Starting phenix.real_space_refine on Thu Mar 5 16:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ry3_24732/03_2026/7ry3_24732_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ry3_24732/03_2026/7ry3_24732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ry3_24732/03_2026/7ry3_24732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ry3_24732/03_2026/7ry3_24732.map" model { file = "/net/cci-nas-00/data/ceres_data/7ry3_24732/03_2026/7ry3_24732_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ry3_24732/03_2026/7ry3_24732_trim.cif" } resolution = 2.91 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.217 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 102 5.16 5 C 15423 2.51 5 N 3973 2.21 5 O 4463 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23964 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 7979 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 47, 'TRANS': 999} Chain: "B" Number of atoms: 7958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 7958 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 47, 'TRANS': 997} Chain: "C" Number of atoms: 7986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 7986 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 48, 'TRANS': 999} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'80P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.56, per 1000 atoms: 0.23 Number of scatterers: 23964 At special positions: 0 Unit cell: (126.36, 124.2, 154.44, 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 102 16.00 F 3 9.00 O 4463 8.00 N 3973 7.00 C 15423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5764 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 26 sheets defined 61.3% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.528A pdb=" N HIS A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.694A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.616A pdb=" N GLN A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.535A pdb=" N VAL A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.965A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.680A pdb=" N TYR A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.786A pdb=" N ILE A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.740A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 removed outlier: 4.019A pdb=" N LYS A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.645A pdb=" N ILE A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 386 removed outlier: 4.009A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.610A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 406 removed outlier: 4.723A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 removed outlier: 3.901A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 removed outlier: 3.567A pdb=" N GLN A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.224A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 459' Processing helix chain 'A' and resid 460 through 497 removed outlier: 3.561A pdb=" N GLY A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.614A pdb=" N LEU A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 539 removed outlier: 3.853A pdb=" N ASP A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 561 Processing helix chain 'A' and resid 585 through 602 removed outlier: 3.602A pdb=" N VAL A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 694 through 710 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 778 through 782 removed outlier: 3.939A pdb=" N MET A 782 " --> pdb=" O GLY A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 789 Processing helix chain 'A' and resid 802 through 805 No H-bonds generated for 'chain 'A' and resid 802 through 805' Processing helix chain 'A' and resid 837 through 856 removed outlier: 3.638A pdb=" N LEU A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Proline residue: A 853 - end of helix Processing helix chain 'A' and resid 866 through 898 removed outlier: 3.661A pdb=" N ALA A 878 " --> pdb=" O SER A 874 " (cutoff:3.500A) Proline residue: A 879 - end of helix Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.602A pdb=" N PHE A 904 " --> pdb=" O TRP A 900 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 929 removed outlier: 4.064A pdb=" N GLY A 913 " --> pdb=" O VAL A 909 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 967 removed outlier: 3.506A pdb=" N LEU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1002 removed outlier: 4.706A pdb=" N ARG A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Proline residue: A 985 - end of helix Proline residue: A 999 - end of helix Processing helix chain 'A' and resid 1007 through 1028 removed outlier: 3.780A pdb=" N GLY A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1044 Proline residue: A1034 - end of helix removed outlier: 3.534A pdb=" N TYR A1037 " --> pdb=" O ILE A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.613A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.887A pdb=" N GLN B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 118 removed outlier: 4.819A pdb=" N SER B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 removed outlier: 4.042A pdb=" N TYR B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.707A pdb=" N PHE B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 359 removed outlier: 4.273A pdb=" N ILE B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 387 removed outlier: 3.603A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.215A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 3.609A pdb=" N GLN B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.580A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 487 removed outlier: 3.512A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 509 through 540 removed outlier: 3.888A pdb=" N SER B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 561 Processing helix chain 'B' and resid 585 through 603 removed outlier: 3.506A pdb=" N THR B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 643 Processing helix chain 'B' and resid 644 through 659 removed outlier: 3.775A pdb=" N LEU B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN B 656 " --> pdb=" O GLY B 652 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N MET B 657 " --> pdb=" O MET B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 711 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.608A pdb=" N ARG B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 789 Processing helix chain 'B' and resid 802 through 805 No H-bonds generated for 'chain 'B' and resid 802 through 805' Processing helix chain 'B' and resid 837 through 851 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 865 through 875 removed outlier: 3.527A pdb=" N GLU B 870 " --> pdb=" O GLY B 866 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 898 removed outlier: 3.940A pdb=" N LEU B 881 " --> pdb=" O GLN B 877 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 882 " --> pdb=" O ALA B 878 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 886 " --> pdb=" O TYR B 882 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 909 removed outlier: 4.252A pdb=" N SER B 905 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 906 " --> pdb=" O ILE B 902 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 909 " --> pdb=" O SER B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 928 removed outlier: 3.749A pdb=" N GLY B 913 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 914 " --> pdb=" O VAL B 910 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 916 " --> pdb=" O LEU B 912 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 917 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 968 Processing helix chain 'B' and resid 970 through 982 Processing helix chain 'B' and resid 982 through 1002 removed outlier: 3.650A pdb=" N THR B 990 " --> pdb=" O ILE B 986 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) Proline residue: B 999 - end of helix Processing helix chain 'B' and resid 1007 through 1044 removed outlier: 4.267A pdb=" N PHE B1031 " --> pdb=" O PHE B1027 " (cutoff:3.500A) Proline residue: B1034 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.685A pdb=" N HIS C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.632A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.651A pdb=" N TYR C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.580A pdb=" N ILE C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 315 removed outlier: 4.306A pdb=" N LYS C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 359 removed outlier: 3.723A pdb=" N PHE C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 387 removed outlier: 4.132A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.311A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 454 removed outlier: 3.580A pdb=" N GLN C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 removed outlier: 3.816A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 459 " --> pdb=" O PRO C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 459' Processing helix chain 'C' and resid 460 through 487 removed outlier: 3.646A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 removed outlier: 3.841A pdb=" N ALA C 491 " --> pdb=" O THR C 487 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 497 " --> pdb=" O CYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 539 Processing helix chain 'C' and resid 539 through 560 removed outlier: 3.555A pdb=" N GLN C 559 " --> pdb=" O VAL C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 604 removed outlier: 3.586A pdb=" N THR C 589 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 604 " --> pdb=" O PHE C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.893A pdb=" N LEU C 648 " --> pdb=" O GLN C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 659 Processing helix chain 'C' and resid 693 through 711 removed outlier: 3.697A pdb=" N SER C 709 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 710 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP C 711 " --> pdb=" O LEU C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 743 through 755 Processing helix chain 'C' and resid 778 through 782 removed outlier: 3.932A pdb=" N MET C 782 " --> pdb=" O GLY C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 789 Processing helix chain 'C' and resid 802 through 805 No H-bonds generated for 'chain 'C' and resid 802 through 805' Processing helix chain 'C' and resid 837 through 851 Processing helix chain 'C' and resid 851 through 856 Processing helix chain 'C' and resid 866 through 875 removed outlier: 3.543A pdb=" N GLU C 870 " --> pdb=" O GLY C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 898 removed outlier: 4.213A pdb=" N PHE C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 908 removed outlier: 4.210A pdb=" N VAL C 906 " --> pdb=" O ILE C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 928 removed outlier: 3.699A pdb=" N GLY C 913 " --> pdb=" O VAL C 909 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 914 " --> pdb=" O VAL C 910 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 917 " --> pdb=" O GLY C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 967 Processing helix chain 'C' and resid 970 through 1002 removed outlier: 4.506A pdb=" N ARG C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Proline residue: C 985 - end of helix removed outlier: 3.594A pdb=" N ALA C 992 " --> pdb=" O MET C 988 " (cutoff:3.500A) Proline residue: C 999 - end of helix Processing helix chain 'C' and resid 1007 through 1044 removed outlier: 3.944A pdb=" N PHE C1031 " --> pdb=" O PHE C1027 " (cutoff:3.500A) Proline residue: C1034 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.762A pdb=" N GLN A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 12.706A pdb=" N ARG A 816 " --> pdb=" O ASN A 827 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N ASN A 827 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 818 " --> pdb=" O SER A 825 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASN A 827 " --> pdb=" O PRO A 719 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN A 829 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL A 717 " --> pdb=" O GLN A 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.762A pdb=" N GLN A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 12.706A pdb=" N ARG A 816 " --> pdb=" O ASN A 827 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N ASN A 827 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 818 " --> pdb=" O SER A 825 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.517A pdb=" N GLN A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.656A pdb=" N TYR A 773 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET A 184 " --> pdb=" O TYR A 773 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLN A 775 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE A 186 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A 772 " --> pdb=" O ILE A 760 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA6, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 806 through 813 removed outlier: 5.166A pdb=" N THR C 233 " --> pdb=" O PRO A 726 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 732 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY C 217 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA C 236 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ALA C 215 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AB1, first strand: chain 'A' and resid 791 through 793 Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.736A pdb=" N GLN B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 12.608A pdb=" N ARG B 816 " --> pdb=" O ASN B 827 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ASN B 827 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 818 " --> pdb=" O SER B 825 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR B 831 " --> pdb=" O GLY B 716 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY B 716 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.736A pdb=" N GLN B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 12.608A pdb=" N ARG B 816 " --> pdb=" O ASN B 827 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ASN B 827 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 818 " --> pdb=" O SER B 825 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 824 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 178 removed outlier: 3.559A pdb=" N GLU B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.619A pdb=" N TYR B 182 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 771 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN B 761 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 774 " --> pdb=" O TYR B 759 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR B 759 " --> pdb=" O VAL B 774 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.960A pdb=" N THR B 233 " --> pdb=" O PRO C 726 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.603A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AB9, first strand: chain 'B' and resid 725 through 732 Processing sheet with id=AC1, first strand: chain 'B' and resid 791 through 793 Processing sheet with id=AC2, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.674A pdb=" N GLN C 87 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER C 82 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER C 89 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C 80 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN C 91 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE C 78 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C 93 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N ARG C 816 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ASN C 827 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 818 " --> pdb=" O SER C 825 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 823 " --> pdb=" O TYR C 820 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR C 831 " --> pdb=" O GLY C 716 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY C 716 " --> pdb=" O THR C 831 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.674A pdb=" N GLN C 87 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER C 82 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER C 89 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C 80 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN C 91 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE C 78 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C 93 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N ARG C 816 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ASN C 827 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 818 " --> pdb=" O SER C 825 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 823 " --> pdb=" O TYR C 820 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER C 824 " --> pdb=" O ASP C 688 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 172 through 178 removed outlier: 4.201A pdb=" N GLY C 288 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 293 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE C 136 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU C 137 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP C 328 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 172 through 178 removed outlier: 4.201A pdb=" N GLY C 288 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS C 631 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE C 610 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 629 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR C 612 " --> pdb=" O ILE C 627 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 627 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER C 614 " --> pdb=" O ALA C 625 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA C 625 " --> pdb=" O SER C 614 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.542A pdb=" N TYR C 182 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS C 771 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN C 761 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 774 " --> pdb=" O TYR C 759 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR C 759 " --> pdb=" O VAL C 774 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.094A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 791 through 793 1624 hydrogen bonds defined for protein. 4698 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: 6.46 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4015 1.31 - 1.44: 6301 1.44 - 1.56: 13909 1.56 - 1.69: 19 1.69 - 1.81: 198 Bond restraints: 24442 Sorted by residual: bond pdb=" C06 80P C1101 " pdb=" C07 80P C1101 " ideal model delta sigma weight residual 1.428 1.597 -0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C04 80P C1101 " pdb=" C21 80P C1101 " ideal model delta sigma weight residual 1.536 1.675 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C04 80P C1101 " pdb=" N03 80P C1101 " ideal model delta sigma weight residual 1.458 1.585 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C06 80P C1101 " pdb=" C36 80P C1101 " ideal model delta sigma weight residual 1.498 1.623 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C18 80P C1101 " pdb=" C19 80P C1101 " ideal model delta sigma weight residual 1.523 1.646 -0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 24437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 31582 3.16 - 6.31: 1341 6.31 - 9.47: 257 9.47 - 12.62: 64 12.62 - 15.78: 3 Bond angle restraints: 33247 Sorted by residual: angle pdb=" N VAL B 376 " pdb=" CA VAL B 376 " pdb=" C VAL B 376 " ideal model delta sigma weight residual 110.42 122.13 -11.71 9.60e-01 1.09e+00 1.49e+02 angle pdb=" N LYS C 796 " pdb=" CA LYS C 796 " pdb=" C LYS C 796 " ideal model delta sigma weight residual 113.30 97.52 15.78 1.34e+00 5.57e-01 1.39e+02 angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 110.72 120.59 -9.87 1.01e+00 9.80e-01 9.54e+01 angle pdb=" N GLN A 276 " pdb=" CA GLN A 276 " pdb=" C GLN A 276 " ideal model delta sigma weight residual 111.36 121.72 -10.36 1.09e+00 8.42e-01 9.03e+01 angle pdb=" N ALA A 236 " pdb=" CA ALA A 236 " pdb=" C ALA A 236 " ideal model delta sigma weight residual 108.00 121.88 -13.88 1.48e+00 4.57e-01 8.79e+01 ... (remaining 33242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 13356 17.24 - 34.49: 1006 34.49 - 51.73: 205 51.73 - 68.97: 50 68.97 - 86.22: 6 Dihedral angle restraints: 14623 sinusoidal: 5642 harmonic: 8981 Sorted by residual: dihedral pdb=" C VAL A 172 " pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" CB VAL A 172 " ideal model delta harmonic sigma weight residual -122.00 -136.68 14.68 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" C VAL C 454 " pdb=" N VAL C 454 " pdb=" CA VAL C 454 " pdb=" CB VAL C 454 " ideal model delta harmonic sigma weight residual -122.00 -135.39 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" N VAL C 454 " pdb=" C VAL C 454 " pdb=" CA VAL C 454 " pdb=" CB VAL C 454 " ideal model delta harmonic sigma weight residual 123.40 136.50 -13.10 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 14620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 3448 0.166 - 0.331: 396 0.331 - 0.497: 59 0.497 - 0.662: 9 0.662 - 0.828: 1 Chirality restraints: 3913 Sorted by residual: chirality pdb=" C08 80P C1101 " pdb=" C07 80P C1101 " pdb=" C09 80P C1101 " pdb=" C21 80P C1101 " both_signs ideal model delta sigma weight residual False -2.30 -3.13 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C04 80P C1101 " pdb=" C05 80P C1101 " pdb=" C21 80P C1101 " pdb=" N03 80P C1101 " both_signs ideal model delta sigma weight residual False 2.32 2.98 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA LEU C 852 " pdb=" N LEU C 852 " pdb=" C LEU C 852 " pdb=" CB LEU C 852 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.59 2.00e-01 2.50e+01 8.56e+00 ... (remaining 3910 not shown) Planarity restraints: 4261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 233 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C THR C 233 " -0.059 2.00e-02 2.50e+03 pdb=" O THR C 233 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL C 234 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 926 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE B 926 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE B 926 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 927 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 852 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO C 853 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 853 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 853 " 0.049 5.00e-02 4.00e+02 ... (remaining 4258 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7068 2.81 - 3.34: 23158 3.34 - 3.86: 40390 3.86 - 4.38: 49429 4.38 - 4.90: 79578 Nonbonded interactions: 199623 Sorted by model distance: nonbonded pdb=" N LYS C 796 " pdb=" N GLY C 797 " model vdw 2.293 2.560 nonbonded pdb=" N GLN B 775 " pdb=" O GLN B 775 " model vdw 2.395 2.496 nonbonded pdb=" N ASN C 509 " pdb=" O ASN C 509 " model vdw 2.412 2.496 nonbonded pdb=" N GLY A 756 " pdb=" O GLY A 756 " model vdw 2.433 2.496 nonbonded pdb=" OG1 THR B 589 " pdb=" O GLN B 623 " model vdw 2.455 3.040 ... (remaining 199618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 1045) selection = chain 'B' selection = (chain 'C' and resid 1 through 1045) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.120 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.011 0.169 24442 Z= 0.836 Angle : 1.560 15.778 33247 Z= 1.069 Chirality : 0.114 0.828 3913 Planarity : 0.009 0.083 4261 Dihedral : 12.858 86.216 8859 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.37 % Rotamer: Outliers : 3.21 % Allowed : 8.19 % Favored : 88.60 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3134 helix: 0.66 (0.12), residues: 1720 sheet: 0.86 (0.23), residues: 453 loop : -0.43 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 816 TYR 0.030 0.003 TYR A 327 PHE 0.022 0.002 PHE A 277 TRP 0.013 0.002 TRP C 810 HIS 0.011 0.002 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.01124 (24442) covalent geometry : angle 1.55999 (33247) hydrogen bonds : bond 0.23705 ( 1554) hydrogen bonds : angle 7.25317 ( 4698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 720 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7513 (ttt) cc_final: 0.7286 (ttt) REVERT: A 58 GLU cc_start: 0.8051 (tt0) cc_final: 0.7549 (tt0) REVERT: A 64 ILE cc_start: 0.7830 (mm) cc_final: 0.7583 (OUTLIER) REVERT: A 66 GLU cc_start: 0.7033 (tt0) cc_final: 0.6576 (tt0) REVERT: A 68 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: A 87 GLN cc_start: 0.8316 (mt0) cc_final: 0.8037 (mt0) REVERT: A 99 ASP cc_start: 0.7750 (t70) cc_final: 0.7374 (t0) REVERT: A 101 ASP cc_start: 0.7885 (m-30) cc_final: 0.7675 (m-30) REVERT: A 128 THR cc_start: 0.8244 (m) cc_final: 0.7963 (p) REVERT: A 153 ASP cc_start: 0.7485 (m-30) cc_final: 0.7242 (m-30) REVERT: A 199 THR cc_start: 0.8256 (p) cc_final: 0.8013 (t) REVERT: A 244 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6404 (mp0) REVERT: A 252 LYS cc_start: 0.7241 (ttpt) cc_final: 0.6878 (ptmt) REVERT: A 278 ASP cc_start: 0.7341 (t0) cc_final: 0.6969 (t0) REVERT: A 292 LYS cc_start: 0.6950 (mttt) cc_final: 0.6461 (mttm) REVERT: A 307 GLU cc_start: 0.6935 (tp30) cc_final: 0.6627 (tp30) REVERT: A 308 GLN cc_start: 0.7255 (tp-100) cc_final: 0.6662 (tp-100) REVERT: A 338 GLU cc_start: 0.6873 (tt0) cc_final: 0.6666 (tt0) REVERT: A 339 SER cc_start: 0.8378 (t) cc_final: 0.7978 (p) REVERT: A 389 SER cc_start: 0.8518 (p) cc_final: 0.8315 (p) REVERT: A 525 MET cc_start: 0.5015 (tpt) cc_final: 0.4679 (tpt) REVERT: A 559 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7224 (mm-40) REVERT: A 601 MET cc_start: 0.8495 (mtm) cc_final: 0.8287 (mtp) REVERT: A 606 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8006 (t) REVERT: A 617 SER cc_start: 0.8139 (t) cc_final: 0.7924 (p) REVERT: A 633 LYS cc_start: 0.7520 (mttm) cc_final: 0.7241 (mttt) REVERT: A 673 MET cc_start: 0.6744 (mtt) cc_final: 0.6397 (mtm) REVERT: A 687 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8113 (mtpt) REVERT: A 692 GLN cc_start: 0.7935 (mt0) cc_final: 0.7654 (mt0) REVERT: A 729 GLN cc_start: 0.7257 (tt0) cc_final: 0.6937 (tt0) REVERT: A 752 ARG cc_start: 0.7025 (ttp80) cc_final: 0.6774 (ptt90) REVERT: A 765 ASP cc_start: 0.7361 (t0) cc_final: 0.6939 (t0) REVERT: A 777 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7036 (OUTLIER) REVERT: A 840 ASP cc_start: 0.7714 (m-30) cc_final: 0.7270 (m-30) REVERT: A 843 LYS cc_start: 0.7209 (mttt) cc_final: 0.6839 (mtpt) REVERT: A 857 LEU cc_start: 0.7688 (mm) cc_final: 0.7157 (mp) REVERT: A 884 LEU cc_start: 0.8056 (tp) cc_final: 0.7734 (mt) REVERT: A 904 PHE cc_start: 0.7201 (m-80) cc_final: 0.6975 (m-10) REVERT: A 955 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7877 (tp) REVERT: A 959 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: A 975 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7950 (m) REVERT: A 980 LYS cc_start: 0.7194 (ttmt) cc_final: 0.6932 (ttmm) REVERT: A 988 MET cc_start: 0.7579 (ttm) cc_final: 0.7332 (mtp) REVERT: B 17 LEU cc_start: 0.7732 (mt) cc_final: 0.7458 (mt) REVERT: B 20 MET cc_start: 0.7621 (mtp) cc_final: 0.7262 (mtm) REVERT: B 66 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7426 (mt-10) REVERT: B 79 SER cc_start: 0.8506 (t) cc_final: 0.8214 (p) REVERT: B 117 LEU cc_start: 0.8460 (mt) cc_final: 0.8204 (mt) REVERT: B 138 GLN cc_start: 0.8033 (pt0) cc_final: 0.7796 (mt0) REVERT: B 146 ASP cc_start: 0.7494 (m-30) cc_final: 0.7239 (m-30) REVERT: B 151 ASP cc_start: 0.5979 (p0) cc_final: 0.5635 (p0) REVERT: B 252 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.7063 (ptpt) REVERT: B 284 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7021 (tmmt) REVERT: B 325 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6740 (tp) REVERT: B 328 ASP cc_start: 0.7557 (t0) cc_final: 0.7290 (t0) REVERT: B 338 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6498 (tm-30) REVERT: B 395 MET cc_start: 0.7291 (mmm) cc_final: 0.7079 (tpp) REVERT: B 481 SER cc_start: 0.7581 (t) cc_final: 0.7235 (p) REVERT: B 574 VAL cc_start: 0.8257 (p) cc_final: 0.8006 (t) REVERT: B 575 MET cc_start: 0.7124 (ttp) cc_final: 0.6558 (ttp) REVERT: B 594 ASP cc_start: 0.6930 (m-30) cc_final: 0.6568 (m-30) REVERT: B 653 MET cc_start: 0.7571 (tpp) cc_final: 0.7268 (tpp) REVERT: B 687 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7689 (mtpp) REVERT: B 733 ASP cc_start: 0.6936 (t0) cc_final: 0.6584 (t0) REVERT: B 740 MET cc_start: 0.7253 (mtp) cc_final: 0.6977 (mtt) REVERT: B 742 VAL cc_start: 0.8471 (t) cc_final: 0.8150 (t) REVERT: B 818 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7474 (mp0) REVERT: B 849 ILE cc_start: 0.8772 (mt) cc_final: 0.8512 (mp) REVERT: C 30 MET cc_start: 0.8457 (ttp) cc_final: 0.8151 (ttt) REVERT: C 69 MET cc_start: 0.8290 (mmt) cc_final: 0.5621 (mmp) REVERT: C 95 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6644 (mm-30) REVERT: C 99 ASP cc_start: 0.7691 (t70) cc_final: 0.7440 (t0) REVERT: C 110 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7719 (mmtm) REVERT: C 120 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6525 (tm-30) REVERT: C 130 THR cc_start: 0.8726 (p) cc_final: 0.8448 (t) REVERT: C 136 PHE cc_start: 0.7304 (m-80) cc_final: 0.7060 (m-10) REVERT: C 140 ILE cc_start: 0.8218 (mt) cc_final: 0.7882 (mp) REVERT: C 174 GLU cc_start: 0.7188 (tt0) cc_final: 0.5900 (tp30) REVERT: C 218 GLN cc_start: 0.8448 (mt0) cc_final: 0.8047 (mt0) REVERT: C 284 LYS cc_start: 0.5851 (mmtp) cc_final: 0.5646 (mtpp) REVERT: C 293 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7079 (mm) REVERT: C 314 ARG cc_start: 0.6078 (mtm-85) cc_final: 0.5787 (mtm180) REVERT: C 324 LYS cc_start: 0.6332 (ttpp) cc_final: 0.5714 (mtpt) REVERT: C 363 ARG cc_start: 0.7648 (mmt90) cc_final: 0.7348 (mtt180) REVERT: C 423 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.6002 (p0) REVERT: C 463 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7569 (m) REVERT: C 499 GLN cc_start: 0.7357 (tt0) cc_final: 0.7054 (tm-30) REVERT: C 587 ASP cc_start: 0.5873 (m-30) cc_final: 0.5489 (t0) REVERT: C 599 PHE cc_start: 0.6281 (t80) cc_final: 0.5867 (t80) REVERT: C 603 GLU cc_start: 0.5814 (mm-30) cc_final: 0.4966 (mm-30) REVERT: C 633 LYS cc_start: 0.6125 (mttm) cc_final: 0.5892 (mtmm) REVERT: C 666 MET cc_start: 0.6163 (ttm) cc_final: 0.5264 (tpp) REVERT: C 687 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7463 (mtpt) REVERT: C 729 GLN cc_start: 0.7158 (tt0) cc_final: 0.6942 (tt0) REVERT: C 768 ARG cc_start: 0.6373 (mmt180) cc_final: 0.5750 (mmm160) REVERT: C 771 LYS cc_start: 0.8215 (mttm) cc_final: 0.7590 (mtpp) REVERT: C 789 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7263 (mttt) REVERT: C 809 GLU cc_start: 0.7284 (pt0) cc_final: 0.6919 (pt0) REVERT: C 845 MET cc_start: 0.7303 (mmm) cc_final: 0.7054 (mmm) REVERT: C 863 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7426 (mt-10) REVERT: C 873 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5873 (mt-10) REVERT: C 904 PHE cc_start: 0.7950 (m-80) cc_final: 0.7402 (m-80) REVERT: C 911 PRO cc_start: 0.7994 (Cg_exo) cc_final: 0.7726 (Cg_endo) REVERT: C 912 LEU cc_start: 0.7808 (mt) cc_final: 0.7523 (mp) REVERT: C 932 ASN cc_start: 0.7695 (m-40) cc_final: 0.7441 (m-40) REVERT: C 937 ILE cc_start: 0.7812 (pp) cc_final: 0.7521 (mt) REVERT: C 1038 VAL cc_start: 0.7656 (t) cc_final: 0.7317 (m) outliers start: 83 outliers final: 21 residues processed: 775 average time/residue: 0.4960 time to fit residues: 452.3481 Evaluate side-chains 606 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 574 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 688 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 108 GLN A 125 GLN A 231 ASN A 241 GLN A 274 ASN A 298 ASN A 531 ASN A 669 GLN A 977 HIS B 87 GLN B 108 GLN B 391 ASN B 415 ASN B 579 GLN B 729 GLN B 731 ASN C 123 GLN C 125 GLN C 274 ASN C 531 ASN C 795 ASN C 829 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.163900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.133557 restraints weight = 25510.563| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.24 r_work: 0.3154 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24442 Z= 0.187 Angle : 0.641 7.476 33247 Z= 0.349 Chirality : 0.045 0.262 3913 Planarity : 0.006 0.063 4261 Dihedral : 7.767 86.446 3464 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.60 % Allowed : 15.07 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.14), residues: 3134 helix: 1.67 (0.12), residues: 1729 sheet: 0.96 (0.24), residues: 411 loop : -0.06 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 8 TYR 0.023 0.002 TYR B 157 PHE 0.025 0.002 PHE B 993 TRP 0.008 0.001 TRP A 755 HIS 0.005 0.001 HIS A1012 Details of bonding type rmsd covalent geometry : bond 0.00406 (24442) covalent geometry : angle 0.64133 (33247) hydrogen bonds : bond 0.06708 ( 1554) hydrogen bonds : angle 4.97535 ( 4698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 616 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7957 (tt0) cc_final: 0.7625 (mt-10) REVERT: A 69 MET cc_start: 0.8726 (mmt) cc_final: 0.8260 (mmt) REVERT: A 99 ASP cc_start: 0.8091 (t70) cc_final: 0.7875 (t0) REVERT: A 208 GLN cc_start: 0.8464 (mm110) cc_final: 0.7947 (mm110) REVERT: A 244 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7381 (mp0) REVERT: A 252 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7381 (ttmt) REVERT: A 292 LYS cc_start: 0.7407 (mttt) cc_final: 0.7163 (mttm) REVERT: A 307 GLU cc_start: 0.7934 (tp30) cc_final: 0.7566 (tp30) REVERT: A 338 GLU cc_start: 0.8112 (tt0) cc_final: 0.7514 (tp30) REVERT: A 420 MET cc_start: 0.8284 (mtp) cc_final: 0.7829 (mtp) REVERT: A 438 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7049 (mp) REVERT: A 525 MET cc_start: 0.5578 (tpt) cc_final: 0.5109 (tpt) REVERT: A 568 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 606 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8221 (t) REVERT: A 637 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7544 (mmmm) REVERT: A 673 MET cc_start: 0.7935 (mtt) cc_final: 0.7585 (mtm) REVERT: A 729 GLN cc_start: 0.7600 (tt0) cc_final: 0.7328 (tt0) REVERT: A 740 MET cc_start: 0.7189 (mmm) cc_final: 0.6855 (mmt) REVERT: A 759 TYR cc_start: 0.8420 (t80) cc_final: 0.8193 (t80) REVERT: A 762 ASP cc_start: 0.8238 (m-30) cc_final: 0.7776 (m-30) REVERT: A 765 ASP cc_start: 0.7936 (t0) cc_final: 0.7520 (t0) REVERT: A 777 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7555 (OUTLIER) REVERT: A 840 ASP cc_start: 0.8342 (m-30) cc_final: 0.8081 (m-30) REVERT: A 843 LYS cc_start: 0.8003 (mttt) cc_final: 0.7721 (mtpt) REVERT: A 884 LEU cc_start: 0.8699 (tp) cc_final: 0.8452 (mt) REVERT: A 904 PHE cc_start: 0.7914 (m-80) cc_final: 0.7661 (m-10) REVERT: A 980 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7827 (ttmm) REVERT: B 8 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7123 (mtt180) REVERT: B 17 LEU cc_start: 0.8584 (mt) cc_final: 0.8299 (mt) REVERT: B 20 MET cc_start: 0.8449 (mtp) cc_final: 0.8248 (mtm) REVERT: B 66 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8160 (mt-10) REVERT: B 151 ASP cc_start: 0.6747 (p0) cc_final: 0.6450 (p0) REVERT: B 263 LYS cc_start: 0.8389 (ptpt) cc_final: 0.8184 (pttt) REVERT: B 284 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7853 (tmmt) REVERT: B 325 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7496 (tp) REVERT: B 338 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7189 (tm-30) REVERT: B 395 MET cc_start: 0.7748 (mmm) cc_final: 0.7530 (mmm) REVERT: B 420 MET cc_start: 0.8003 (ttp) cc_final: 0.7724 (ttt) REVERT: B 574 VAL cc_start: 0.8576 (p) cc_final: 0.8332 (t) REVERT: B 575 MET cc_start: 0.7886 (ttp) cc_final: 0.7258 (ttp) REVERT: B 579 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8083 (tp40) REVERT: B 594 ASP cc_start: 0.7754 (m-30) cc_final: 0.7544 (m-30) REVERT: B 733 ASP cc_start: 0.7192 (t0) cc_final: 0.6871 (t0) REVERT: B 736 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6247 (mm110) REVERT: B 740 MET cc_start: 0.7722 (mtp) cc_final: 0.7153 (mtt) REVERT: B 742 VAL cc_start: 0.8872 (t) cc_final: 0.8647 (t) REVERT: B 818 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8146 (mp0) REVERT: B 848 ILE cc_start: 0.8742 (mt) cc_final: 0.8508 (mt) REVERT: B 849 ILE cc_start: 0.8558 (mt) cc_final: 0.8281 (mp) REVERT: B 863 GLU cc_start: 0.7572 (tt0) cc_final: 0.7257 (tt0) REVERT: B 892 CYS cc_start: 0.8927 (m) cc_final: 0.8461 (m) REVERT: B 925 MET cc_start: 0.8006 (tmt) cc_final: 0.7595 (tmm) REVERT: B 987 ILE cc_start: 0.7746 (mm) cc_final: 0.7478 (OUTLIER) REVERT: B 988 MET cc_start: 0.7712 (ptm) cc_final: 0.7190 (mtm) REVERT: C 20 MET cc_start: 0.7825 (mtp) cc_final: 0.7374 (mtm) REVERT: C 64 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 69 MET cc_start: 0.8572 (mmt) cc_final: 0.5911 (mmp) REVERT: C 99 ASP cc_start: 0.7861 (t70) cc_final: 0.7633 (t0) REVERT: C 110 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8485 (mmtm) REVERT: C 120 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7913 (tm-30) REVERT: C 130 THR cc_start: 0.8840 (p) cc_final: 0.8550 (t) REVERT: C 136 PHE cc_start: 0.8105 (m-80) cc_final: 0.7638 (m-10) REVERT: C 168 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7572 (mtt90) REVERT: C 218 GLN cc_start: 0.8957 (mt0) cc_final: 0.8606 (mt0) REVERT: C 324 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7717 (mttm) REVERT: C 342 HIS cc_start: 0.7058 (t70) cc_final: 0.6730 (m90) REVERT: C 363 ARG cc_start: 0.8174 (mmt90) cc_final: 0.7879 (mtt180) REVERT: C 422 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7318 (mt-10) REVERT: C 468 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7924 (ttp-110) REVERT: C 499 GLN cc_start: 0.7258 (tt0) cc_final: 0.7009 (tm-30) REVERT: C 530 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7568 (mm-40) REVERT: C 536 MET cc_start: 0.8176 (mmm) cc_final: 0.7597 (mtt) REVERT: C 599 PHE cc_start: 0.8022 (t80) cc_final: 0.7434 (t80) REVERT: C 603 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6135 (mm-30) REVERT: C 629 PHE cc_start: 0.8177 (m-80) cc_final: 0.7969 (m-80) REVERT: C 666 MET cc_start: 0.6976 (ttm) cc_final: 0.6657 (tpp) REVERT: C 668 LEU cc_start: 0.7498 (mt) cc_final: 0.7286 (mp) REVERT: C 683 ASN cc_start: 0.8099 (t0) cc_final: 0.7677 (t0) REVERT: C 687 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8523 (mtpt) REVERT: C 768 ARG cc_start: 0.7385 (mmt180) cc_final: 0.6895 (mtp180) REVERT: C 800 VAL cc_start: 0.8193 (t) cc_final: 0.7907 (m) REVERT: C 887 LEU cc_start: 0.7923 (tp) cc_final: 0.7711 (tm) REVERT: C 904 PHE cc_start: 0.8243 (m-80) cc_final: 0.7853 (m-80) REVERT: C 943 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8417 (mm) REVERT: C 963 GLU cc_start: 0.7825 (tt0) cc_final: 0.7073 (mm-30) REVERT: C 982 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8645 (mmm160) REVERT: C 1012 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.8378 (m170) REVERT: C 1045 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7854 (ttmm) outliers start: 119 outliers final: 43 residues processed: 680 average time/residue: 0.4844 time to fit residues: 388.2631 Evaluate side-chains 606 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 551 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 669 GLN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1012 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 290 optimal weight: 9.9990 chunk 171 optimal weight: 50.0000 chunk 119 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 87 GLN A 241 GLN A 316 ASN A 669 GLN A 749 ASN B 87 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 213 GLN C 138 GLN C 148 ASN C 274 ASN C 531 ASN C 579 GLN C 795 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.161703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.131150 restraints weight = 25609.316| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.23 r_work: 0.3114 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24442 Z= 0.190 Angle : 0.613 8.020 33247 Z= 0.327 Chirality : 0.044 0.218 3913 Planarity : 0.005 0.056 4261 Dihedral : 7.046 81.481 3428 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.75 % Allowed : 17.23 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3134 helix: 2.04 (0.12), residues: 1729 sheet: 0.61 (0.24), residues: 438 loop : -0.02 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 8 TYR 0.020 0.002 TYR A 897 PHE 0.019 0.002 PHE B 993 TRP 0.008 0.001 TRP A 790 HIS 0.005 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00429 (24442) covalent geometry : angle 0.61271 (33247) hydrogen bonds : bond 0.06120 ( 1554) hydrogen bonds : angle 4.75668 ( 4698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 568 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8061 (tt0) cc_final: 0.7771 (mt-10) REVERT: A 69 MET cc_start: 0.8772 (mmt) cc_final: 0.8418 (mmt) REVERT: A 99 ASP cc_start: 0.8174 (t70) cc_final: 0.7904 (t0) REVERT: A 174 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: A 208 GLN cc_start: 0.8444 (mm110) cc_final: 0.7927 (mm110) REVERT: A 252 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7482 (ttmt) REVERT: A 269 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7572 (pp20) REVERT: A 292 LYS cc_start: 0.7438 (mttt) cc_final: 0.7215 (mttm) REVERT: A 304 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7595 (pp20) REVERT: A 307 GLU cc_start: 0.7966 (tp30) cc_final: 0.7648 (tp30) REVERT: A 438 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7288 (mm) REVERT: A 525 MET cc_start: 0.5850 (tpt) cc_final: 0.5378 (tpt) REVERT: A 568 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: A 657 MET cc_start: 0.7356 (mmm) cc_final: 0.7109 (mmp) REVERT: A 669 GLN cc_start: 0.8076 (mt0) cc_final: 0.7786 (mt0) REVERT: A 673 MET cc_start: 0.7921 (mtt) cc_final: 0.7576 (mtm) REVERT: A 718 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8684 (ptt-90) REVERT: A 729 GLN cc_start: 0.7668 (tt0) cc_final: 0.7421 (tt0) REVERT: A 740 MET cc_start: 0.7348 (mmm) cc_final: 0.6956 (mmt) REVERT: A 759 TYR cc_start: 0.8451 (t80) cc_final: 0.8163 (t80) REVERT: A 765 ASP cc_start: 0.8054 (t0) cc_final: 0.7538 (t0) REVERT: A 777 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7566 (OUTLIER) REVERT: A 783 MET cc_start: 0.7166 (mmm) cc_final: 0.6960 (mmm) REVERT: A 816 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7378 (ttp-110) REVERT: A 840 ASP cc_start: 0.8331 (m-30) cc_final: 0.8024 (m-30) REVERT: A 884 LEU cc_start: 0.8784 (tp) cc_final: 0.8506 (mt) REVERT: A 904 PHE cc_start: 0.7931 (m-80) cc_final: 0.7666 (m-10) REVERT: A 975 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.8016 (m) REVERT: B 8 ARG cc_start: 0.7239 (mpt180) cc_final: 0.6966 (mtt180) REVERT: B 17 LEU cc_start: 0.8630 (mt) cc_final: 0.8342 (mt) REVERT: B 66 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 151 ASP cc_start: 0.6691 (p0) cc_final: 0.6401 (p0) REVERT: B 184 MET cc_start: 0.8974 (mmt) cc_final: 0.8132 (tpp) REVERT: B 263 LYS cc_start: 0.8459 (ptpt) cc_final: 0.8221 (pttt) REVERT: B 284 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7891 (tmmt) REVERT: B 325 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7118 (tt) REVERT: B 338 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7156 (tm-30) REVERT: B 386 PHE cc_start: 0.7876 (m-10) cc_final: 0.7647 (m-80) REVERT: B 398 MET cc_start: 0.7573 (tpt) cc_final: 0.7164 (mmt) REVERT: B 420 MET cc_start: 0.7961 (ttp) cc_final: 0.7543 (ttt) REVERT: B 575 MET cc_start: 0.8084 (ttp) cc_final: 0.7325 (ttp) REVERT: B 579 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8065 (tp40) REVERT: B 594 ASP cc_start: 0.7735 (m-30) cc_final: 0.7491 (m-30) REVERT: B 653 MET cc_start: 0.7421 (tpp) cc_final: 0.6974 (mmt) REVERT: B 733 ASP cc_start: 0.7167 (t0) cc_final: 0.6885 (t0) REVERT: B 736 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6356 (mm110) REVERT: B 740 MET cc_start: 0.7790 (mtp) cc_final: 0.7248 (mtt) REVERT: B 742 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8721 (t) REVERT: B 789 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7601 (mtmt) REVERT: B 793 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7865 (ttp-170) REVERT: B 818 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8498 (mt-10) REVERT: B 849 ILE cc_start: 0.8576 (mt) cc_final: 0.8313 (mp) REVERT: B 891 LEU cc_start: 0.8140 (mt) cc_final: 0.7829 (mm) REVERT: B 892 CYS cc_start: 0.8866 (m) cc_final: 0.8404 (m) REVERT: B 925 MET cc_start: 0.8027 (tmt) cc_final: 0.7803 (tmm) REVERT: B 987 ILE cc_start: 0.7931 (mm) cc_final: 0.7668 (OUTLIER) REVERT: C 8 ARG cc_start: 0.8317 (mtm-85) cc_final: 0.8071 (mtm-85) REVERT: C 20 MET cc_start: 0.7783 (mtp) cc_final: 0.7338 (mtm) REVERT: C 99 ASP cc_start: 0.7970 (t70) cc_final: 0.7753 (t0) REVERT: C 120 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7940 (tm-30) REVERT: C 218 GLN cc_start: 0.9027 (mt0) cc_final: 0.8674 (mt0) REVERT: C 324 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7750 (mttt) REVERT: C 342 HIS cc_start: 0.7112 (t70) cc_final: 0.6852 (m90) REVERT: C 363 ARG cc_start: 0.8169 (mmt90) cc_final: 0.7886 (mtt180) REVERT: C 422 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7169 (mt-10) REVERT: C 433 ARG cc_start: 0.8364 (ttt90) cc_final: 0.7973 (ttt-90) REVERT: C 499 GLN cc_start: 0.7409 (tt0) cc_final: 0.7150 (tm-30) REVERT: C 530 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7519 (mm-40) REVERT: C 536 MET cc_start: 0.8171 (mmm) cc_final: 0.7817 (mtt) REVERT: C 591 LYS cc_start: 0.8308 (mttt) cc_final: 0.8046 (mtpt) REVERT: C 666 MET cc_start: 0.7017 (ttm) cc_final: 0.6763 (tpp) REVERT: C 668 LEU cc_start: 0.7539 (mt) cc_final: 0.7307 (mp) REVERT: C 683 ASN cc_start: 0.8073 (t0) cc_final: 0.7755 (t0) REVERT: C 696 LYS cc_start: 0.8328 (mmmt) cc_final: 0.8082 (tppp) REVERT: C 718 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6963 (ptm-80) REVERT: C 768 ARG cc_start: 0.7421 (mmt180) cc_final: 0.6899 (mmm160) REVERT: C 800 VAL cc_start: 0.8225 (t) cc_final: 0.7951 (m) REVERT: C 887 LEU cc_start: 0.7864 (tp) cc_final: 0.7602 (tm) REVERT: C 904 PHE cc_start: 0.8339 (m-80) cc_final: 0.7969 (m-80) REVERT: C 943 ILE cc_start: 0.8639 (mt) cc_final: 0.8423 (mm) REVERT: C 963 GLU cc_start: 0.7793 (tt0) cc_final: 0.7193 (mm-30) REVERT: C 982 ARG cc_start: 0.8881 (mmm160) cc_final: 0.8447 (mmm160) REVERT: C 1012 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8427 (m170) REVERT: C 1045 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7899 (ttmm) outliers start: 123 outliers final: 57 residues processed: 635 average time/residue: 0.4957 time to fit residues: 369.8505 Evaluate side-chains 620 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 547 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 793 ARG Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1012 HIS Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 227 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 156 optimal weight: 40.0000 chunk 4 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 274 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 87 GLN A 241 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN C 731 ASN C 795 ASN C 829 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.159741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.129177 restraints weight = 25478.298| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.15 r_work: 0.3115 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 24442 Z= 0.242 Angle : 0.655 7.900 33247 Z= 0.346 Chirality : 0.046 0.253 3913 Planarity : 0.005 0.059 4261 Dihedral : 6.919 78.324 3419 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.49 % Allowed : 17.85 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.15), residues: 3134 helix: 1.90 (0.12), residues: 1722 sheet: 0.35 (0.23), residues: 450 loop : -0.14 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 314 TYR 0.021 0.002 TYR A 327 PHE 0.027 0.002 PHE C 599 TRP 0.010 0.002 TRP A 790 HIS 0.009 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00572 (24442) covalent geometry : angle 0.65480 (33247) hydrogen bonds : bond 0.06244 ( 1554) hydrogen bonds : angle 4.82729 ( 4698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 568 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8127 (tt0) cc_final: 0.7578 (tt0) REVERT: A 69 MET cc_start: 0.8761 (mmt) cc_final: 0.8271 (mmt) REVERT: A 99 ASP cc_start: 0.8139 (t70) cc_final: 0.7873 (t0) REVERT: A 208 GLN cc_start: 0.8355 (mm110) cc_final: 0.7794 (mm110) REVERT: A 252 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7371 (ttmt) REVERT: A 269 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: A 292 LYS cc_start: 0.7471 (mttt) cc_final: 0.7255 (mttm) REVERT: A 304 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7597 (pp20) REVERT: A 307 GLU cc_start: 0.7886 (tp30) cc_final: 0.7553 (tp30) REVERT: A 342 HIS cc_start: 0.7603 (t70) cc_final: 0.7326 (t-170) REVERT: A 525 MET cc_start: 0.5815 (tpt) cc_final: 0.5295 (tpt) REVERT: A 568 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: A 657 MET cc_start: 0.7321 (mmm) cc_final: 0.7063 (mmp) REVERT: A 673 MET cc_start: 0.7766 (mtt) cc_final: 0.7497 (mtm) REVERT: A 695 GLU cc_start: 0.8257 (mp0) cc_final: 0.8019 (mp0) REVERT: A 718 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8659 (ptt-90) REVERT: A 727 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6820 (mt0) REVERT: A 729 GLN cc_start: 0.7745 (tt0) cc_final: 0.7489 (tt0) REVERT: A 740 MET cc_start: 0.7154 (mmm) cc_final: 0.6749 (mmt) REVERT: A 759 TYR cc_start: 0.8508 (t80) cc_final: 0.8202 (t80) REVERT: A 777 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7532 (OUTLIER) REVERT: A 783 MET cc_start: 0.7188 (mmm) cc_final: 0.6947 (mmm) REVERT: A 816 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7367 (ttp-110) REVERT: A 840 ASP cc_start: 0.8172 (m-30) cc_final: 0.7819 (m-30) REVERT: A 884 LEU cc_start: 0.8806 (tp) cc_final: 0.8485 (mt) REVERT: A 904 PHE cc_start: 0.7839 (m-80) cc_final: 0.7581 (m-10) REVERT: A 955 ILE cc_start: 0.8791 (tp) cc_final: 0.8526 (pp) REVERT: B 66 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 67 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: B 151 ASP cc_start: 0.6675 (p0) cc_final: 0.6405 (p0) REVERT: B 184 MET cc_start: 0.8975 (mmt) cc_final: 0.7877 (tpp) REVERT: B 263 LYS cc_start: 0.8390 (ptpt) cc_final: 0.8137 (pttt) REVERT: B 284 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7907 (tmmt) REVERT: B 388 PHE cc_start: 0.7996 (m-80) cc_final: 0.7795 (m-80) REVERT: B 398 MET cc_start: 0.7507 (tpt) cc_final: 0.7089 (mmt) REVERT: B 420 MET cc_start: 0.7966 (ttp) cc_final: 0.7526 (ttt) REVERT: B 575 MET cc_start: 0.8125 (ttp) cc_final: 0.7307 (tpp) REVERT: B 594 ASP cc_start: 0.7638 (m-30) cc_final: 0.7292 (m-30) REVERT: B 733 ASP cc_start: 0.7193 (t0) cc_final: 0.6895 (t0) REVERT: B 736 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6356 (mm110) REVERT: B 740 MET cc_start: 0.7670 (mtp) cc_final: 0.7239 (mtt) REVERT: B 789 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7510 (mtmt) REVERT: B 818 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 891 LEU cc_start: 0.8201 (mt) cc_final: 0.7849 (mm) REVERT: B 892 CYS cc_start: 0.8856 (m) cc_final: 0.8375 (m) REVERT: B 925 MET cc_start: 0.8046 (tmt) cc_final: 0.7844 (tmm) REVERT: B 987 ILE cc_start: 0.7927 (mm) cc_final: 0.7647 (OUTLIER) REVERT: B 988 MET cc_start: 0.7961 (ptm) cc_final: 0.7448 (mtm) REVERT: B 1013 SER cc_start: 0.6943 (p) cc_final: 0.6694 (m) REVERT: C 8 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7989 (mtm-85) REVERT: C 20 MET cc_start: 0.7768 (mtp) cc_final: 0.7314 (mtm) REVERT: C 117 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8439 (mm) REVERT: C 120 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7982 (tm-30) REVERT: C 218 GLN cc_start: 0.9002 (mt0) cc_final: 0.8662 (mt0) REVERT: C 298 ASN cc_start: 0.8254 (t0) cc_final: 0.7942 (t0) REVERT: C 342 HIS cc_start: 0.7070 (t70) cc_final: 0.6810 (m90) REVERT: C 363 ARG cc_start: 0.8194 (mmt90) cc_final: 0.7876 (mtt180) REVERT: C 422 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6965 (mt-10) REVERT: C 499 GLN cc_start: 0.7379 (tt0) cc_final: 0.7125 (tm-30) REVERT: C 530 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7463 (mm-40) REVERT: C 536 MET cc_start: 0.8106 (mmm) cc_final: 0.7765 (mtt) REVERT: C 591 LYS cc_start: 0.8333 (mttt) cc_final: 0.8036 (mtpt) REVERT: C 666 MET cc_start: 0.7055 (ttm) cc_final: 0.6774 (tpp) REVERT: C 668 LEU cc_start: 0.7491 (mt) cc_final: 0.7262 (mp) REVERT: C 718 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6916 (ptm-80) REVERT: C 768 ARG cc_start: 0.7513 (mmt180) cc_final: 0.7022 (mmm160) REVERT: C 800 VAL cc_start: 0.8198 (t) cc_final: 0.7900 (m) REVERT: C 857 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7111 (mp) REVERT: C 887 LEU cc_start: 0.8051 (tp) cc_final: 0.7791 (tm) REVERT: C 963 GLU cc_start: 0.7807 (tt0) cc_final: 0.7143 (mm-30) REVERT: C 982 ARG cc_start: 0.8841 (mmm160) cc_final: 0.8569 (mmm160) REVERT: C 1045 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7946 (ttmm) outliers start: 142 outliers final: 73 residues processed: 654 average time/residue: 0.4863 time to fit residues: 375.0494 Evaluate side-chains 630 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 546 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 905 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 77 optimal weight: 0.0040 chunk 242 optimal weight: 20.0000 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 722 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 384 ASN C 67 GLN C 123 GLN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 583 ASN C 720 ASN C 795 ASN C 827 ASN C 829 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.160263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.129238 restraints weight = 25185.926| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.26 r_work: 0.3093 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24442 Z= 0.168 Angle : 0.591 8.416 33247 Z= 0.308 Chirality : 0.043 0.221 3913 Planarity : 0.005 0.057 4261 Dihedral : 6.611 74.799 3417 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.75 % Allowed : 19.40 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.15), residues: 3134 helix: 2.09 (0.12), residues: 1731 sheet: 0.28 (0.23), residues: 454 loop : -0.09 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 314 TYR 0.017 0.002 TYR A 664 PHE 0.023 0.001 PHE C 599 TRP 0.007 0.001 TRP B 187 HIS 0.005 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00383 (24442) covalent geometry : angle 0.59088 (33247) hydrogen bonds : bond 0.05430 ( 1554) hydrogen bonds : angle 4.63613 ( 4698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 564 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7941 (tt0) cc_final: 0.7625 (mt-10) REVERT: A 69 MET cc_start: 0.8750 (mmt) cc_final: 0.8246 (mmt) REVERT: A 99 ASP cc_start: 0.8179 (t70) cc_final: 0.7877 (t0) REVERT: A 208 GLN cc_start: 0.8373 (mm110) cc_final: 0.7831 (mm110) REVERT: A 252 LYS cc_start: 0.7733 (ttpt) cc_final: 0.7411 (ttmt) REVERT: A 269 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7593 (pp20) REVERT: A 292 LYS cc_start: 0.7432 (mttt) cc_final: 0.7193 (mttm) REVERT: A 304 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7615 (pp20) REVERT: A 307 GLU cc_start: 0.8001 (tp30) cc_final: 0.7721 (tp30) REVERT: A 342 HIS cc_start: 0.7685 (t70) cc_final: 0.7412 (t-170) REVERT: A 525 MET cc_start: 0.5831 (tpt) cc_final: 0.5363 (tpt) REVERT: A 568 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: A 657 MET cc_start: 0.7388 (mmm) cc_final: 0.7128 (mmp) REVERT: A 673 MET cc_start: 0.7952 (mtt) cc_final: 0.7697 (mtm) REVERT: A 695 GLU cc_start: 0.8331 (mp0) cc_final: 0.8101 (mp0) REVERT: A 718 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8655 (ptt-90) REVERT: A 727 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6896 (mt0) REVERT: A 729 GLN cc_start: 0.7723 (tt0) cc_final: 0.7476 (tt0) REVERT: A 740 MET cc_start: 0.7191 (mmm) cc_final: 0.6853 (mmt) REVERT: A 759 TYR cc_start: 0.8458 (t80) cc_final: 0.8118 (t80) REVERT: A 777 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7531 (OUTLIER) REVERT: A 816 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7391 (ttp-110) REVERT: A 840 ASP cc_start: 0.8231 (m-30) cc_final: 0.7878 (m-30) REVERT: A 857 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7245 (mp) REVERT: A 884 LEU cc_start: 0.8785 (tp) cc_final: 0.8465 (mt) REVERT: A 904 PHE cc_start: 0.7876 (m-80) cc_final: 0.7626 (m-10) REVERT: A 955 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8573 (pp) REVERT: B 67 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: B 151 ASP cc_start: 0.6758 (p0) cc_final: 0.6513 (p0) REVERT: B 184 MET cc_start: 0.8943 (mmt) cc_final: 0.7861 (tpp) REVERT: B 207 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8711 (mt) REVERT: B 263 LYS cc_start: 0.8458 (ptpt) cc_final: 0.8166 (pttt) REVERT: B 284 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7906 (tmmt) REVERT: B 398 MET cc_start: 0.7523 (tpt) cc_final: 0.7067 (mmt) REVERT: B 420 MET cc_start: 0.7934 (ttp) cc_final: 0.7574 (ttt) REVERT: B 575 MET cc_start: 0.8157 (ttp) cc_final: 0.7294 (tpp) REVERT: B 594 ASP cc_start: 0.7844 (m-30) cc_final: 0.7514 (m-30) REVERT: B 657 MET cc_start: 0.7346 (tmm) cc_final: 0.7069 (ttp) REVERT: B 733 ASP cc_start: 0.7208 (t0) cc_final: 0.6935 (t0) REVERT: B 736 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6310 (mm110) REVERT: B 740 MET cc_start: 0.7851 (mtp) cc_final: 0.7377 (mtt) REVERT: B 742 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8834 (t) REVERT: B 789 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7458 (mtmt) REVERT: B 891 LEU cc_start: 0.8172 (mt) cc_final: 0.7877 (mm) REVERT: B 892 CYS cc_start: 0.8925 (m) cc_final: 0.8476 (m) REVERT: B 925 MET cc_start: 0.8012 (tmt) cc_final: 0.7757 (tmm) REVERT: B 987 ILE cc_start: 0.8028 (mm) cc_final: 0.7770 (OUTLIER) REVERT: B 1013 SER cc_start: 0.6856 (p) cc_final: 0.6616 (m) REVERT: C 20 MET cc_start: 0.7828 (mtp) cc_final: 0.7358 (mtm) REVERT: C 120 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7962 (tm-30) REVERT: C 218 GLN cc_start: 0.8942 (mt0) cc_final: 0.8640 (mt0) REVERT: C 324 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7706 (mttm) REVERT: C 342 HIS cc_start: 0.7035 (t70) cc_final: 0.6742 (m90) REVERT: C 363 ARG cc_start: 0.8146 (mmt90) cc_final: 0.7808 (mtt180) REVERT: C 422 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6900 (mt-10) REVERT: C 459 PHE cc_start: 0.7605 (m-80) cc_final: 0.7337 (m-80) REVERT: C 499 GLN cc_start: 0.7394 (tt0) cc_final: 0.7144 (tm-30) REVERT: C 530 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7499 (mm-40) REVERT: C 536 MET cc_start: 0.8093 (mmm) cc_final: 0.7776 (mtt) REVERT: C 591 LYS cc_start: 0.8170 (mttt) cc_final: 0.7910 (mttt) REVERT: C 603 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6469 (mm-30) REVERT: C 666 MET cc_start: 0.7164 (ttm) cc_final: 0.6822 (tpp) REVERT: C 668 LEU cc_start: 0.7520 (mt) cc_final: 0.7274 (mp) REVERT: C 696 LYS cc_start: 0.8292 (mmmt) cc_final: 0.8051 (tppp) REVERT: C 718 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6908 (ptm-80) REVERT: C 768 ARG cc_start: 0.7580 (mmt180) cc_final: 0.7061 (mmm160) REVERT: C 800 VAL cc_start: 0.8199 (t) cc_final: 0.7896 (m) REVERT: C 887 LEU cc_start: 0.8069 (tp) cc_final: 0.7807 (tm) REVERT: C 963 GLU cc_start: 0.7840 (tt0) cc_final: 0.7160 (mm-30) REVERT: C 982 ARG cc_start: 0.8817 (mmm160) cc_final: 0.8579 (mmm160) REVERT: C 1045 LYS cc_start: 0.8250 (mtpt) cc_final: 0.8026 (ttmm) outliers start: 123 outliers final: 64 residues processed: 635 average time/residue: 0.4875 time to fit residues: 366.0576 Evaluate side-chains 614 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 537 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 278 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 271 optimal weight: 0.9990 chunk 147 optimal weight: 50.0000 chunk 173 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 50 optimal weight: 50.0000 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 176 GLN A 722 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 720 ASN B 827 ASN C 123 GLN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 598 ASN C 720 ASN C 795 ASN C 827 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.161403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.130517 restraints weight = 25458.841| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.30 r_work: 0.3118 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24442 Z= 0.145 Angle : 0.571 8.466 33247 Z= 0.294 Chirality : 0.042 0.211 3913 Planarity : 0.005 0.055 4261 Dihedral : 6.412 71.409 3417 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.68 % Allowed : 19.67 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 3134 helix: 2.24 (0.12), residues: 1727 sheet: 0.30 (0.23), residues: 455 loop : -0.12 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.016 0.001 TYR A 664 PHE 0.023 0.001 PHE C 599 TRP 0.008 0.001 TRP A 755 HIS 0.004 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00325 (24442) covalent geometry : angle 0.57093 (33247) hydrogen bonds : bond 0.05006 ( 1554) hydrogen bonds : angle 4.51026 ( 4698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 551 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7903 (tt0) cc_final: 0.7594 (mt-10) REVERT: A 69 MET cc_start: 0.8750 (mmt) cc_final: 0.8229 (mmt) REVERT: A 81 ASN cc_start: 0.7690 (m-40) cc_final: 0.7369 (m-40) REVERT: A 99 ASP cc_start: 0.8141 (t70) cc_final: 0.7841 (t0) REVERT: A 208 GLN cc_start: 0.8318 (mm110) cc_final: 0.7792 (mm110) REVERT: A 252 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7424 (ttmt) REVERT: A 269 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7573 (pp20) REVERT: A 292 LYS cc_start: 0.7479 (mttt) cc_final: 0.7217 (mttm) REVERT: A 304 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7599 (pp20) REVERT: A 307 GLU cc_start: 0.7868 (tp30) cc_final: 0.7591 (tp30) REVERT: A 342 HIS cc_start: 0.7647 (t70) cc_final: 0.7371 (t-170) REVERT: A 438 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7039 (mp) REVERT: A 525 MET cc_start: 0.5693 (tpt) cc_final: 0.5233 (tpt) REVERT: A 568 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 657 MET cc_start: 0.7391 (mmm) cc_final: 0.7095 (mmp) REVERT: A 673 MET cc_start: 0.7785 (mtt) cc_final: 0.7450 (mtm) REVERT: A 695 GLU cc_start: 0.8346 (mp0) cc_final: 0.8105 (mp0) REVERT: A 718 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8681 (ptt-90) REVERT: A 727 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6898 (mt0) REVERT: A 729 GLN cc_start: 0.7690 (tt0) cc_final: 0.7444 (tt0) REVERT: A 740 MET cc_start: 0.7211 (mmm) cc_final: 0.6834 (mmt) REVERT: A 759 TYR cc_start: 0.8431 (t80) cc_final: 0.8080 (t80) REVERT: A 777 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: A 816 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7118 (ttp-110) REVERT: A 840 ASP cc_start: 0.8238 (m-30) cc_final: 0.7889 (m-30) REVERT: A 884 LEU cc_start: 0.8777 (tp) cc_final: 0.8464 (mt) REVERT: A 904 PHE cc_start: 0.7882 (m-80) cc_final: 0.7641 (m-10) REVERT: A 955 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8563 (pp) REVERT: A 975 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7863 (m) REVERT: B 67 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: B 184 MET cc_start: 0.8932 (mmt) cc_final: 0.7853 (tpp) REVERT: B 207 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 284 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7905 (tmmt) REVERT: B 398 MET cc_start: 0.7529 (tpt) cc_final: 0.7084 (mmt) REVERT: B 420 MET cc_start: 0.7952 (ttp) cc_final: 0.7575 (ttt) REVERT: B 575 MET cc_start: 0.8162 (ttp) cc_final: 0.7383 (tpp) REVERT: B 579 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8119 (tp40) REVERT: B 594 ASP cc_start: 0.7828 (m-30) cc_final: 0.7445 (m-30) REVERT: B 657 MET cc_start: 0.7294 (tmm) cc_final: 0.7005 (ttp) REVERT: B 733 ASP cc_start: 0.7176 (t0) cc_final: 0.6869 (t0) REVERT: B 736 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6379 (mm110) REVERT: B 740 MET cc_start: 0.7836 (mtp) cc_final: 0.7357 (mtt) REVERT: B 855 MET cc_start: 0.8116 (mmm) cc_final: 0.7829 (mmt) REVERT: B 891 LEU cc_start: 0.8210 (mt) cc_final: 0.7934 (mm) REVERT: B 892 CYS cc_start: 0.8928 (m) cc_final: 0.8495 (m) REVERT: B 925 MET cc_start: 0.8014 (tmt) cc_final: 0.7754 (tmm) REVERT: B 987 ILE cc_start: 0.7939 (mm) cc_final: 0.7681 (OUTLIER) REVERT: C 8 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8010 (mtm-85) REVERT: C 20 MET cc_start: 0.7771 (mtp) cc_final: 0.7299 (mtm) REVERT: C 120 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7890 (tm-30) REVERT: C 149 LEU cc_start: 0.7743 (mm) cc_final: 0.7522 (mp) REVERT: C 218 GLN cc_start: 0.8945 (mt0) cc_final: 0.8600 (mt0) REVERT: C 298 ASN cc_start: 0.8198 (t0) cc_final: 0.7907 (t0) REVERT: C 324 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7648 (mttm) REVERT: C 342 HIS cc_start: 0.7021 (t70) cc_final: 0.6682 (m90) REVERT: C 422 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6843 (mt-10) REVERT: C 499 GLN cc_start: 0.7377 (tt0) cc_final: 0.7051 (tm-30) REVERT: C 530 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7518 (mm-40) REVERT: C 536 MET cc_start: 0.7997 (mmm) cc_final: 0.7678 (mtt) REVERT: C 591 LYS cc_start: 0.8151 (mttt) cc_final: 0.7882 (mttt) REVERT: C 603 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6395 (mm-30) REVERT: C 666 MET cc_start: 0.7126 (ttm) cc_final: 0.6773 (tpp) REVERT: C 668 LEU cc_start: 0.7569 (mt) cc_final: 0.7331 (mp) REVERT: C 696 LYS cc_start: 0.8251 (mmmt) cc_final: 0.8018 (tppp) REVERT: C 768 ARG cc_start: 0.7558 (mmt180) cc_final: 0.7021 (mmm160) REVERT: C 800 VAL cc_start: 0.8192 (t) cc_final: 0.7916 (m) REVERT: C 887 LEU cc_start: 0.8083 (tp) cc_final: 0.7821 (tm) REVERT: C 963 GLU cc_start: 0.7836 (tt0) cc_final: 0.7137 (mm-30) REVERT: C 1045 LYS cc_start: 0.8249 (mtpt) cc_final: 0.8024 (ttmm) outliers start: 121 outliers final: 64 residues processed: 624 average time/residue: 0.4809 time to fit residues: 356.4951 Evaluate side-chains 613 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 533 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 192 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 206 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 241 GLN A 722 GLN B 87 GLN B 91 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN C 67 GLN C 123 GLN C 138 GLN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 598 ASN C 795 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.161643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.131068 restraints weight = 25336.606| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.30 r_work: 0.3112 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24442 Z= 0.143 Angle : 0.567 7.851 33247 Z= 0.292 Chirality : 0.042 0.208 3913 Planarity : 0.004 0.055 4261 Dihedral : 6.262 68.242 3417 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.52 % Allowed : 20.36 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.15), residues: 3134 helix: 2.28 (0.12), residues: 1728 sheet: 0.32 (0.24), residues: 457 loop : -0.09 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 8 TYR 0.016 0.001 TYR A 664 PHE 0.023 0.001 PHE C 599 TRP 0.009 0.001 TRP A 755 HIS 0.004 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00322 (24442) covalent geometry : angle 0.56665 (33247) hydrogen bonds : bond 0.04885 ( 1554) hydrogen bonds : angle 4.47969 ( 4698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 548 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7871 (tt0) cc_final: 0.7571 (mt-10) REVERT: A 69 MET cc_start: 0.8758 (mmt) cc_final: 0.8257 (mmt) REVERT: A 81 ASN cc_start: 0.7677 (m-40) cc_final: 0.7361 (m-40) REVERT: A 99 ASP cc_start: 0.8150 (t70) cc_final: 0.7861 (t0) REVERT: A 208 GLN cc_start: 0.8293 (mm110) cc_final: 0.7775 (mm110) REVERT: A 252 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7444 (ttmt) REVERT: A 269 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: A 292 LYS cc_start: 0.7478 (mttt) cc_final: 0.7224 (mtpt) REVERT: A 304 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7580 (pp20) REVERT: A 307 GLU cc_start: 0.7869 (tp30) cc_final: 0.7625 (tp30) REVERT: A 342 HIS cc_start: 0.7657 (t70) cc_final: 0.7369 (t-170) REVERT: A 355 MET cc_start: 0.8156 (mtm) cc_final: 0.7864 (mtm) REVERT: A 438 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7035 (mp) REVERT: A 525 MET cc_start: 0.5739 (tpt) cc_final: 0.5295 (tpt) REVERT: A 568 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: A 657 MET cc_start: 0.7395 (mmm) cc_final: 0.7121 (mmp) REVERT: A 673 MET cc_start: 0.7709 (mtt) cc_final: 0.7371 (mtm) REVERT: A 695 GLU cc_start: 0.8343 (mp0) cc_final: 0.8088 (mp0) REVERT: A 718 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8699 (ptt-90) REVERT: A 727 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6953 (mt0) REVERT: A 729 GLN cc_start: 0.7710 (tt0) cc_final: 0.7459 (tt0) REVERT: A 740 MET cc_start: 0.7218 (mmm) cc_final: 0.6838 (mmt) REVERT: A 759 TYR cc_start: 0.8350 (t80) cc_final: 0.8041 (t80) REVERT: A 777 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: A 816 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7110 (ttp-110) REVERT: A 840 ASP cc_start: 0.8348 (m-30) cc_final: 0.8011 (m-30) REVERT: A 904 PHE cc_start: 0.7897 (m-80) cc_final: 0.7626 (m-10) REVERT: B 67 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: B 95 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: B 184 MET cc_start: 0.8907 (mmt) cc_final: 0.7713 (tpp) REVERT: B 207 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8749 (mt) REVERT: B 284 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7916 (tmmt) REVERT: B 338 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6495 (mm-30) REVERT: B 398 MET cc_start: 0.7515 (tpt) cc_final: 0.7160 (mmt) REVERT: B 420 MET cc_start: 0.7921 (ttp) cc_final: 0.7595 (ttt) REVERT: B 575 MET cc_start: 0.8139 (ttp) cc_final: 0.7390 (tpp) REVERT: B 579 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8117 (tp40) REVERT: B 594 ASP cc_start: 0.7814 (m-30) cc_final: 0.7593 (m-30) REVERT: B 657 MET cc_start: 0.7129 (tmm) cc_final: 0.6890 (ttp) REVERT: B 733 ASP cc_start: 0.7268 (t0) cc_final: 0.6945 (t0) REVERT: B 736 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6397 (mm110) REVERT: B 740 MET cc_start: 0.7822 (mtp) cc_final: 0.7350 (mtt) REVERT: B 855 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7802 (mmt) REVERT: B 891 LEU cc_start: 0.8228 (mt) cc_final: 0.7954 (mm) REVERT: B 892 CYS cc_start: 0.8936 (m) cc_final: 0.8521 (m) REVERT: B 925 MET cc_start: 0.8139 (tmt) cc_final: 0.7796 (tmm) REVERT: B 987 ILE cc_start: 0.7893 (mm) cc_final: 0.7660 (mp) REVERT: C 8 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7937 (mtm-85) REVERT: C 20 MET cc_start: 0.7783 (mtp) cc_final: 0.7306 (mtm) REVERT: C 120 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8007 (tm-30) REVERT: C 149 LEU cc_start: 0.7731 (mm) cc_final: 0.7510 (mp) REVERT: C 208 GLN cc_start: 0.7499 (tt0) cc_final: 0.7254 (tp40) REVERT: C 218 GLN cc_start: 0.8938 (mt0) cc_final: 0.8597 (mt0) REVERT: C 298 ASN cc_start: 0.8279 (t0) cc_final: 0.7989 (t0) REVERT: C 324 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7626 (mttm) REVERT: C 342 HIS cc_start: 0.7020 (t70) cc_final: 0.6696 (m90) REVERT: C 363 ARG cc_start: 0.8295 (mtt180) cc_final: 0.8039 (mtp85) REVERT: C 422 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6884 (mt-10) REVERT: C 459 PHE cc_start: 0.7490 (m-80) cc_final: 0.7222 (m-80) REVERT: C 499 GLN cc_start: 0.7415 (tt0) cc_final: 0.7065 (tm-30) REVERT: C 530 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: C 536 MET cc_start: 0.7962 (mmm) cc_final: 0.7661 (mtt) REVERT: C 591 LYS cc_start: 0.8159 (mttt) cc_final: 0.7914 (mttt) REVERT: C 603 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6432 (mm-30) REVERT: C 608 GLU cc_start: 0.7639 (tp30) cc_final: 0.7367 (tt0) REVERT: C 666 MET cc_start: 0.7135 (ttm) cc_final: 0.6846 (tpp) REVERT: C 668 LEU cc_start: 0.7529 (mt) cc_final: 0.7295 (mp) REVERT: C 696 LYS cc_start: 0.8263 (mmmt) cc_final: 0.8044 (tppp) REVERT: C 768 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7032 (mmm160) REVERT: C 799 MET cc_start: 0.8028 (mmp) cc_final: 0.7700 (mmp) REVERT: C 800 VAL cc_start: 0.8166 (t) cc_final: 0.7870 (m) REVERT: C 887 LEU cc_start: 0.8074 (tp) cc_final: 0.7815 (tm) REVERT: C 963 GLU cc_start: 0.7806 (tt0) cc_final: 0.7178 (mm-30) REVERT: C 982 ARG cc_start: 0.8831 (mmm160) cc_final: 0.8571 (mmm160) REVERT: C 1012 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.8339 (m170) REVERT: C 1045 LYS cc_start: 0.8252 (mtpt) cc_final: 0.8048 (ttmm) outliers start: 117 outliers final: 69 residues processed: 618 average time/residue: 0.5012 time to fit residues: 366.7530 Evaluate side-chains 610 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 522 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1012 HIS Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 182 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 87 GLN B 108 GLN B 112 GLN B 384 ASN C 123 GLN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 531 ASN C 598 ASN C 795 ASN C1011 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.162675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.131998 restraints weight = 25370.234| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.24 r_work: 0.3135 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24442 Z= 0.127 Angle : 0.557 8.422 33247 Z= 0.285 Chirality : 0.041 0.201 3913 Planarity : 0.004 0.054 4261 Dihedral : 6.073 65.019 3416 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.67 % Allowed : 21.56 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.15), residues: 3134 helix: 2.40 (0.12), residues: 1729 sheet: 0.43 (0.24), residues: 441 loop : -0.07 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 314 TYR 0.016 0.001 TYR A 664 PHE 0.023 0.001 PHE C 599 TRP 0.008 0.001 TRP A 755 HIS 0.003 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00275 (24442) covalent geometry : angle 0.55667 (33247) hydrogen bonds : bond 0.04554 ( 1554) hydrogen bonds : angle 4.38547 ( 4698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 542 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7810 (tt0) cc_final: 0.7512 (mt-10) REVERT: A 69 MET cc_start: 0.8753 (mmt) cc_final: 0.8168 (mmt) REVERT: A 81 ASN cc_start: 0.7580 (m-40) cc_final: 0.7292 (m-40) REVERT: A 99 ASP cc_start: 0.8126 (t70) cc_final: 0.7830 (t0) REVERT: A 208 GLN cc_start: 0.8247 (mm110) cc_final: 0.7735 (mm110) REVERT: A 252 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7415 (ttmt) REVERT: A 269 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: A 292 LYS cc_start: 0.7457 (mttt) cc_final: 0.7206 (mtpt) REVERT: A 307 GLU cc_start: 0.7844 (tp30) cc_final: 0.7617 (tp30) REVERT: A 355 MET cc_start: 0.8118 (mtm) cc_final: 0.7843 (mtm) REVERT: A 438 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7003 (mp) REVERT: A 525 MET cc_start: 0.5707 (tpt) cc_final: 0.5269 (tpt) REVERT: A 568 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: A 657 MET cc_start: 0.7306 (mmm) cc_final: 0.7039 (mmp) REVERT: A 673 MET cc_start: 0.7651 (mtt) cc_final: 0.7393 (mtm) REVERT: A 695 GLU cc_start: 0.8335 (mp0) cc_final: 0.8067 (mp0) REVERT: A 727 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: A 729 GLN cc_start: 0.7652 (tt0) cc_final: 0.7420 (tt0) REVERT: A 740 MET cc_start: 0.7154 (mmm) cc_final: 0.6789 (mmt) REVERT: A 759 TYR cc_start: 0.8333 (t80) cc_final: 0.8023 (t80) REVERT: A 777 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: A 816 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7161 (ttp-110) REVERT: A 840 ASP cc_start: 0.8332 (m-30) cc_final: 0.7984 (m-30) REVERT: A 904 PHE cc_start: 0.7906 (m-80) cc_final: 0.7625 (m-10) REVERT: A 975 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7809 (m) REVERT: B 67 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: B 95 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: B 184 MET cc_start: 0.8892 (mmt) cc_final: 0.7731 (tpp) REVERT: B 207 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (mt) REVERT: B 267 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.8018 (ttt180) REVERT: B 284 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7910 (tmmt) REVERT: B 398 MET cc_start: 0.7441 (tpt) cc_final: 0.7085 (mmt) REVERT: B 420 MET cc_start: 0.7905 (ttp) cc_final: 0.7673 (ttt) REVERT: B 571 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: B 575 MET cc_start: 0.8120 (ttp) cc_final: 0.7326 (tpp) REVERT: B 579 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8097 (tp40) REVERT: B 594 ASP cc_start: 0.7747 (m-30) cc_final: 0.7498 (m-30) REVERT: B 653 MET cc_start: 0.7313 (tpp) cc_final: 0.6868 (tpp) REVERT: B 657 MET cc_start: 0.7280 (tmm) cc_final: 0.7011 (ttp) REVERT: B 733 ASP cc_start: 0.7285 (t0) cc_final: 0.6913 (t0) REVERT: B 736 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6286 (mm110) REVERT: B 740 MET cc_start: 0.7814 (mtp) cc_final: 0.7378 (mtt) REVERT: B 855 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7760 (mmt) REVERT: B 891 LEU cc_start: 0.8227 (mt) cc_final: 0.7966 (mm) REVERT: B 892 CYS cc_start: 0.8943 (m) cc_final: 0.8535 (m) REVERT: B 925 MET cc_start: 0.8129 (tmt) cc_final: 0.7769 (tmm) REVERT: B 987 ILE cc_start: 0.7993 (mm) cc_final: 0.7750 (mp) REVERT: C 3 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7903 (mp10) REVERT: C 8 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8009 (mtm-85) REVERT: C 20 MET cc_start: 0.7752 (mtp) cc_final: 0.7272 (mtm) REVERT: C 120 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7961 (tm-30) REVERT: C 208 GLN cc_start: 0.7475 (tt0) cc_final: 0.7248 (tp40) REVERT: C 218 GLN cc_start: 0.8938 (mt0) cc_final: 0.8605 (mt0) REVERT: C 298 ASN cc_start: 0.8307 (t0) cc_final: 0.8013 (t0) REVERT: C 342 HIS cc_start: 0.6990 (t70) cc_final: 0.6645 (m90) REVERT: C 363 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7948 (mtp85) REVERT: C 422 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6756 (mt-10) REVERT: C 459 PHE cc_start: 0.7445 (m-80) cc_final: 0.7193 (m-80) REVERT: C 499 GLN cc_start: 0.7397 (tt0) cc_final: 0.7078 (tm-30) REVERT: C 530 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: C 536 MET cc_start: 0.7880 (mmm) cc_final: 0.7590 (mtt) REVERT: C 591 LYS cc_start: 0.8119 (mttt) cc_final: 0.7864 (mttt) REVERT: C 608 GLU cc_start: 0.7525 (tp30) cc_final: 0.7167 (tp30) REVERT: C 666 MET cc_start: 0.7157 (ttm) cc_final: 0.6849 (tpp) REVERT: C 668 LEU cc_start: 0.7458 (mt) cc_final: 0.7228 (mp) REVERT: C 696 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7971 (tppp) REVERT: C 768 ARG cc_start: 0.7595 (mmt180) cc_final: 0.7022 (mmm160) REVERT: C 783 MET cc_start: 0.8134 (mpp) cc_final: 0.7868 (mmm) REVERT: C 799 MET cc_start: 0.8023 (mmp) cc_final: 0.7706 (mmp) REVERT: C 800 VAL cc_start: 0.8138 (t) cc_final: 0.7888 (m) REVERT: C 887 LEU cc_start: 0.8108 (tp) cc_final: 0.7859 (tm) REVERT: C 904 PHE cc_start: 0.8055 (m-80) cc_final: 0.7799 (m-80) REVERT: C 963 GLU cc_start: 0.7751 (tt0) cc_final: 0.7112 (mm-30) REVERT: C 1012 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8276 (m170) outliers start: 95 outliers final: 59 residues processed: 601 average time/residue: 0.5097 time to fit residues: 361.4965 Evaluate side-chains 598 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 521 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1012 HIS Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 309 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 264 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 722 GLN A 877 GLN B 87 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 598 ASN C 795 ASN C1011 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.161857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.130965 restraints weight = 25482.339| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.35 r_work: 0.3124 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24442 Z= 0.145 Angle : 0.577 8.289 33247 Z= 0.297 Chirality : 0.042 0.212 3913 Planarity : 0.004 0.054 4261 Dihedral : 6.029 62.254 3414 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.83 % Allowed : 21.83 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.15), residues: 3134 helix: 2.33 (0.12), residues: 1729 sheet: 0.40 (0.24), residues: 441 loop : -0.09 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 314 TYR 0.017 0.001 TYR A 664 PHE 0.030 0.001 PHE B 358 TRP 0.007 0.001 TRP A 864 HIS 0.004 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00331 (24442) covalent geometry : angle 0.57704 (33247) hydrogen bonds : bond 0.04734 ( 1554) hydrogen bonds : angle 4.44034 ( 4698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 536 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7837 (tt0) cc_final: 0.7554 (mt-10) REVERT: A 69 MET cc_start: 0.8759 (mmt) cc_final: 0.8269 (mmt) REVERT: A 81 ASN cc_start: 0.7666 (m-40) cc_final: 0.7373 (m-40) REVERT: A 99 ASP cc_start: 0.8145 (t70) cc_final: 0.7844 (t0) REVERT: A 208 GLN cc_start: 0.8324 (mm110) cc_final: 0.7803 (mm110) REVERT: A 252 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7408 (ttmt) REVERT: A 269 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: A 292 LYS cc_start: 0.7484 (mttt) cc_final: 0.7233 (mtpt) REVERT: A 304 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7642 (pp20) REVERT: A 307 GLU cc_start: 0.7867 (tp30) cc_final: 0.7645 (tp30) REVERT: A 355 MET cc_start: 0.8157 (mtm) cc_final: 0.7916 (mtm) REVERT: A 438 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7104 (mp) REVERT: A 525 MET cc_start: 0.5606 (tpt) cc_final: 0.5164 (tpt) REVERT: A 568 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: A 657 MET cc_start: 0.7358 (mmm) cc_final: 0.7081 (mmp) REVERT: A 673 MET cc_start: 0.7672 (mtt) cc_final: 0.7412 (mtm) REVERT: A 695 GLU cc_start: 0.8374 (mp0) cc_final: 0.8105 (mp0) REVERT: A 718 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8659 (ptt-90) REVERT: A 729 GLN cc_start: 0.7679 (tt0) cc_final: 0.7434 (tt0) REVERT: A 740 MET cc_start: 0.7096 (mmm) cc_final: 0.6752 (mmt) REVERT: A 759 TYR cc_start: 0.8365 (t80) cc_final: 0.8046 (t80) REVERT: A 777 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: A 816 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7120 (ttp-110) REVERT: A 840 ASP cc_start: 0.8362 (m-30) cc_final: 0.8016 (m-30) REVERT: A 904 PHE cc_start: 0.7916 (m-80) cc_final: 0.7638 (m-10) REVERT: A 975 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7814 (m) REVERT: B 67 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: B 95 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: B 184 MET cc_start: 0.8900 (mmt) cc_final: 0.7709 (tpp) REVERT: B 207 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8747 (mt) REVERT: B 267 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.8044 (ttt180) REVERT: B 284 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7915 (tmmt) REVERT: B 398 MET cc_start: 0.7497 (tpt) cc_final: 0.7137 (mmt) REVERT: B 420 MET cc_start: 0.7938 (ttp) cc_final: 0.7714 (ttt) REVERT: B 575 MET cc_start: 0.8155 (ttp) cc_final: 0.7339 (tpp) REVERT: B 579 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8109 (tp40) REVERT: B 594 ASP cc_start: 0.7748 (m-30) cc_final: 0.7542 (m-30) REVERT: B 653 MET cc_start: 0.7307 (tpp) cc_final: 0.6790 (tpp) REVERT: B 657 MET cc_start: 0.7292 (tmm) cc_final: 0.6997 (ttp) REVERT: B 733 ASP cc_start: 0.7407 (t0) cc_final: 0.6963 (t0) REVERT: B 736 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6159 (mm110) REVERT: B 740 MET cc_start: 0.7796 (mtp) cc_final: 0.7369 (mtt) REVERT: B 855 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7708 (mmt) REVERT: B 891 LEU cc_start: 0.8240 (mt) cc_final: 0.7960 (mm) REVERT: B 892 CYS cc_start: 0.8974 (m) cc_final: 0.8564 (m) REVERT: B 925 MET cc_start: 0.8125 (tmt) cc_final: 0.7761 (tmm) REVERT: B 987 ILE cc_start: 0.7992 (mm) cc_final: 0.7743 (mp) REVERT: C 8 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7969 (mtm-85) REVERT: C 20 MET cc_start: 0.7774 (mtp) cc_final: 0.7290 (mtm) REVERT: C 120 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7952 (tm-30) REVERT: C 149 LEU cc_start: 0.7741 (mm) cc_final: 0.7518 (mp) REVERT: C 218 GLN cc_start: 0.8973 (mt0) cc_final: 0.8643 (mt0) REVERT: C 298 ASN cc_start: 0.8346 (t0) cc_final: 0.8057 (t0) REVERT: C 342 HIS cc_start: 0.7021 (t70) cc_final: 0.6635 (m90) REVERT: C 363 ARG cc_start: 0.8272 (mtt180) cc_final: 0.8053 (mtp85) REVERT: C 422 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6906 (mt-10) REVERT: C 459 PHE cc_start: 0.7536 (m-80) cc_final: 0.7253 (m-80) REVERT: C 499 GLN cc_start: 0.7437 (tt0) cc_final: 0.7105 (tm-30) REVERT: C 530 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: C 536 MET cc_start: 0.7915 (mmm) cc_final: 0.7629 (mtt) REVERT: C 591 LYS cc_start: 0.8133 (mttt) cc_final: 0.7886 (mttt) REVERT: C 603 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6377 (mm-30) REVERT: C 608 GLU cc_start: 0.7517 (tp30) cc_final: 0.7169 (tp30) REVERT: C 666 MET cc_start: 0.7175 (ttm) cc_final: 0.6848 (tpp) REVERT: C 668 LEU cc_start: 0.7490 (mt) cc_final: 0.7246 (mp) REVERT: C 696 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7977 (tppp) REVERT: C 768 ARG cc_start: 0.7598 (mmt180) cc_final: 0.7064 (mmm160) REVERT: C 783 MET cc_start: 0.8149 (mpp) cc_final: 0.7863 (mmm) REVERT: C 796 LYS cc_start: 0.7879 (tttm) cc_final: 0.7470 (ttmm) REVERT: C 799 MET cc_start: 0.8031 (mmp) cc_final: 0.7736 (mmp) REVERT: C 800 VAL cc_start: 0.8166 (t) cc_final: 0.7850 (m) REVERT: C 887 LEU cc_start: 0.8117 (tp) cc_final: 0.7859 (tm) REVERT: C 963 GLU cc_start: 0.7782 (tt0) cc_final: 0.7130 (mm-30) REVERT: C 1012 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.8313 (m170) outliers start: 99 outliers final: 67 residues processed: 597 average time/residue: 0.5153 time to fit residues: 362.5197 Evaluate side-chains 602 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 518 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1012 HIS Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 142 optimal weight: 10.0000 chunk 204 optimal weight: 50.0000 chunk 264 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 171 optimal weight: 0.2980 chunk 301 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 722 GLN B 87 GLN B 720 ASN B 827 ASN C 123 GLN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 598 ASN C 795 ASN C1011 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.159975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.128961 restraints weight = 25467.877| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.27 r_work: 0.3091 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24442 Z= 0.190 Angle : 0.624 8.727 33247 Z= 0.322 Chirality : 0.044 0.277 3913 Planarity : 0.005 0.056 4261 Dihedral : 6.178 59.535 3414 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.55 % Allowed : 22.18 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.15), residues: 3134 helix: 2.15 (0.12), residues: 1729 sheet: 0.27 (0.24), residues: 445 loop : -0.16 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 314 TYR 0.019 0.002 TYR A 664 PHE 0.023 0.002 PHE B 358 TRP 0.012 0.002 TRP A 864 HIS 0.008 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00449 (24442) covalent geometry : angle 0.62354 (33247) hydrogen bonds : bond 0.05311 ( 1554) hydrogen bonds : angle 4.59698 ( 4698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 537 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7977 (tt0) cc_final: 0.7610 (mt-10) REVERT: A 69 MET cc_start: 0.8697 (mmt) cc_final: 0.8128 (mmt) REVERT: A 99 ASP cc_start: 0.8144 (t70) cc_final: 0.7858 (t0) REVERT: A 208 GLN cc_start: 0.8345 (mm110) cc_final: 0.7823 (mm110) REVERT: A 252 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7435 (ttmt) REVERT: A 269 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: A 292 LYS cc_start: 0.7524 (mttt) cc_final: 0.7273 (mtpt) REVERT: A 304 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7627 (pp20) REVERT: A 307 GLU cc_start: 0.7914 (tp30) cc_final: 0.7662 (tp30) REVERT: A 342 HIS cc_start: 0.7705 (t70) cc_final: 0.7439 (t-170) REVERT: A 386 PHE cc_start: 0.8140 (m-80) cc_final: 0.7931 (m-80) REVERT: A 438 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7106 (mp) REVERT: A 525 MET cc_start: 0.5694 (tpt) cc_final: 0.5261 (tpt) REVERT: A 568 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: A 657 MET cc_start: 0.7396 (mmm) cc_final: 0.7112 (mmp) REVERT: A 673 MET cc_start: 0.7639 (mtt) cc_final: 0.7409 (mtm) REVERT: A 695 GLU cc_start: 0.8385 (mp0) cc_final: 0.8088 (mp0) REVERT: A 718 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8644 (ptt-90) REVERT: A 729 GLN cc_start: 0.7785 (tt0) cc_final: 0.7531 (tt0) REVERT: A 740 MET cc_start: 0.7086 (mmm) cc_final: 0.6745 (mmt) REVERT: A 759 TYR cc_start: 0.8435 (t80) cc_final: 0.8096 (t80) REVERT: A 777 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: A 816 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7391 (ttp-110) REVERT: A 840 ASP cc_start: 0.8226 (m-30) cc_final: 0.7872 (m-30) REVERT: A 904 PHE cc_start: 0.7888 (m-80) cc_final: 0.7607 (m-10) REVERT: A 975 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7884 (m) REVERT: B 67 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: B 69 MET cc_start: 0.8681 (mmt) cc_final: 0.7864 (mmp) REVERT: B 95 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: B 151 ASP cc_start: 0.6716 (p0) cc_final: 0.6482 (p0) REVERT: B 184 MET cc_start: 0.8937 (mmt) cc_final: 0.7735 (tpp) REVERT: B 207 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8718 (mt) REVERT: B 284 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7925 (tmmt) REVERT: B 398 MET cc_start: 0.7477 (tpt) cc_final: 0.7077 (mmt) REVERT: B 420 MET cc_start: 0.7960 (ttp) cc_final: 0.7756 (ttt) REVERT: B 449 LEU cc_start: 0.8533 (mp) cc_final: 0.8247 (mm) REVERT: B 456 MET cc_start: 0.8432 (ttp) cc_final: 0.8182 (ttt) REVERT: B 575 MET cc_start: 0.8187 (ttp) cc_final: 0.7371 (tpp) REVERT: B 579 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8148 (tp40) REVERT: B 653 MET cc_start: 0.7304 (tpp) cc_final: 0.6871 (tpp) REVERT: B 657 MET cc_start: 0.7292 (tmm) cc_final: 0.6953 (ttp) REVERT: B 733 ASP cc_start: 0.7407 (t0) cc_final: 0.7007 (t0) REVERT: B 736 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6572 (mt0) REVERT: B 740 MET cc_start: 0.7777 (mtp) cc_final: 0.7385 (mtt) REVERT: B 855 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7690 (mmt) REVERT: B 891 LEU cc_start: 0.8277 (mt) cc_final: 0.7990 (mm) REVERT: B 892 CYS cc_start: 0.8938 (m) cc_final: 0.8516 (m) REVERT: B 925 MET cc_start: 0.8135 (tmt) cc_final: 0.7776 (tmm) REVERT: B 987 ILE cc_start: 0.7998 (mm) cc_final: 0.7744 (mp) REVERT: B 1016 PHE cc_start: 0.7582 (m-80) cc_final: 0.7312 (m-10) REVERT: C 8 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7981 (mtm-85) REVERT: C 20 MET cc_start: 0.7798 (mtp) cc_final: 0.7311 (mtm) REVERT: C 120 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7989 (tm-30) REVERT: C 208 GLN cc_start: 0.7569 (tt0) cc_final: 0.7334 (tp40) REVERT: C 298 ASN cc_start: 0.8400 (t0) cc_final: 0.8018 (t0) REVERT: C 342 HIS cc_start: 0.7052 (t70) cc_final: 0.6687 (m90) REVERT: C 363 ARG cc_start: 0.8355 (mtt180) cc_final: 0.8055 (mtt90) REVERT: C 422 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6855 (mt-10) REVERT: C 459 PHE cc_start: 0.7623 (m-80) cc_final: 0.7348 (m-80) REVERT: C 499 GLN cc_start: 0.7434 (tt0) cc_final: 0.7142 (tm-30) REVERT: C 530 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: C 536 MET cc_start: 0.8054 (mmm) cc_final: 0.7729 (mtt) REVERT: C 591 LYS cc_start: 0.8267 (mttt) cc_final: 0.8003 (mttt) REVERT: C 603 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6441 (mm-30) REVERT: C 608 GLU cc_start: 0.7608 (tp30) cc_final: 0.7311 (tp30) REVERT: C 666 MET cc_start: 0.7056 (ttm) cc_final: 0.6776 (tpp) REVERT: C 668 LEU cc_start: 0.7479 (mt) cc_final: 0.7224 (mp) REVERT: C 768 ARG cc_start: 0.7703 (mmt180) cc_final: 0.7141 (mmm160) REVERT: C 796 LYS cc_start: 0.7864 (tttm) cc_final: 0.7474 (ttmm) REVERT: C 800 VAL cc_start: 0.8169 (t) cc_final: 0.7857 (m) REVERT: C 887 LEU cc_start: 0.8120 (tp) cc_final: 0.7875 (tm) REVERT: C 904 PHE cc_start: 0.8213 (m-80) cc_final: 0.7856 (m-80) REVERT: C 963 GLU cc_start: 0.7820 (tt0) cc_final: 0.7174 (mm-30) outliers start: 92 outliers final: 60 residues processed: 590 average time/residue: 0.5087 time to fit residues: 354.9445 Evaluate side-chains 604 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 528 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 579 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 575 MET Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 94 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 877 GLN B 87 GLN B 123 GLN B 159 ASN C 123 GLN C 148 ASN C 274 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN C 598 ASN C 795 ASN C1011 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.159379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.128921 restraints weight = 25220.357| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.24 r_work: 0.3065 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24442 Z= 0.205 Angle : 0.640 9.829 33247 Z= 0.332 Chirality : 0.045 0.286 3913 Planarity : 0.005 0.057 4261 Dihedral : 6.238 59.401 3414 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.17 % Allowed : 22.68 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.15), residues: 3134 helix: 2.02 (0.12), residues: 1729 sheet: 0.20 (0.24), residues: 445 loop : -0.22 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 314 TYR 0.019 0.002 TYR A 664 PHE 0.022 0.002 PHE C 599 TRP 0.011 0.002 TRP A 864 HIS 0.007 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00483 (24442) covalent geometry : angle 0.64036 (33247) hydrogen bonds : bond 0.05504 ( 1554) hydrogen bonds : angle 4.68106 ( 4698) =============================================================================== Job complete usr+sys time: 8753.04 seconds wall clock time: 149 minutes 23.08 seconds (8963.08 seconds total)