc_final: 0.6330 (t80) REVERT: F 186 LYS cc_start: 0.7686 (mtmm) cc_final: 0.7316 (mtmm) REVERT: F 193 TYR cc_start: 0.7810 (t80) cc_final: 0.7471 (t80) outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.4197 time to fit residues: 419.1970 Evaluate side-chains 643 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 212 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 483 GLN B 563 ASN B 658 HIS B 852 HIS ** F 93 ASN ** 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 = 0.4295 r_free = 0.4295 target = 0.176047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.136368 restraints weight = 122386.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.144158 restraints weight = 57959.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148923 restraints weight = 33056.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.151827 restraints weight = 21791.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.153477 restraints weight = 16264.949| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 23772 Z= 0.294 Angle : 0.668 16.562 32072 Z= 0.388 Chirality : 0.043 0.307 3422 Planarity : 0.005 0.065 4114 Dihedral : 5.708 46.824 3097 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.96 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.15), residues: 2801 helix: -0.86 (0.12), residues: 1518 sheet: -1.90 (0.34), residues: 208 loop : -2.30 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 747 TYR 0.023 0.002 TYR B 800 PHE 0.032 0.002 PHE A 550 TRP 0.014 0.002 TRP A 231 HIS 0.009 0.002 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00548 (23772) covalent geometry : angle 0.66775 (32072) hydrogen bonds : bond 0.06094 ( 1049) hydrogen bonds : angle 6.28630 ( 3006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 1.186 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.6831 (tptp) cc_final: 0.6475 (mtpt) REVERT: D 192 TYR cc_start: 0.7005 (m-80) cc_final: 0.6641 (m-80) REVERT: D 199 SER cc_start: 0.8317 (t) cc_final: 0.8035 (t) REVERT: D 221 GLU cc_start: 0.5890 (tm-30) cc_final: 0.5649 (tm-30) REVERT: C 58 GLU cc_start: 0.5632 (pm20) cc_final: 0.5244 (pm20) REVERT: C 64 LYS cc_start: 0.6899 (mtpp) cc_final: 0.6087 (mtpp) REVERT: C 75 MET cc_start: 0.2093 (tmm) cc_final: 0.1819 (tmm) REVERT: C 206 MET cc_start: 0.6987 (tpt) cc_final: 0.6340 (tpt) REVERT: C 208 LEU cc_start: 0.7925 (pt) cc_final: 0.7661 (pt) REVERT: C 223 LEU cc_start: 0.6416 (mm) cc_final: 0.6198 (mm) REVERT: A 28 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 33 ILE cc_start: 0.8746 (mt) cc_final: 0.8495 (mm) REVERT: A 35 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 39 ASN cc_start: 0.8425 (m-40) cc_final: 0.8199 (m-40) REVERT: A 41 LYS cc_start: 0.7840 (ttpp) cc_final: 0.7605 (ttpp) REVERT: A 182 ASN cc_start: 0.8154 (m110) cc_final: 0.7849 (m110) REVERT: A 196 ASN cc_start: 0.7865 (m-40) cc_final: 0.7640 (m-40) REVERT: A 249 ASP cc_start: 0.7932 (t70) cc_final: 0.7652 (t70) REVERT: A 306 ASP cc_start: 0.8187 (t70) cc_final: 0.7873 (t0) REVERT: A 307 GLU cc_start: 0.7107 (tp30) cc_final: 0.6777 (tp30) REVERT: A 337 ASP cc_start: 0.7482 (m-30) cc_final: 0.7178 (m-30) REVERT: A 385 PHE cc_start: 0.7666 (t80) cc_final: 0.7448 (t80) REVERT: A 409 ILE cc_start: 0.8179 (mt) cc_final: 0.7880 (mm) REVERT: A 424 PHE cc_start: 0.8384 (t80) cc_final: 0.8161 (t80) REVERT: A 442 LEU cc_start: 0.8797 (mt) cc_final: 0.8480 (mt) REVERT: A 477 ASN cc_start: 0.9104 (m-40) cc_final: 0.8896 (m-40) REVERT: A 560 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 571 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6902 (mm-30) REVERT: A 580 SER cc_start: 0.9115 (p) cc_final: 0.8888 (m) REVERT: A 582 ILE cc_start: 0.8867 (tp) cc_final: 0.8612 (tp) REVERT: A 630 ASP cc_start: 0.6990 (t0) cc_final: 0.6752 (t0) REVERT: A 657 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.8310 (ttm-80) REVERT: A 660 LYS cc_start: 0.8148 (mmmm) cc_final: 0.7871 (mtpp) REVERT: A 685 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8539 (mt-10) REVERT: A 709 TYR cc_start: 0.7888 (t80) cc_final: 0.7266 (t80) REVERT: A 711 GLN cc_start: 0.7430 (mp10) cc_final: 0.7043 (mp10) REVERT: A 737 VAL cc_start: 0.8790 (p) cc_final: 0.8519 (m) REVERT: A 741 LEU cc_start: 0.8504 (mm) cc_final: 0.8216 (mm) REVERT: A 822 GLU cc_start: 0.8775 (mp0) cc_final: 0.7903 (mm-30) REVERT: A 913 MET cc_start: 0.6468 (mmp) cc_final: 0.6209 (mmp) REVERT: A 924 GLU cc_start: 0.8295 (tp30) cc_final: 0.7981 (tp30) REVERT: A 965 LYS cc_start: 0.8445 (pttm) cc_final: 0.7806 (tppp) REVERT: A 976 MET cc_start: 0.7591 (mtp) cc_final: 0.7180 (mtp) REVERT: B 196 ASN cc_start: 0.8451 (m-40) cc_final: 0.8161 (m110) REVERT: B 291 ASP cc_start: 0.8522 (m-30) cc_final: 0.8271 (m-30) REVERT: B 410 ASN cc_start: 0.6557 (t0) cc_final: 0.5905 (t0) REVERT: B 411 SER cc_start: 0.8546 (t) cc_final: 0.8110 (p) REVERT: B 434 ASP cc_start: 0.7776 (m-30) cc_final: 0.7387 (m-30) REVERT: B 445 LEU cc_start: 0.9038 (mt) cc_final: 0.8531 (tp) REVERT: B 459 ILE cc_start: 0.7777 (tp) cc_final: 0.7526 (tp) REVERT: B 477 ASN cc_start: 0.7989 (t160) cc_final: 0.7751 (t0) REVERT: B 499 THR cc_start: 0.8438 (m) cc_final: 0.8011 (t) REVERT: B 503 HIS cc_start: 0.7197 (t-90) cc_final: 0.6813 (t-170) REVERT: B 508 THR cc_start: 0.8381 (p) cc_final: 0.7804 (t) REVERT: B 510 GLU cc_start: 0.7343 (mp0) cc_final: 0.6843 (mp0) REVERT: B 511 PHE cc_start: 0.7925 (t80) cc_final: 0.7645 (t80) REVERT: B 517 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.8160 (mtt-85) REVERT: B 562 THR cc_start: 0.8690 (t) cc_final: 0.8428 (p) REVERT: B 568 GLU cc_start: 0.8475 (pt0) cc_final: 0.8121 (pt0) REVERT: B 569 MET cc_start: 0.7884 (tmm) cc_final: 0.7168 (tmm) REVERT: B 590 ASP cc_start: 0.7936 (m-30) cc_final: 0.7495 (m-30) REVERT: B 658 HIS cc_start: 0.8029 (m90) cc_final: 0.7485 (m-70) REVERT: B 667 LEU cc_start: 0.8472 (tp) cc_final: 0.8249 (tp) REVERT: B 682 GLU cc_start: 0.6800 (pm20) cc_final: 0.6565 (mp0) REVERT: B 696 THR cc_start: 0.8326 (p) cc_final: 0.8047 (p) REVERT: B 727 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8242 (ttpp) REVERT: B 746 GLU cc_start: 0.8122 (pm20) cc_final: 0.7725 (pm20) REVERT: B 850 LYS cc_start: 0.7770 (mttm) cc_final: 0.7367 (mtpt) REVERT: B 947 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8193 (mm-30) REVERT: B 976 MET cc_start: 0.6696 (mtm) cc_final: 0.6245 (mtm) REVERT: B 982 GLU cc_start: 0.7780 (mp0) cc_final: 0.7332 (mp0) REVERT: B 1001 MET cc_start: 0.8462 (tpp) cc_final: 0.8176 (tpp) REVERT: E 69 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6150 (tm-30) REVERT: E 92 TYR cc_start: 0.7559 (t80) cc_final: 0.7323 (t80) REVERT: E 187 GLU cc_start: 0.6379 (tt0) cc_final: 0.6144 (tt0) REVERT: E 244 PHE cc_start: 0.3292 (m-10) cc_final: 0.2990 (m-80) REVERT: F 46 VAL cc_start: 0.8033 (t) cc_final: 0.7818 (p) REVERT: F 69 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5553 (mm-30) REVERT: F 92 TYR cc_start: 0.6900 (t80) cc_final: 0.6368 (t80) REVERT: F 186 LYS cc_start: 0.7735 (mtmm) cc_final: 0.7380 (mtmm) REVERT: F 193 TYR cc_start: 0.7843 (t80) cc_final: 0.7521 (t80) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 0.4178 time to fit residues: 424.6358 Evaluate side-chains 650 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 191 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 205 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 548 ASN A 961 ASN B 263 ASN B 477 ASN B 483 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS F 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.189333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148216 restraints weight = 120341.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.156408 restraints weight = 58149.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.161457 restraints weight = 33503.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.164573 restraints weight = 22180.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.166449 restraints weight = 16423.790| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 23772 Z= 0.129 Angle : 0.560 16.271 32072 Z= 0.314 Chirality : 0.040 0.293 3422 Planarity : 0.004 0.056 4114 Dihedral : 5.210 44.578 3097 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.18 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.15), residues: 2801 helix: -0.21 (0.13), residues: 1525 sheet: -1.80 (0.33), residues: 215 loop : -2.18 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 613 TYR 0.024 0.001 TYR A 755 PHE 0.025 0.001 PHE B 856 TRP 0.029 0.001 TRP C 72 HIS 0.007 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00262 (23772) covalent geometry : angle 0.55963 (32072) hydrogen bonds : bond 0.05083 ( 1049) hydrogen bonds : angle 5.44444 ( 3006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 1.210 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.6820 (tptp) cc_final: 0.6528 (mtpt) REVERT: D 34 GLN cc_start: 0.7318 (tp40) cc_final: 0.6975 (tm-30) REVERT: D 192 TYR cc_start: 0.6745 (m-80) cc_final: 0.6539 (m-80) REVERT: D 221 GLU cc_start: 0.5948 (tm-30) cc_final: 0.5725 (tm-30) REVERT: C 34 GLN cc_start: 0.8047 (tt0) cc_final: 0.7782 (tt0) REVERT: C 58 GLU cc_start: 0.5666 (pm20) cc_final: 0.5289 (pm20) REVERT: C 64 LYS cc_start: 0.6691 (mtpp) cc_final: 0.5962 (mtpp) REVERT: C 75 MET cc_start: 0.2286 (tmm) cc_final: 0.1929 (tmm) REVERT: C 206 MET cc_start: 0.6797 (tpt) cc_final: 0.6219 (tpt) REVERT: C 208 LEU cc_start: 0.7983 (pt) cc_final: 0.7695 (pt) REVERT: A 28 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 35 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7818 (mm-30) REVERT: A 39 ASN cc_start: 0.8388 (m-40) cc_final: 0.8093 (m-40) REVERT: A 182 ASN cc_start: 0.8157 (m110) cc_final: 0.7776 (m110) REVERT: A 196 ASN cc_start: 0.7889 (m-40) cc_final: 0.7671 (m-40) REVERT: A 249 ASP cc_start: 0.7933 (t70) cc_final: 0.7650 (t70) REVERT: A 304 LYS cc_start: 0.8678 (pttm) cc_final: 0.8434 (pttm) REVERT: A 307 GLU cc_start: 0.6921 (tp30) cc_final: 0.6549 (tp30) REVERT: A 337 ASP cc_start: 0.7215 (m-30) cc_final: 0.6970 (m-30) REVERT: A 364 LYS cc_start: 0.8949 (tttt) cc_final: 0.8341 (tppt) REVERT: A 407 ILE cc_start: 0.8185 (mm) cc_final: 0.7490 (pt) REVERT: A 424 PHE cc_start: 0.8381 (t80) cc_final: 0.8153 (t80) REVERT: A 442 LEU cc_start: 0.8777 (mt) cc_final: 0.8406 (mt) REVERT: A 450 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8150 (mp0) REVERT: A 453 ASP cc_start: 0.8045 (m-30) cc_final: 0.7673 (m-30) REVERT: A 493 ASN cc_start: 0.9082 (m-40) cc_final: 0.8862 (t0) REVERT: A 521 ASN cc_start: 0.7329 (t0) cc_final: 0.6986 (t0) REVERT: A 543 GLU cc_start: 0.8179 (tt0) cc_final: 0.7963 (tt0) REVERT: A 548 ASN cc_start: 0.5465 (p0) cc_final: 0.5252 (p0) REVERT: A 560 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8017 (mt-10) REVERT: A 571 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6681 (mm-30) REVERT: A 582 ILE cc_start: 0.8839 (tp) cc_final: 0.8535 (tp) REVERT: A 657 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8235 (ttm-80) REVERT: A 685 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8518 (mt-10) REVERT: A 709 TYR cc_start: 0.7856 (t80) cc_final: 0.7300 (t80) REVERT: A 711 GLN cc_start: 0.7413 (mp10) cc_final: 0.7028 (mp10) REVERT: A 737 VAL cc_start: 0.8644 (p) cc_final: 0.8254 (m) REVERT: A 784 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 822 GLU cc_start: 0.8740 (mp0) cc_final: 0.7580 (mm-30) REVERT: A 913 MET cc_start: 0.6337 (mmp) cc_final: 0.6089 (mmp) REVERT: A 976 MET cc_start: 0.7389 (mtp) cc_final: 0.6984 (mtp) REVERT: B 196 ASN cc_start: 0.8402 (m-40) cc_final: 0.8112 (m110) REVERT: B 291 ASP cc_start: 0.8426 (m-30) cc_final: 0.8188 (m-30) REVERT: B 410 ASN cc_start: 0.6563 (t0) cc_final: 0.6052 (m-40) REVERT: B 411 SER cc_start: 0.8511 (t) cc_final: 0.8200 (p) REVERT: B 421 MET cc_start: 0.8430 (ptp) cc_final: 0.8167 (ptp) REVERT: B 445 LEU cc_start: 0.8928 (mt) cc_final: 0.8581 (tp) REVERT: B 477 ASN cc_start: 0.7797 (t160) cc_final: 0.7528 (t0) REVERT: B 503 HIS cc_start: 0.7262 (t-90) cc_final: 0.6865 (t-170) REVERT: B 508 THR cc_start: 0.8303 (p) cc_final: 0.7924 (t) REVERT: B 510 GLU cc_start: 0.7214 (mp0) cc_final: 0.6910 (mp0) REVERT: B 511 PHE cc_start: 0.7852 (t80) cc_final: 0.7598 (t80) REVERT: B 517 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8106 (mtt-85) REVERT: B 568 GLU cc_start: 0.8447 (pt0) cc_final: 0.8011 (pt0) REVERT: B 569 MET cc_start: 0.7776 (tmm) cc_final: 0.7189 (tmm) REVERT: B 590 ASP cc_start: 0.7840 (m-30) cc_final: 0.7279 (m-30) REVERT: B 663 ASP cc_start: 0.8311 (m-30) cc_final: 0.7856 (m-30) REVERT: B 667 LEU cc_start: 0.8422 (tp) cc_final: 0.8153 (tp) REVERT: B 693 GLU cc_start: 0.8044 (tp30) cc_final: 0.7472 (tp30) REVERT: B 708 PHE cc_start: 0.8307 (t80) cc_final: 0.7770 (t80) REVERT: B 727 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8230 (ttpp) REVERT: B 850 LYS cc_start: 0.7633 (mttm) cc_final: 0.7280 (mtpt) REVERT: B 947 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8165 (mm-30) REVERT: B 976 MET cc_start: 0.6570 (mtm) cc_final: 0.6123 (mtm) REVERT: B 982 GLU cc_start: 0.7667 (mp0) cc_final: 0.7363 (mp0) REVERT: B 985 LYS cc_start: 0.8221 (ptpp) cc_final: 0.7878 (ptmm) REVERT: B 1001 MET cc_start: 0.8392 (tpp) cc_final: 0.8049 (tpp) REVERT: E 92 TYR cc_start: 0.7469 (t80) cc_final: 0.7263 (t80) REVERT: E 244 PHE cc_start: 0.3133 (m-10) cc_final: 0.2875 (m-80) REVERT: F 46 VAL cc_start: 0.8030 (t) cc_final: 0.7799 (p) REVERT: F 92 TYR cc_start: 0.6839 (t80) cc_final: 0.6306 (t80) REVERT: F 118 HIS cc_start: 0.3942 (m90) cc_final: 0.3610 (m90) REVERT: F 186 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7427 (mtmm) REVERT: F 193 TYR cc_start: 0.7759 (t80) cc_final: 0.7429 (t80) REVERT: F 195 GLN cc_start: 0.6576 (tp-100) cc_final: 0.5889 (mm-40) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.4093 time to fit residues: 411.8045 Evaluate side-chains 645 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 152 optimal weight: 0.0980 chunk 116 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN A 961 ASN B 477 ASN B 483 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.182422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141488 restraints weight = 120543.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149457 restraints weight = 58466.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.154331 restraints weight = 33817.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157163 restraints weight = 22519.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159008 restraints weight = 17149.874| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 23772 Z= 0.215 Angle : 0.593 16.361 32072 Z= 0.341 Chirality : 0.041 0.301 3422 Planarity : 0.004 0.054 4114 Dihedral : 5.315 45.674 3097 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.35 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.15), residues: 2801 helix: -0.27 (0.13), residues: 1536 sheet: -1.79 (0.34), residues: 207 loop : -2.30 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 747 TYR 0.021 0.002 TYR B 800 PHE 0.026 0.002 PHE B 856 TRP 0.023 0.002 TRP C 72 HIS 0.009 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00417 (23772) covalent geometry : angle 0.59278 (32072) hydrogen bonds : bond 0.05182 ( 1049) hydrogen bonds : angle 5.69043 ( 3006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 675 time to evaluate : 1.254 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.6917 (tptp) cc_final: 0.6680 (mtpt) REVERT: D 34 GLN cc_start: 0.7290 (tp40) cc_final: 0.6994 (tm-30) REVERT: D 192 TYR cc_start: 0.6972 (m-80) cc_final: 0.6689 (m-80) REVERT: D 206 MET cc_start: 0.5893 (tpt) cc_final: 0.4971 (tpt) REVERT: D 208 LEU cc_start: 0.7647 (pt) cc_final: 0.6865 (pt) REVERT: D 220 PHE cc_start: 0.7476 (m-10) cc_final: 0.7169 (m-10) REVERT: C 34 GLN cc_start: 0.7701 (tt0) cc_final: 0.7401 (tt0) REVERT: C 58 GLU cc_start: 0.5709 (pm20) cc_final: 0.5323 (pm20) REVERT: C 64 LYS cc_start: 0.7049 (mtpp) cc_final: 0.6172 (mtpp) REVERT: C 68 PHE cc_start: 0.7499 (t80) cc_final: 0.7174 (t80) REVERT: C 75 MET cc_start: 0.2496 (tmm) cc_final: 0.2237 (tmm) REVERT: C 197 ASN cc_start: 0.8165 (t0) cc_final: 0.7741 (t0) REVERT: C 206 MET cc_start: 0.6994 (tpt) cc_final: 0.6426 (tpt) REVERT: C 208 LEU cc_start: 0.7971 (pt) cc_final: 0.7725 (pt) REVERT: C 223 LEU cc_start: 0.6539 (mm) cc_final: 0.6153 (mm) REVERT: A 28 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 33 ILE cc_start: 0.8730 (mt) cc_final: 0.8487 (mm) REVERT: A 35 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 41 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7631 (ptpp) REVERT: A 182 ASN cc_start: 0.8237 (m110) cc_final: 0.7818 (m110) REVERT: A 249 ASP cc_start: 0.7970 (t70) cc_final: 0.7723 (t70) REVERT: A 298 GLU cc_start: 0.7260 (pt0) cc_final: 0.7028 (pt0) REVERT: A 304 LYS cc_start: 0.8724 (pttm) cc_final: 0.8473 (pttm) REVERT: A 307 GLU cc_start: 0.7047 (tp30) cc_final: 0.6648 (tp30) REVERT: A 315 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7994 (mptt) REVERT: A 334 PHE cc_start: 0.8273 (m-10) cc_final: 0.8070 (m-80) REVERT: A 337 ASP cc_start: 0.7486 (m-30) cc_final: 0.7192 (m-30) REVERT: A 424 PHE cc_start: 0.8402 (t80) cc_final: 0.8172 (t80) REVERT: A 442 LEU cc_start: 0.8782 (mt) cc_final: 0.8411 (mt) REVERT: A 450 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8163 (mp0) REVERT: A 493 ASN cc_start: 0.9094 (m-40) cc_final: 0.8875 (t0) REVERT: A 560 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 571 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6828 (mm-30) REVERT: A 582 ILE cc_start: 0.8834 (tp) cc_final: 0.8559 (tp) REVERT: A 657 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: A 685 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8493 (mt-10) REVERT: A 709 TYR cc_start: 0.7858 (t80) cc_final: 0.6421 (t80) REVERT: A 711 GLN cc_start: 0.7439 (mp10) cc_final: 0.7048 (mp10) REVERT: A 737 VAL cc_start: 0.8670 (p) cc_final: 0.8366 (m) REVERT: A 766 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 784 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7903 (mm-30) REVERT: A 913 MET cc_start: 0.6439 (mmp) cc_final: 0.6200 (mmp) REVERT: A 924 GLU cc_start: 0.8292 (tp30) cc_final: 0.7968 (tp30) REVERT: A 939 GLN cc_start: 0.7733 (tt0) cc_final: 0.7365 (tt0) REVERT: A 976 MET cc_start: 0.7466 (mtp) cc_final: 0.7079 (mtp) REVERT: B 196 ASN cc_start: 0.8461 (m-40) cc_final: 0.8143 (m110) REVERT: B 291 ASP cc_start: 0.8429 (m-30) cc_final: 0.8213 (m-30) REVERT: B 410 ASN cc_start: 0.6629 (t0) cc_final: 0.6141 (m-40) REVERT: B 411 SER cc_start: 0.8479 (t) cc_final: 0.8249 (p) REVERT: B 445 LEU cc_start: 0.8996 (mt) cc_final: 0.8589 (tp) REVERT: B 477 ASN cc_start: 0.7867 (t160) cc_final: 0.7632 (t0) REVERT: B 503 HIS cc_start: 0.7334 (t-90) cc_final: 0.6930 (t-170) REVERT: B 508 THR cc_start: 0.8310 (p) cc_final: 0.7943 (t) REVERT: B 510 GLU cc_start: 0.7307 (mp0) cc_final: 0.6982 (mp0) REVERT: B 511 PHE cc_start: 0.7897 (t80) cc_final: 0.7694 (t80) REVERT: B 517 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.8153 (mtt-85) REVERT: B 568 GLU cc_start: 0.8440 (pt0) cc_final: 0.8036 (pt0) REVERT: B 569 MET cc_start: 0.7873 (tmm) cc_final: 0.7165 (tmm) REVERT: B 590 ASP cc_start: 0.7907 (m-30) cc_final: 0.7411 (m-30) REVERT: B 667 LEU cc_start: 0.8412 (tp) cc_final: 0.8197 (tp) REVERT: B 693 GLU cc_start: 0.8094 (tp30) cc_final: 0.7559 (tp30) REVERT: B 708 PHE cc_start: 0.8352 (t80) cc_final: 0.8001 (t80) REVERT: B 727 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8231 (ttpp) REVERT: B 738 LYS cc_start: 0.8766 (tptt) cc_final: 0.8515 (tptt) REVERT: B 947 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8195 (mm-30) REVERT: B 976 MET cc_start: 0.6609 (mtm) cc_final: 0.6187 (mtm) REVERT: B 1001 MET cc_start: 0.8383 (tpp) cc_final: 0.8029 (tpp) REVERT: E 244 PHE cc_start: 0.3207 (m-10) cc_final: 0.2962 (m-80) REVERT: F 69 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5543 (mm-30) REVERT: F 92 TYR cc_start: 0.7000 (t80) cc_final: 0.6410 (t80) REVERT: F 118 HIS cc_start: 0.4008 (m90) cc_final: 0.3726 (m-70) REVERT: F 186 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7433 (mtmm) REVERT: F 193 TYR cc_start: 0.7780 (t80) cc_final: 0.7469 (t80) REVERT: F 262 GLU cc_start: 0.7331 (tp30) cc_final: 0.7094 (tp30) REVERT: F 290 MET cc_start: 0.7174 (mmm) cc_final: 0.6969 (mmm) outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.4037 time to fit residues: 403.2498 Evaluate side-chains 645 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 208 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 254 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 961 ASN B 39 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 483 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 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 = 0.4298 r_free = 0.4298 target = 0.177355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136729 restraints weight = 122771.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144604 restraints weight = 59327.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.149365 restraints weight = 34101.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.152223 restraints weight = 22770.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.153845 restraints weight = 17218.538| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23772 Z= 0.260 Angle : 0.630 16.249 32072 Z= 0.365 Chirality : 0.042 0.305 3422 Planarity : 0.005 0.060 4114 Dihedral : 5.500 45.442 3097 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.28 % Favored : 89.08 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.15), residues: 2801 helix: -0.49 (0.13), residues: 1540 sheet: -1.80 (0.35), residues: 193 loop : -2.34 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 747 TYR 0.022 0.002 TYR B 791 PHE 0.033 0.002 PHE B 744 TRP 0.028 0.002 TRP E 60 HIS 0.015 0.002 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00487 (23772) covalent geometry : angle 0.62998 (32072) hydrogen bonds : bond 0.05360 ( 1049) hydrogen bonds : angle 5.90186 ( 3006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 670 time to evaluate : 1.234 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 LYS cc_start: 0.7111 (tptp) cc_final: 0.6847 (mtmt) REVERT: D 34 GLN cc_start: 0.7268 (tp40) cc_final: 0.7040 (tm-30) REVERT: D 75 MET cc_start: 0.8376 (mmm) cc_final: 0.8165 (mmm) REVERT: D 192 TYR cc_start: 0.7069 (m-80) cc_final: 0.6725 (m-80) REVERT: D 206 MET cc_start: 0.5966 (tpt) cc_final: 0.5282 (tpt) REVERT: D 220 PHE cc_start: 0.7485 (m-10) cc_final: 0.7179 (m-10) REVERT: C 34 GLN cc_start: 0.7828 (tt0) cc_final: 0.7600 (tt0) REVERT: C 58 GLU cc_start: 0.5642 (pm20) cc_final: 0.5242 (pm20) REVERT: C 64 LYS cc_start: 0.7169 (mtpp) cc_final: 0.6273 (mtpp) REVERT: C 68 PHE cc_start: 0.7575 (t80) cc_final: 0.7153 (t80) REVERT: C 168 SER cc_start: 0.8413 (m) cc_final: 0.8110 (p) REVERT: C 197 ASN cc_start: 0.8470 (t0) cc_final: 0.7939 (t0) REVERT: C 206 MET cc_start: 0.6913 (tpt) cc_final: 0.6307 (tpt) REVERT: C 208 LEU cc_start: 0.7894 (pt) cc_final: 0.7608 (pt) REVERT: C 223 LEU cc_start: 0.6562 (mm) cc_final: 0.6298 (mm) REVERT: A 28 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 33 ILE cc_start: 0.8719 (mt) cc_final: 0.8481 (mm) REVERT: A 35 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 41 LYS cc_start: 0.7861 (ptpp) cc_final: 0.7622 (ptpp) REVERT: A 182 ASN cc_start: 0.8283 (m110) cc_final: 0.7877 (m110) REVERT: A 196 ASN cc_start: 0.7831 (m110) cc_final: 0.7628 (m-40) REVERT: A 249 ASP cc_start: 0.8034 (t70) cc_final: 0.7745 (t70) REVERT: A 306 ASP cc_start: 0.8123 (t70) cc_final: 0.7898 (t0) REVERT: A 307 GLU cc_start: 0.7174 (tp30) cc_final: 0.6735 (tp30) REVERT: A 310 ASP cc_start: 0.8218 (p0) cc_final: 0.7990 (p0) REVERT: A 334 PHE cc_start: 0.8260 (m-10) cc_final: 0.7893 (m-80) REVERT: A 335 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7982 (mt-10) REVERT: A 337 ASP cc_start: 0.7465 (m-30) cc_final: 0.7155 (m-30) REVERT: A 424 PHE cc_start: 0.8329 (t80) cc_final: 0.8115 (t80) REVERT: A 442 LEU cc_start: 0.8790 (mt) cc_final: 0.8403 (mt) REVERT: A 450 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8178 (mp0) REVERT: A 493 ASN cc_start: 0.9113 (m-40) cc_final: 0.8901 (t0) REVERT: A 543 GLU cc_start: 0.8383 (tt0) cc_final: 0.7993 (tt0) REVERT: A 560 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 569 MET cc_start: 0.7028 (tmm) cc_final: 0.6339 (tmm) REVERT: A 571 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6844 (mm-30) REVERT: A 582 ILE cc_start: 0.8816 (tp) cc_final: 0.8525 (tp) REVERT: A 625 TYR cc_start: 0.8283 (t80) cc_final: 0.7881 (t80) REVERT: A 657 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8256 (ttm-80) REVERT: A 668 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8172 (mt-10) REVERT: A 685 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8503 (mt-10) REVERT: A 708 PHE cc_start: 0.7581 (t80) cc_final: 0.7153 (t80) REVERT: A 709 TYR cc_start: 0.7852 (t80) cc_final: 0.7241 (t80) REVERT: A 711 GLN cc_start: 0.7441 (mp10) cc_final: 0.7039 (mp10) REVERT: A 737 VAL cc_start: 0.8688 (p) cc_final: 0.8397 (m) REVERT: A 784 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 826 CYS cc_start: 0.9019 (t) cc_final: 0.8773 (p) REVERT: A 924 GLU cc_start: 0.8365 (tp30) cc_final: 0.8018 (tp30) REVERT: A 939 GLN cc_start: 0.7568 (tt0) cc_final: 0.7351 (tt0) REVERT: A 976 MET cc_start: 0.7506 (mtp) cc_final: 0.7076 (mtp) REVERT: B 196 ASN cc_start: 0.8475 (m-40) cc_final: 0.8147 (m110) REVERT: B 291 ASP cc_start: 0.8485 (m-30) cc_final: 0.8244 (m-30) REVERT: B 360 PHE cc_start: 0.8306 (t80) cc_final: 0.8092 (t80) REVERT: B 410 ASN cc_start: 0.6756 (t0) cc_final: 0.6143 (m-40) REVERT: B 411 SER cc_start: 0.8552 (t) cc_final: 0.8189 (p) REVERT: B 438 LYS cc_start: 0.8903 (mttp) cc_final: 0.8424 (mttt) REVERT: B 445 LEU cc_start: 0.9046 (mt) cc_final: 0.8831 (mm) REVERT: B 473 LEU cc_start: 0.7939 (mt) cc_final: 0.7322 (mt) REVERT: B 474 SER cc_start: 0.8607 (t) cc_final: 0.8380 (t) REVERT: B 503 HIS cc_start: 0.7616 (t-90) cc_final: 0.7107 (t-170) REVERT: B 508 THR cc_start: 0.8406 (p) cc_final: 0.8032 (t) REVERT: B 510 GLU cc_start: 0.7360 (mp0) cc_final: 0.7033 (mp0) REVERT: B 511 PHE cc_start: 0.7864 (t80) cc_final: 0.7651 (t80) REVERT: B 517 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8177 (mtt-85) REVERT: B 558 LEU cc_start: 0.8711 (tp) cc_final: 0.8507 (tp) REVERT: B 562 THR cc_start: 0.8685 (t) cc_final: 0.8476 (p) REVERT: B 568 GLU cc_start: 0.8483 (pt0) cc_final: 0.8096 (pt0) REVERT: B 569 MET cc_start: 0.7891 (tmm) cc_final: 0.7187 (tmm) REVERT: B 590 ASP cc_start: 0.7912 (m-30) cc_final: 0.7441 (m-30) REVERT: B 663 ASP cc_start: 0.8284 (m-30) cc_final: 0.7912 (m-30) REVERT: B 667 LEU cc_start: 0.8427 (tp) cc_final: 0.8222 (tp) REVERT: B 668 GLU cc_start: 0.8355 (tp30) cc_final: 0.8151 (tp30) REVERT: B 682 GLU cc_start: 0.6747 (pm20) cc_final: 0.6518 (mp0) REVERT: B 769 LYS cc_start: 0.9046 (tptp) cc_final: 0.8844 (tptp) REVERT: B 947 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8185 (mm-30) REVERT: B 966 LEU cc_start: 0.8840 (tp) cc_final: 0.8619 (tp) REVERT: B 976 MET cc_start: 0.6740 (mtm) cc_final: 0.6259 (mtm) REVERT: B 985 LYS cc_start: 0.8288 (ptpp) cc_final: 0.7998 (ptmm) REVERT: B 1001 MET cc_start: 0.8412 (tpp) cc_final: 0.8028 (tpp) REVERT: E 68 GLU cc_start: 0.9046 (mp0) cc_final: 0.8845 (mp0) REVERT: E 92 TYR cc_start: 0.7544 (t80) cc_final: 0.7219 (t80) REVERT: E 192 ASN cc_start: 0.8322 (m-40) cc_final: 0.8117 (m-40) REVERT: E 193 TYR cc_start: 0.7813 (p90) cc_final: 0.6580 (t80) REVERT: E 227 MET cc_start: 0.7365 (tmm) cc_final: 0.7152 (tmm) REVERT: E 244 PHE cc_start: 0.3522 (m-10) cc_final: 0.3228 (m-80) REVERT: F 69 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5637 (mm-30) REVERT: F 92 TYR cc_start: 0.7025 (t80) cc_final: 0.6378 (t80) REVERT: F 186 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7482 (mtmm) REVERT: F 193 TYR cc_start: 0.7764 (t80) cc_final: 0.7471 (t80) REVERT: F 262 GLU cc_start: 0.7425 (tp30) cc_final: 0.7144 (tp30) REVERT: F 290 MET cc_start: 0.7320 (mmm) cc_final: 0.6845 (mmm) outliers start: 0 outliers final: 0 residues processed: 670 average time/residue: 0.4076 time to fit residues: 405.9723 Evaluate side-chains 647 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 115 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 212 optimal weight: 0.0170 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN ** F 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.180393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140057 restraints weight = 121289.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147925 restraints weight = 58173.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.152769 restraints weight = 33348.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155562 restraints weight = 22172.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157234 restraints weight = 16713.628| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 23772 Z= 0.248 Angle : 0.619 16.144 32072 Z= 0.358 Chirality : 0.041 0.304 3422 Planarity : 0.005 0.070 4114 Dihedral : 5.511 45.088 3097 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.14 % Favored : 89.22 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.15), residues: 2801 helix: -0.48 (0.13), residues: 1536 sheet: -1.99 (0.33), residues: 204 loop : -2.40 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 760 TYR 0.025 0.002 TYR E 79 PHE 0.028 0.002 PHE B 856 TRP 0.015 0.002 TRP C 72 HIS 0.015 0.002 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00470 (23772) covalent geometry : angle 0.61857 (32072) hydrogen bonds : bond 0.05275 ( 1049) hydrogen bonds : angle 5.82133 ( 3006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 1.208 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 GLN cc_start: 0.7325 (tp40) cc_final: 0.7060 (tm-30) REVERT: D 75 MET cc_start: 0.8372 (mmm) cc_final: 0.8162 (mmm) REVERT: D 192 TYR cc_start: 0.7090 (m-80) cc_final: 0.6718 (m-80) REVERT: D 206 MET cc_start: 0.5913 (tpt) cc_final: 0.5222 (tpt) REVERT: D 220 PHE cc_start: 0.7481 (m-10) cc_final: 0.7159 (m-10) REVERT: C 34 GLN cc_start: 0.7862 (tt0) cc_final: 0.7622 (tt0) REVERT: C 58 GLU cc_start: 0.5565 (pm20) cc_final: 0.5124 (pm20) REVERT: C 64 LYS cc_start: 0.7145 (mtpp) cc_final: 0.6233 (mtpp) REVERT: C 68 PHE cc_start: 0.7650 (t80) cc_final: 0.7270 (t80) REVERT: C 168 SER cc_start: 0.8441 (m) cc_final: 0.8145 (p) REVERT: C 172 GLU cc_start: 0.4435 (mp0) cc_final: 0.4090 (mp0) REVERT: C 197 ASN cc_start: 0.8512 (t0) cc_final: 0.8087 (t0) REVERT: C 206 MET cc_start: 0.6971 (tpt) cc_final: 0.6420 (tpt) REVERT: C 208 LEU cc_start: 0.7857 (pt) cc_final: 0.7556 (pt) REVERT: C 223 LEU cc_start: 0.6708 (mm) cc_final: 0.6459 (mm) REVERT: A 28 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 33 ILE cc_start: 0.8705 (mt) cc_final: 0.8466 (mm) REVERT: A 35 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7891 (mm-30) REVERT: A 41 LYS cc_start: 0.7865 (ptpp) cc_final: 0.7648 (ptpp) REVERT: A 182 ASN cc_start: 0.8223 (m110) cc_final: 0.7755 (m110) REVERT: A 249 ASP cc_start: 0.8077 (t70) cc_final: 0.7781 (t70) REVERT: A 306 ASP cc_start: 0.8140 (t70) cc_final: 0.7867 (t0) REVERT: A 307 GLU cc_start: 0.7192 (tp30) cc_final: 0.6780 (tp30) REVERT: A 310 ASP cc_start: 0.8228 (p0) cc_final: 0.7975 (p0) REVERT: A 334 PHE cc_start: 0.8311 (m-10) cc_final: 0.8007 (m-80) REVERT: A 337 ASP cc_start: 0.7484 (m-30) cc_final: 0.7190 (m-30) REVERT: A 424 PHE cc_start: 0.8306 (t80) cc_final: 0.8102 (t80) REVERT: A 442 LEU cc_start: 0.8767 (mt) cc_final: 0.8371 (mt) REVERT: A 450 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8194 (mp0) REVERT: A 493 ASN cc_start: 0.9148 (m-40) cc_final: 0.8935 (t0) REVERT: A 560 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 569 MET cc_start: 0.7032 (tmm) cc_final: 0.6377 (tmm) REVERT: A 571 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7050 (mm-30) REVERT: A 582 ILE cc_start: 0.8775 (tp) cc_final: 0.8502 (tp) REVERT: A 589 TYR cc_start: 0.7497 (m-80) cc_final: 0.7275 (m-80) REVERT: A 602 SER cc_start: 0.8740 (p) cc_final: 0.8459 (m) REVERT: A 621 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 625 TYR cc_start: 0.8297 (t80) cc_final: 0.7876 (t80) REVERT: A 663 ASP cc_start: 0.7942 (t70) cc_final: 0.7615 (t0) REVERT: A 670 SER cc_start: 0.8373 (m) cc_final: 0.8039 (m) REVERT: A 685 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8506 (mt-10) REVERT: A 709 TYR cc_start: 0.7852 (t80) cc_final: 0.6381 (t80) REVERT: A 737 VAL cc_start: 0.8704 (p) cc_final: 0.8409 (m) REVERT: A 766 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 800 TYR cc_start: 0.7310 (m-80) cc_final: 0.7013 (m-80) REVERT: A 822 GLU cc_start: 0.8763 (mp0) cc_final: 0.8326 (mp0) REVERT: A 826 CYS cc_start: 0.8995 (t) cc_final: 0.8734 (p) REVERT: A 913 MET cc_start: 0.6449 (mmp) cc_final: 0.6042 (mmp) REVERT: A 924 GLU cc_start: 0.8404 (tp30) cc_final: 0.8000 (tp30) REVERT: A 939 GLN cc_start: 0.7849 (tt0) cc_final: 0.7453 (tt0) REVERT: A 976 MET cc_start: 0.7412 (mtp) cc_final: 0.6957 (mtp) REVERT: B 104 LEU cc_start: 0.8240 (mt) cc_final: 0.7918 (mt) REVERT: B 160 ASN cc_start: 0.8556 (m-40) cc_final: 0.7809 (p0) REVERT: B 196 ASN cc_start: 0.8494 (m-40) cc_final: 0.8164 (m110) REVERT: B 240 PHE cc_start: 0.8318 (t80) cc_final: 0.8045 (t80) REVERT: B 291 ASP cc_start: 0.8497 (m-30) cc_final: 0.8254 (m-30) REVERT: B 360 PHE cc_start: 0.8270 (t80) cc_final: 0.8048 (t80) REVERT: B 410 ASN cc_start: 0.6711 (t0) cc_final: 0.5958 (m-40) REVERT: B 411 SER cc_start: 0.8561 (t) cc_final: 0.8247 (p) REVERT: B 438 LYS cc_start: 0.8832 (mttp) cc_final: 0.8299 (mttt) REVERT: B 445 LEU cc_start: 0.9017 (mt) cc_final: 0.8603 (tt) REVERT: B 473 LEU cc_start: 0.7706 (mt) cc_final: 0.7324 (mt) REVERT: B 477 ASN cc_start: 0.8507 (m110) cc_final: 0.8196 (m-40) REVERT: B 503 HIS cc_start: 0.7650 (t-90) cc_final: 0.7104 (t-170) REVERT: B 508 THR cc_start: 0.8402 (p) cc_final: 0.7906 (t) REVERT: B 510 GLU cc_start: 0.7384 (mp0) cc_final: 0.7035 (mp0) REVERT: B 511 PHE cc_start: 0.7898 (t80) cc_final: 0.7672 (t80) REVERT: B 517 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8168 (mtt-85) REVERT: B 568 GLU cc_start: 0.8466 (pt0) cc_final: 0.8083 (pt0) REVERT: B 569 MET cc_start: 0.7990 (tmm) cc_final: 0.7205 (tmm) REVERT: B 598 ASN cc_start: 0.8485 (m-40) cc_final: 0.8134 (m-40) REVERT: B 613 ARG cc_start: 0.7215 (ttm110) cc_final: 0.6880 (ttm110) REVERT: B 663 ASP cc_start: 0.8332 (m-30) cc_final: 0.8047 (m-30) REVERT: B 666 ASN cc_start: 0.8393 (m-40) cc_final: 0.8047 (t0) REVERT: B 667 LEU cc_start: 0.8453 (tp) cc_final: 0.8188 (tp) REVERT: B 693 GLU cc_start: 0.8134 (tp30) cc_final: 0.7513 (tp30) REVERT: B 738 LYS cc_start: 0.8755 (tptt) cc_final: 0.8508 (tptt) REVERT: B 746 GLU cc_start: 0.8025 (pm20) cc_final: 0.7755 (pm20) REVERT: B 913 MET cc_start: 0.8656 (ttm) cc_final: 0.8433 (ttm) REVERT: B 966 LEU cc_start: 0.8870 (tp) cc_final: 0.8649 (tp) REVERT: B 976 MET cc_start: 0.6751 (mtm) cc_final: 0.6296 (mtm) REVERT: B 985 LYS cc_start: 0.8231 (ptpp) cc_final: 0.7977 (ptmm) REVERT: B 1001 MET cc_start: 0.8410 (tpp) cc_final: 0.7967 (tpp) REVERT: B 1003 TYR cc_start: 0.8025 (m-10) cc_final: 0.7802 (m-10) REVERT: E 92 TYR cc_start: 0.7514 (t80) cc_final: 0.7189 (t80) REVERT: F 69 GLU cc_start: 0.6241 (mm-30) cc_final: 0.5702 (mm-30) REVERT: F 186 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7474 (mtmm) REVERT: F 193 TYR cc_start: 0.7773 (t80) cc_final: 0.7479 (t80) REVERT: F 195 GLN cc_start: 0.6894 (tp-100) cc_final: 0.5826 (mt0) REVERT: F 262 GLU cc_start: 0.7498 (tp30) cc_final: 0.7204 (tp30) REVERT: F 290 MET cc_start: 0.7426 (mmm) cc_final: 0.7172 (mmm) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.4161 time to fit residues: 419.0023 Evaluate side-chains 657 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 180 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN B 563 ASN F 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.182096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142584 restraints weight = 119832.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150489 restraints weight = 56977.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155270 restraints weight = 32331.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.158095 restraints weight = 21257.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159591 restraints weight = 15881.054| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 23772 Z= 0.202 Angle : 0.593 16.090 32072 Z= 0.339 Chirality : 0.041 0.304 3422 Planarity : 0.005 0.080 4114 Dihedral : 5.392 44.990 3097 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.50 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.15), residues: 2801 helix: -0.37 (0.13), residues: 1540 sheet: -2.01 (0.34), residues: 208 loop : -2.33 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 657 TYR 0.030 0.002 TYR B 134 PHE 0.028 0.002 PHE B 856 TRP 0.017 0.002 TRP C 72 HIS 0.011 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00390 (23772) covalent geometry : angle 0.59258 (32072) hydrogen bonds : bond 0.05004 ( 1049) hydrogen bonds : angle 5.62295 ( 3006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 0.972 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 GLN cc_start: 0.7280 (tp40) cc_final: 0.6984 (tm-30) REVERT: D 75 MET cc_start: 0.8373 (mmm) cc_final: 0.8167 (mmm) REVERT: D 192 TYR cc_start: 0.7048 (m-80) cc_final: 0.6705 (m-80) REVERT: D 206 MET cc_start: 0.5797 (tpt) cc_final: 0.5096 (tpt) REVERT: D 220 PHE cc_start: 0.7413 (m-10) cc_final: 0.7144 (m-10) REVERT: C 34 GLN cc_start: 0.7883 (tt0) cc_final: 0.7645 (tt0) REVERT: C 58 GLU cc_start: 0.5551 (pm20) cc_final: 0.5157 (pm20) REVERT: C 64 LYS cc_start: 0.7170 (mtpp) cc_final: 0.6232 (mtpp) REVERT: C 68 PHE cc_start: 0.7662 (t80) cc_final: 0.7237 (t80) REVERT: C 197 ASN cc_start: 0.8516 (t0) cc_final: 0.8130 (t0) REVERT: C 206 MET cc_start: 0.6867 (tpt) cc_final: 0.6273 (tpt) REVERT: C 208 LEU cc_start: 0.7866 (pt) cc_final: 0.7540 (pt) REVERT: C 223 LEU cc_start: 0.6738 (mm) cc_final: 0.6505 (mm) REVERT: C 231 MET cc_start: 0.4955 (ptm) cc_final: 0.4705 (ppp) REVERT: A 28 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 35 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 182 ASN cc_start: 0.8253 (m110) cc_final: 0.7799 (m110) REVERT: A 196 ASN cc_start: 0.7797 (m-40) cc_final: 0.7581 (m-40) REVERT: A 298 GLU cc_start: 0.7419 (pt0) cc_final: 0.7211 (pt0) REVERT: A 306 ASP cc_start: 0.8132 (t70) cc_final: 0.7848 (t0) REVERT: A 307 GLU cc_start: 0.7179 (tp30) cc_final: 0.6791 (tp30) REVERT: A 310 ASP cc_start: 0.8236 (p0) cc_final: 0.7979 (p0) REVERT: A 334 PHE cc_start: 0.8277 (m-10) cc_final: 0.7921 (m-80) REVERT: A 335 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 337 ASP cc_start: 0.7420 (m-30) cc_final: 0.7110 (m-30) REVERT: A 424 PHE cc_start: 0.8303 (t80) cc_final: 0.8084 (t80) REVERT: A 442 LEU cc_start: 0.8769 (mt) cc_final: 0.8351 (mt) REVERT: A 450 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8151 (mp0) REVERT: A 493 ASN cc_start: 0.9125 (m-40) cc_final: 0.8903 (t0) REVERT: A 560 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8014 (mt-10) REVERT: A 569 MET cc_start: 0.6977 (tmm) cc_final: 0.6445 (tmm) REVERT: A 582 ILE cc_start: 0.8759 (tp) cc_final: 0.8469 (tp) REVERT: A 602 SER cc_start: 0.8719 (p) cc_final: 0.8443 (m) REVERT: A 613 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7713 (ttp80) REVERT: A 663 ASP cc_start: 0.7980 (t70) cc_final: 0.7635 (t0) REVERT: A 670 SER cc_start: 0.8300 (m) cc_final: 0.7994 (m) REVERT: A 685 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8471 (mt-10) REVERT: A 709 TYR cc_start: 0.7840 (t80) cc_final: 0.6432 (t80) REVERT: A 712 PHE cc_start: 0.7853 (t80) cc_final: 0.7649 (t80) REVERT: A 737 VAL cc_start: 0.8684 (p) cc_final: 0.8391 (m) REVERT: A 766 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 800 TYR cc_start: 0.7266 (m-80) cc_final: 0.6952 (m-80) REVERT: A 826 CYS cc_start: 0.8987 (t) cc_final: 0.8713 (p) REVERT: A 913 MET cc_start: 0.6468 (mmp) cc_final: 0.6003 (mmp) REVERT: A 924 GLU cc_start: 0.8393 (tp30) cc_final: 0.8011 (tp30) REVERT: A 976 MET cc_start: 0.7358 (mtp) cc_final: 0.6900 (mtp) REVERT: B 104 LEU cc_start: 0.8240 (mt) cc_final: 0.7903 (mt) REVERT: B 160 ASN cc_start: 0.8549 (m-40) cc_final: 0.7810 (p0) REVERT: B 196 ASN cc_start: 0.8444 (m-40) cc_final: 0.8110 (m110) REVERT: B 291 ASP cc_start: 0.8504 (m-30) cc_final: 0.8276 (m-30) REVERT: B 410 ASN cc_start: 0.6845 (t0) cc_final: 0.6081 (m-40) REVERT: B 411 SER cc_start: 0.8612 (t) cc_final: 0.8275 (p) REVERT: B 438 LYS cc_start: 0.8822 (mttp) cc_final: 0.8282 (mttt) REVERT: B 445 LEU cc_start: 0.9008 (mt) cc_final: 0.8598 (tt) REVERT: B 473 LEU cc_start: 0.7640 (mt) cc_final: 0.7238 (mt) REVERT: B 477 ASN cc_start: 0.8511 (m110) cc_final: 0.8187 (m-40) REVERT: B 503 HIS cc_start: 0.7663 (t-90) cc_final: 0.7143 (t-170) REVERT: B 508 THR cc_start: 0.8379 (p) cc_final: 0.7892 (t) REVERT: B 510 GLU cc_start: 0.7389 (mp0) cc_final: 0.7070 (mp0) REVERT: B 511 PHE cc_start: 0.7908 (t80) cc_final: 0.7637 (t80) REVERT: B 539 TYR cc_start: 0.7976 (m-10) cc_final: 0.7759 (m-10) REVERT: B 569 MET cc_start: 0.7915 (tmm) cc_final: 0.7338 (tmm) REVERT: B 590 ASP cc_start: 0.7871 (m-30) cc_final: 0.7396 (m-30) REVERT: B 613 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6826 (ttm110) REVERT: B 663 ASP cc_start: 0.8243 (m-30) cc_final: 0.7935 (m-30) REVERT: B 668 GLU cc_start: 0.8264 (tp30) cc_final: 0.8037 (tp30) REVERT: B 693 GLU cc_start: 0.8097 (tp30) cc_final: 0.7484 (tp30) REVERT: B 738 LYS cc_start: 0.8750 (tptt) cc_final: 0.8498 (tptt) REVERT: B 746 GLU cc_start: 0.8033 (pm20) cc_final: 0.7744 (pm20) REVERT: B 936 MET cc_start: 0.7704 (mtt) cc_final: 0.7477 (mtt) REVERT: B 966 LEU cc_start: 0.8865 (tp) cc_final: 0.8638 (tp) REVERT: B 976 MET cc_start: 0.6720 (mtm) cc_final: 0.6250 (mtm) REVERT: B 985 LYS cc_start: 0.8230 (ptpp) cc_final: 0.7958 (ptmm) REVERT: B 1001 MET cc_start: 0.8389 (tpp) cc_final: 0.7925 (tpp) REVERT: B 1003 TYR cc_start: 0.7989 (m-10) cc_final: 0.7772 (m-10) REVERT: E 92 TYR cc_start: 0.7468 (t80) cc_final: 0.7140 (t80) REVERT: E 192 ASN cc_start: 0.8377 (m-40) cc_final: 0.8165 (m-40) REVERT: E 193 TYR cc_start: 0.7591 (p90) cc_final: 0.6279 (t80) REVERT: F 69 GLU cc_start: 0.6205 (mm-30) cc_final: 0.5681 (mm-30) REVERT: F 92 TYR cc_start: 0.7073 (t80) cc_final: 0.6630 (t80) REVERT: F 186 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7453 (mtmm) REVERT: F 193 TYR cc_start: 0.7743 (t80) cc_final: 0.7439 (t80) REVERT: F 195 GLN cc_start: 0.6930 (tp-100) cc_final: 0.5908 (mt0) REVERT: F 262 GLU cc_start: 0.7384 (tp30) cc_final: 0.7098 (tp30) REVERT: F 290 MET cc_start: 0.7559 (mmm) cc_final: 0.7152 (mmm) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.3922 time to fit residues: 391.1911 Evaluate side-chains 639 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 483 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN ** F 236 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 = 0.4283 r_free = 0.4283 target = 0.180018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140415 restraints weight = 120455.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148153 restraints weight = 57282.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.152800 restraints weight = 32603.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.155507 restraints weight = 21635.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.157206 restraints weight = 16346.040| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 23772 Z= 0.300 Angle : 0.667 16.069 32072 Z= 0.388 Chirality : 0.043 0.311 3422 Planarity : 0.005 0.074 4114 Dihedral : 5.697 45.279 3097 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.53 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.15), residues: 2801 helix: -0.70 (0.12), residues: 1540 sheet: -2.20 (0.34), residues: 192 loop : -2.47 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 747 TYR 0.030 0.002 TYR B 791 PHE 0.036 0.002 PHE B 646 TRP 0.015 0.002 TRP A 601 HIS 0.016 0.002 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00563 (23772) covalent geometry : angle 0.66693 (32072) hydrogen bonds : bond 0.05524 ( 1049) hydrogen bonds : angle 6.07050 ( 3006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9647.23 seconds wall clock time: 164 minutes 51.44 seconds (9891.44 seconds total)