Starting phenix.real_space_refine on Thu Mar 5 14:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b8q_12089/03_2026/7b8q_12089.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b8q_12089/03_2026/7b8q_12089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b8q_12089/03_2026/7b8q_12089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b8q_12089/03_2026/7b8q_12089.map" model { file = "/net/cci-nas-00/data/ceres_data/7b8q_12089/03_2026/7b8q_12089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b8q_12089/03_2026/7b8q_12089.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 14987 2.51 5 N 3770 2.21 5 O 4286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 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: 23178 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7710 Classifications: {'peptide': 1011} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 964} Chain breaks: 2 Chain: "B" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Chain: "C" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Time building chain proxies: 5.28, per 1000 atoms: 0.23 Number of scatterers: 23178 At special positions: 0 Unit cell: (118.65, 113.4, 139.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4286 8.00 N 3770 7.00 C 14987 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: 1.97 Conformation dependent library (CDL) restraints added in 809.5 milliseconds 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 23 sheets defined 59.7% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.513A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.701A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.572A pdb=" N ALA A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.691A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.817A pdb=" N VAL A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.716A pdb=" N THR A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 423 removed outlier: 4.510A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.483A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 460 through 496 removed outlier: 3.523A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.973A pdb=" N SER A 516 " --> pdb=" O TRP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 555 Processing helix chain 'A' and resid 580 through 597 removed outlier: 4.460A pdb=" N ASP A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 removed outlier: 3.763A pdb=" N ARG A 632 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 648 Processing helix chain 'A' and resid 683 through 700 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 791 through 794 Processing helix chain 'A' and resid 827 through 840 removed outlier: 3.617A pdb=" N ALA A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.631A pdb=" N LYS A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 4.363A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 removed outlier: 4.139A pdb=" N SER A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 892 " --> pdb=" O ILE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 911 removed outlier: 3.666A pdb=" N GLY A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.642A pdb=" N GLU A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 982 removed outlier: 4.230A pdb=" N VAL A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1022 removed outlier: 3.660A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.613A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.515A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.568A pdb=" N VAL B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 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 360 Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.329A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.775A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 461 through 496 removed outlier: 4.090A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 512 through 534 removed outlier: 3.768A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 698 Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 747 removed outlier: 3.634A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER B 747 " --> pdb=" O THR B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 removed outlier: 4.416A pdb=" N ARG B 771 " --> pdb=" O ALA B 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 771' Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.971A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 795 No H-bonds generated for 'chain 'B' and resid 793 through 795' Processing helix chain 'B' and resid 827 through 841 Processing helix chain 'B' and resid 852 through 862 Processing helix chain 'B' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU B 867 " --> pdb=" O GLN B 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 868 " --> pdb=" O MET B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 Processing helix chain 'B' and resid 895 through 911 Processing helix chain 'B' and resid 915 through 946 removed outlier: 3.784A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 982 removed outlier: 4.611A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL B1014 " --> pdb=" O PHE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 27 removed outlier: 3.677A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.854A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.792A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 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 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.328A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 453 removed outlier: 6.280A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.777A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 461 through 488 removed outlier: 4.090A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 512 through 534 removed outlier: 3.768A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 580 through 595 Processing helix chain 'C' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP C 642 " --> pdb=" O LYS C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 698 removed outlier: 4.020A pdb=" N ALA C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 747 removed outlier: 3.597A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER C 747 " --> pdb=" O THR C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 773 through 778 removed outlier: 3.954A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 Processing helix chain 'C' and resid 852 through 862 Processing helix chain 'C' and resid 863 through 884 removed outlier: 3.575A pdb=" N LEU C 867 " --> pdb=" O GLN C 863 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 868 " --> pdb=" O MET C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 894 Processing helix chain 'C' and resid 895 through 911 Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.784A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 982 removed outlier: 4.610A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL C1014 " --> pdb=" O PHE C1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.496A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.496A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.682A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 293 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N LEU A 137 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASP A 328 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.769A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 603 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 605 " --> pdb=" O PHE A 623 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.540A pdb=" N LYS A 182 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLN A 761 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 796 through 804 removed outlier: 8.334A pdb=" N SER B 235 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 718 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 782 through 783 Processing sheet with id=AA8, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 821 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.623A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.831A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 605 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 572 " --> pdb=" O MET B 656 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB5, first strand: chain 'B' and resid 715 through 719 Processing sheet with id=AB6, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB7, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.832A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR C 605 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER C 572 " --> pdb=" O MET C 656 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.777A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC4, first strand: chain 'C' and resid 715 through 722 Processing sheet with id=AC5, first strand: chain 'C' and resid 781 through 783 1575 hydrogen bonds defined for protein. 4566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3817 1.31 - 1.44: 5659 1.44 - 1.56: 13851 1.56 - 1.69: 4 1.69 - 1.81: 264 Bond restraints: 23595 Sorted by residual: bond pdb=" C GLU A 423 " pdb=" N GLY A 424 " ideal model delta sigma weight residual 1.329 1.404 -0.075 1.09e-02 8.42e+03 4.76e+01 bond pdb=" CA LEU B 198 " pdb=" C LEU B 198 " ideal model delta sigma weight residual 1.526 1.593 -0.068 1.36e-02 5.41e+03 2.50e+01 bond pdb=" N LEU B 720 " pdb=" CA LEU B 720 " ideal model delta sigma weight residual 1.454 1.398 0.056 1.15e-02 7.56e+03 2.40e+01 bond pdb=" CA LEU C 198 " pdb=" C LEU C 198 " ideal model delta sigma weight residual 1.526 1.591 -0.066 1.36e-02 5.41e+03 2.35e+01 bond pdb=" CA VAL B 259 " pdb=" CB VAL B 259 " ideal model delta sigma weight residual 1.533 1.481 0.052 1.13e-02 7.83e+03 2.15e+01 ... (remaining 23590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 31637 3.70 - 7.40: 317 7.40 - 11.09: 39 11.09 - 14.79: 10 14.79 - 18.49: 1 Bond angle restraints: 32004 Sorted by residual: angle pdb=" N ILE C 750 " pdb=" CA ILE C 750 " pdb=" C ILE C 750 " ideal model delta sigma weight residual 111.67 125.08 -13.41 9.50e-01 1.11e+00 1.99e+02 angle pdb=" N ILE B 750 " pdb=" CA ILE B 750 " pdb=" C ILE B 750 " ideal model delta sigma weight residual 111.67 124.70 -13.03 9.50e-01 1.11e+00 1.88e+02 angle pdb=" N SER A 132 " pdb=" CA SER A 132 " pdb=" C SER A 132 " ideal model delta sigma weight residual 111.52 126.06 -14.54 1.40e+00 5.10e-01 1.08e+02 angle pdb=" N LYS B 226 " pdb=" CA LYS B 226 " pdb=" C LYS B 226 " ideal model delta sigma weight residual 110.24 96.81 13.43 1.47e+00 4.63e-01 8.35e+01 angle pdb=" C GLY A 238 " pdb=" N GLN A 239 " pdb=" CA GLN A 239 " ideal model delta sigma weight residual 123.00 135.40 -12.40 1.38e+00 5.25e-01 8.08e+01 ... (remaining 31999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 12663 17.69 - 35.38: 1281 35.38 - 53.07: 283 53.07 - 70.76: 61 70.76 - 88.45: 20 Dihedral angle restraints: 14308 sinusoidal: 5547 harmonic: 8761 Sorted by residual: dihedral pdb=" CA TYR C 49 " pdb=" C TYR C 49 " pdb=" N PRO C 50 " pdb=" CA PRO C 50 " ideal model delta harmonic sigma weight residual -180.00 -159.24 -20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR B 49 " pdb=" C TYR B 49 " pdb=" N PRO B 50 " pdb=" CA PRO B 50 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C ASN A 248 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " pdb=" CB ASN A 248 " ideal model delta harmonic sigma weight residual -122.60 -132.82 10.22 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 14305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3470 0.092 - 0.183: 341 0.183 - 0.275: 29 0.275 - 0.367: 4 0.367 - 0.458: 4 Chirality restraints: 3848 Sorted by residual: chirality pdb=" CA SER A 132 " pdb=" N SER A 132 " pdb=" C SER A 132 " pdb=" CB SER A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA ASN A 248 " pdb=" N ASN A 248 " pdb=" C ASN A 248 " pdb=" CB ASN A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA LYS C 254 " pdb=" N LYS C 254 " pdb=" C LYS C 254 " pdb=" CB LYS C 254 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 3845 not shown) Planarity restraints: 4027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 666 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C LEU A 666 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU A 666 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY A 667 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 561 " 0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 562 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 562 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 562 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 35 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO B 36 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.049 5.00e-02 4.00e+02 ... (remaining 4024 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 695 2.70 - 3.25: 24659 3.25 - 3.80: 37121 3.80 - 4.35: 47745 4.35 - 4.90: 80392 Nonbonded interactions: 190612 Sorted by model distance: nonbonded pdb=" O GLU A 654 " pdb=" OE1 GLU A 654 " model vdw 2.150 3.040 nonbonded pdb=" N ASP B 723 " pdb=" O VAL B 795 " model vdw 2.197 3.120 nonbonded pdb=" O PRO C 216 " pdb=" O LEU C 234 " model vdw 2.229 3.040 nonbonded pdb=" O SER A 747 " pdb=" OG SER A 747 " model vdw 2.238 3.040 nonbonded pdb=" O VAL B 212 " pdb=" O GLY B 238 " model vdw 2.324 3.040 ... (remaining 190607 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 502 or resid 511 through 1023)) selection = (chain 'B' and (resid 1 through 253 or resid 259 through 1023)) selection = (chain 'C' and (resid 1 through 253 or resid 259 through 1023)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.010 Find NCS groups from input model: 0.440 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 23595 Z= 0.323 Angle : 1.008 18.491 32004 Z= 0.688 Chirality : 0.057 0.458 3848 Planarity : 0.006 0.097 4027 Dihedral : 15.131 88.451 8638 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.79 % Allowed : 13.39 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.93 (0.14), residues: 3027 helix: -1.04 (0.12), residues: 1660 sheet: -2.72 (0.21), residues: 464 loop : -2.92 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 724 TYR 0.016 0.001 TYR B 49 PHE 0.015 0.001 PHE B 917 TRP 0.007 0.001 TRP A 886 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00528 (23595) covalent geometry : angle 1.00810 (32004) hydrogen bonds : bond 0.13739 ( 1490) hydrogen bonds : angle 7.05209 ( 4566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 923 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 VAL cc_start: 0.8476 (t) cc_final: 0.8255 (p) REVERT: A 477 SER cc_start: 0.8947 (t) cc_final: 0.8638 (m) REVERT: A 563 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7152 (mt-10) REVERT: A 647 MET cc_start: 0.8439 (mmp) cc_final: 0.7818 (mmm) REVERT: A 701 ASN cc_start: 0.7099 (t0) cc_final: 0.5972 (t0) REVERT: A 759 MET cc_start: 0.8389 (mmm) cc_final: 0.7574 (mmt) REVERT: A 848 TYR cc_start: 0.8485 (p90) cc_final: 0.8220 (p90) REVERT: A 926 ILE cc_start: 0.9577 (mm) cc_final: 0.9209 (mm) REVERT: A 943 LEU cc_start: 0.8597 (mt) cc_final: 0.8348 (tp) REVERT: A 987 SER cc_start: 0.8951 (p) cc_final: 0.8723 (m) REVERT: B 44 ASN cc_start: 0.8222 (m-40) cc_final: 0.7894 (m-40) REVERT: B 49 TYR cc_start: 0.8754 (t80) cc_final: 0.8517 (t80) REVERT: B 102 MET cc_start: 0.8321 (mmm) cc_final: 0.8059 (mmm) REVERT: B 106 ASP cc_start: 0.7627 (m-30) cc_final: 0.7352 (m-30) REVERT: B 240 LEU cc_start: 0.8388 (mt) cc_final: 0.8129 (mt) REVERT: B 272 SER cc_start: 0.9298 (p) cc_final: 0.8987 (m) REVERT: B 404 ILE cc_start: 0.7800 (mt) cc_final: 0.7351 (mt) REVERT: B 460 SER cc_start: 0.8620 (m) cc_final: 0.8382 (p) REVERT: B 570 MET cc_start: 0.8313 (mtm) cc_final: 0.8065 (mtm) REVERT: B 574 GLN cc_start: 0.8475 (tp40) cc_final: 0.7820 (tm-30) REVERT: B 604 ASN cc_start: 0.9016 (t0) cc_final: 0.8681 (t0) REVERT: B 727 LEU cc_start: 0.7779 (mt) cc_final: 0.7272 (mt) REVERT: B 848 TYR cc_start: 0.8084 (p90) cc_final: 0.7786 (p90) REVERT: B 919 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7936 (mttp) REVERT: B 922 LEU cc_start: 0.9264 (tp) cc_final: 0.8912 (tt) REVERT: B 962 LEU cc_start: 0.9017 (tp) cc_final: 0.8778 (tp) REVERT: C 44 ASN cc_start: 0.8028 (m-40) cc_final: 0.7726 (m-40) REVERT: C 102 MET cc_start: 0.8355 (mmm) cc_final: 0.7461 (tpp) REVERT: C 185 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8597 (mmt180) REVERT: C 196 TYR cc_start: 0.7960 (m-80) cc_final: 0.7440 (m-80) REVERT: C 398 MET cc_start: 0.8643 (mtt) cc_final: 0.8431 (mtt) REVERT: C 404 ILE cc_start: 0.9086 (mt) cc_final: 0.8806 (mt) REVERT: C 474 MET cc_start: 0.7875 (mtm) cc_final: 0.7650 (mtm) REVERT: C 524 TYR cc_start: 0.8677 (t80) cc_final: 0.8394 (t80) REVERT: C 545 ILE cc_start: 0.8616 (mt) cc_final: 0.8369 (mt) REVERT: C 604 ASN cc_start: 0.8487 (t0) cc_final: 0.7876 (t0) REVERT: C 697 MET cc_start: 0.7747 (mtp) cc_final: 0.7546 (mtm) REVERT: C 864 MET cc_start: 0.7767 (ptm) cc_final: 0.7541 (tpp) REVERT: C 904 ILE cc_start: 0.8900 (mm) cc_final: 0.8206 (mm) outliers start: 20 outliers final: 1 residues processed: 931 average time/residue: 0.1525 time to fit residues: 222.9130 Evaluate side-chains 534 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 532 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 919 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 677 GLN A 691 GLN A 709 ASN A 779 ASN B 128 GLN B 228 GLN B 239 GLN B 415 ASN B 574 GLN B 617 GLN B 677 GLN ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 ASN B 805 GLN B 823 ASN B 863 GLN C 128 GLN C 148 GLN C 176 GLN C 191 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN C 415 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN C 863 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105861 restraints weight = 40283.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108668 restraints weight = 21491.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110534 restraints weight = 13687.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111787 restraints weight = 9904.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112713 restraints weight = 7818.478| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23595 Z= 0.152 Angle : 0.658 10.597 32004 Z= 0.333 Chirality : 0.043 0.198 3848 Planarity : 0.005 0.059 4027 Dihedral : 4.066 32.241 3183 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.12 % Allowed : 18.88 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.03 (0.15), residues: 3027 helix: 0.52 (0.13), residues: 1685 sheet: -2.25 (0.21), residues: 489 loop : -1.95 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 8 TYR 0.020 0.002 TYR C 77 PHE 0.021 0.002 PHE C1015 TRP 0.015 0.001 TRP B 568 HIS 0.004 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00332 (23595) covalent geometry : angle 0.65764 (32004) hydrogen bonds : bond 0.04278 ( 1490) hydrogen bonds : angle 5.04620 ( 4566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 607 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 VAL cc_start: 0.8648 (t) cc_final: 0.8337 (p) REVERT: A 112 LYS cc_start: 0.7958 (tptt) cc_final: 0.7717 (tptp) REVERT: A 435 MET cc_start: 0.9390 (mmm) cc_final: 0.9170 (mmt) REVERT: A 477 SER cc_start: 0.8910 (t) cc_final: 0.8603 (m) REVERT: A 647 MET cc_start: 0.8230 (mmp) cc_final: 0.7026 (mmm) REVERT: A 695 MET cc_start: 0.8313 (tpp) cc_final: 0.7784 (mmm) REVERT: A 987 SER cc_start: 0.8877 (p) cc_final: 0.8663 (m) REVERT: B 15 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8693 (tp) REVERT: B 44 ASN cc_start: 0.8548 (m-40) cc_final: 0.7967 (m-40) REVERT: B 49 TYR cc_start: 0.8793 (t80) cc_final: 0.8511 (t80) REVERT: B 109 ASN cc_start: 0.8610 (m-40) cc_final: 0.8378 (m-40) REVERT: B 157 TYR cc_start: 0.8380 (t80) cc_final: 0.7972 (t80) REVERT: B 404 ILE cc_start: 0.8403 (mt) cc_final: 0.8057 (mt) REVERT: B 435 MET cc_start: 0.7225 (mmm) cc_final: 0.6781 (mmm) REVERT: B 479 LEU cc_start: 0.8759 (mp) cc_final: 0.8528 (mp) REVERT: B 561 MET cc_start: 0.8278 (mmm) cc_final: 0.8046 (mmm) REVERT: B 574 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8584 (tm-30) REVERT: B 701 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: B 770 SER cc_start: 0.8822 (m) cc_final: 0.8470 (t) REVERT: B 832 MET cc_start: 0.8659 (mtp) cc_final: 0.8135 (mtp) REVERT: B 857 GLU cc_start: 0.8408 (tt0) cc_final: 0.8206 (tp30) REVERT: B 864 MET cc_start: 0.8552 (tpp) cc_final: 0.8351 (tpp) REVERT: B 948 MET cc_start: 0.7637 (ttm) cc_final: 0.7379 (ttm) REVERT: B 962 LEU cc_start: 0.9212 (tp) cc_final: 0.8981 (tp) REVERT: C 102 MET cc_start: 0.8365 (mmm) cc_final: 0.7744 (tpp) REVERT: C 398 MET cc_start: 0.8667 (mtt) cc_final: 0.8464 (mtt) REVERT: C 439 THR cc_start: 0.8042 (t) cc_final: 0.7789 (m) REVERT: C 524 TYR cc_start: 0.8597 (t80) cc_final: 0.8322 (t80) REVERT: C 545 ILE cc_start: 0.8587 (mt) cc_final: 0.8326 (mt) REVERT: C 595 LEU cc_start: 0.8838 (pp) cc_final: 0.8636 (pp) REVERT: C 604 ASN cc_start: 0.8425 (t0) cc_final: 0.8128 (t0) REVERT: C 694 LEU cc_start: 0.9100 (tt) cc_final: 0.8740 (tp) REVERT: C 706 MET cc_start: 0.6219 (ttt) cc_final: 0.5488 (ttp) REVERT: C 770 SER cc_start: 0.9252 (m) cc_final: 0.8887 (t) REVERT: C 864 MET cc_start: 0.7739 (ptm) cc_final: 0.7419 (tpp) REVERT: C 913 MET cc_start: 0.8066 (mmm) cc_final: 0.7309 (mmm) outliers start: 105 outliers final: 55 residues processed: 675 average time/residue: 0.1344 time to fit residues: 150.1450 Evaluate side-chains 520 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 463 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 773 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 136 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 534 HIS A 604 ASN B 691 GLN B 701 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099487 restraints weight = 41380.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102304 restraints weight = 21583.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104191 restraints weight = 13561.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105483 restraints weight = 9748.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106359 restraints weight = 7645.550| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23595 Z= 0.158 Angle : 0.618 9.511 32004 Z= 0.312 Chirality : 0.042 0.163 3848 Planarity : 0.004 0.057 4027 Dihedral : 3.926 19.113 3178 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.59 % Allowed : 20.61 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.39 (0.16), residues: 3027 helix: 0.94 (0.13), residues: 1692 sheet: -1.91 (0.22), residues: 479 loop : -1.54 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 515 TYR 0.025 0.002 TYR B 810 PHE 0.033 0.002 PHE A 629 TRP 0.015 0.001 TRP A 512 HIS 0.007 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00367 (23595) covalent geometry : angle 0.61824 (32004) hydrogen bonds : bond 0.04105 ( 1490) hydrogen bonds : angle 4.83032 ( 4566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 509 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 VAL cc_start: 0.8779 (t) cc_final: 0.8446 (p) REVERT: A 112 LYS cc_start: 0.8020 (tptt) cc_final: 0.7735 (tptp) REVERT: A 193 LEU cc_start: 0.8397 (mt) cc_final: 0.7893 (tt) REVERT: A 202 ASP cc_start: 0.7989 (t0) cc_final: 0.7442 (t0) REVERT: A 415 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8860 (m-40) REVERT: A 477 SER cc_start: 0.8927 (t) cc_final: 0.8653 (m) REVERT: A 575 LEU cc_start: 0.8728 (mm) cc_final: 0.8426 (mp) REVERT: A 647 MET cc_start: 0.8353 (mmp) cc_final: 0.7109 (mmm) REVERT: A 695 MET cc_start: 0.8238 (tpp) cc_final: 0.7817 (mmm) REVERT: A 759 MET cc_start: 0.7984 (mmt) cc_final: 0.7506 (mmm) REVERT: A 987 SER cc_start: 0.8836 (p) cc_final: 0.8580 (m) REVERT: B 232 ILE cc_start: 0.9389 (mt) cc_final: 0.9129 (mt) REVERT: B 404 ILE cc_start: 0.8583 (mt) cc_final: 0.8204 (mt) REVERT: B 435 MET cc_start: 0.7431 (mmm) cc_final: 0.6899 (mmm) REVERT: B 438 ILE cc_start: 0.8669 (pp) cc_final: 0.8434 (pp) REVERT: B 561 MET cc_start: 0.8494 (mmm) cc_final: 0.8245 (mmm) REVERT: B 574 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8496 (tm-30) REVERT: B 745 MET cc_start: 0.6346 (mmm) cc_final: 0.5851 (mmm) REVERT: B 832 MET cc_start: 0.8758 (mtp) cc_final: 0.8302 (mtp) REVERT: B 857 GLU cc_start: 0.8457 (tt0) cc_final: 0.8231 (tt0) REVERT: B 864 MET cc_start: 0.8542 (tpp) cc_final: 0.8222 (tpp) REVERT: B 948 MET cc_start: 0.7698 (ttm) cc_final: 0.7354 (ttm) REVERT: B 962 LEU cc_start: 0.9222 (tp) cc_final: 0.8988 (tp) REVERT: C 93 THR cc_start: 0.8853 (m) cc_final: 0.8596 (m) REVERT: C 130 GLU cc_start: 0.8070 (pp20) cc_final: 0.7588 (pp20) REVERT: C 229 LEU cc_start: 0.8500 (mm) cc_final: 0.8236 (pt) REVERT: C 346 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: C 439 THR cc_start: 0.8128 (t) cc_final: 0.7864 (m) REVERT: C 474 MET cc_start: 0.8264 (mtm) cc_final: 0.7890 (mtm) REVERT: C 524 TYR cc_start: 0.8594 (t80) cc_final: 0.8339 (t80) REVERT: C 604 ASN cc_start: 0.8513 (t0) cc_final: 0.8286 (t0) REVERT: C 651 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7724 (p) REVERT: C 723 ASP cc_start: 0.7201 (t0) cc_final: 0.6921 (t0) REVERT: C 770 SER cc_start: 0.9281 (m) cc_final: 0.8965 (t) REVERT: C 864 MET cc_start: 0.7750 (ptm) cc_final: 0.7378 (tpp) outliers start: 117 outliers final: 78 residues processed: 588 average time/residue: 0.1342 time to fit residues: 131.0338 Evaluate side-chains 528 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 447 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 133 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN A 146 ASN A 534 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 604 ASN B 691 GLN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095556 restraints weight = 41629.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098253 restraints weight = 21813.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100080 restraints weight = 13820.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101286 restraints weight = 10000.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102070 restraints weight = 7969.245| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23595 Z= 0.184 Angle : 0.625 9.884 32004 Z= 0.316 Chirality : 0.042 0.156 3848 Planarity : 0.004 0.056 4027 Dihedral : 3.969 17.454 3178 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.34 % Allowed : 21.63 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.10 (0.16), residues: 3027 helix: 1.08 (0.13), residues: 1686 sheet: -1.78 (0.22), residues: 503 loop : -1.14 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 910 TYR 0.025 0.002 TYR C 883 PHE 0.025 0.002 PHE B 629 TRP 0.010 0.001 TRP B 556 HIS 0.008 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00433 (23595) covalent geometry : angle 0.62477 (32004) hydrogen bonds : bond 0.04098 ( 1490) hydrogen bonds : angle 4.78302 ( 4566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 492 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 112 LYS cc_start: 0.7920 (tptt) cc_final: 0.7720 (tptp) REVERT: A 194 VAL cc_start: 0.8443 (p) cc_final: 0.8212 (t) REVERT: A 202 ASP cc_start: 0.8071 (t0) cc_final: 0.7845 (t70) REVERT: A 383 MET cc_start: 0.8640 (ttm) cc_final: 0.8322 (mtt) REVERT: A 415 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8860 (m-40) REVERT: A 477 SER cc_start: 0.8973 (t) cc_final: 0.8696 (m) REVERT: A 575 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 647 MET cc_start: 0.8455 (mmp) cc_final: 0.7213 (mmm) REVERT: A 695 MET cc_start: 0.8275 (tpp) cc_final: 0.7893 (mmm) REVERT: B 232 ILE cc_start: 0.9370 (mt) cc_final: 0.9153 (mt) REVERT: B 404 ILE cc_start: 0.8744 (mt) cc_final: 0.8331 (mt) REVERT: B 435 MET cc_start: 0.7883 (mmm) cc_final: 0.7382 (mmm) REVERT: B 438 ILE cc_start: 0.8687 (pp) cc_final: 0.8461 (pp) REVERT: B 638 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8461 (tmtt) REVERT: B 710 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 745 MET cc_start: 0.6512 (mmm) cc_final: 0.5965 (mmm) REVERT: B 823 ASN cc_start: 0.7999 (t0) cc_final: 0.7790 (t0) REVERT: B 834 GLU cc_start: 0.8241 (tp30) cc_final: 0.8013 (tm-30) REVERT: B 857 GLU cc_start: 0.8546 (tt0) cc_final: 0.8301 (tt0) REVERT: B 864 MET cc_start: 0.8623 (tpp) cc_final: 0.8329 (tpp) REVERT: B 942 MET cc_start: 0.7914 (mtp) cc_final: 0.7478 (mtt) REVERT: B 948 MET cc_start: 0.7817 (ttm) cc_final: 0.7514 (ttm) REVERT: B 963 ARG cc_start: 0.8810 (ttt90) cc_final: 0.8550 (ttt180) REVERT: C 8 ARG cc_start: 0.7582 (mtt-85) cc_final: 0.7223 (mtt-85) REVERT: C 130 GLU cc_start: 0.8132 (pp20) cc_final: 0.7656 (pp20) REVERT: C 346 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: C 435 MET cc_start: 0.8947 (mmm) cc_final: 0.8737 (mmm) REVERT: C 439 THR cc_start: 0.8398 (t) cc_final: 0.8152 (m) REVERT: C 474 MET cc_start: 0.8109 (mtm) cc_final: 0.7767 (mtm) REVERT: C 647 MET cc_start: 0.7614 (mmt) cc_final: 0.7276 (mmt) REVERT: C 723 ASP cc_start: 0.7473 (t0) cc_final: 0.7165 (t0) REVERT: C 770 SER cc_start: 0.9328 (m) cc_final: 0.8969 (t) outliers start: 136 outliers final: 92 residues processed: 590 average time/residue: 0.1310 time to fit residues: 129.9253 Evaluate side-chains 532 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 437 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 772 MET Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 102 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 284 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096991 restraints weight = 41023.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.099700 restraints weight = 21456.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.101521 restraints weight = 13577.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102746 restraints weight = 9780.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103520 restraints weight = 7743.349| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23595 Z= 0.160 Angle : 0.612 8.402 32004 Z= 0.308 Chirality : 0.042 0.231 3848 Planarity : 0.004 0.053 4027 Dihedral : 3.942 17.650 3178 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.26 % Allowed : 22.30 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.11 (0.16), residues: 3027 helix: 1.18 (0.13), residues: 1684 sheet: -1.54 (0.23), residues: 493 loop : -0.98 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.012 0.001 TYR B 810 PHE 0.022 0.001 PHE C 591 TRP 0.011 0.001 TRP A 187 HIS 0.008 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00368 (23595) covalent geometry : angle 0.61228 (32004) hydrogen bonds : bond 0.03928 ( 1490) hydrogen bonds : angle 4.72657 ( 4566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 467 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7944 (tptt) cc_final: 0.7727 (tptp) REVERT: A 383 MET cc_start: 0.8634 (ttm) cc_final: 0.8319 (mtt) REVERT: A 415 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8841 (m-40) REVERT: A 477 SER cc_start: 0.8937 (t) cc_final: 0.8692 (m) REVERT: A 575 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 647 MET cc_start: 0.8396 (mmp) cc_final: 0.7327 (mmm) REVERT: B 20 ILE cc_start: 0.9191 (mm) cc_final: 0.8942 (mt) REVERT: B 130 GLU cc_start: 0.8245 (pm20) cc_final: 0.8007 (pm20) REVERT: B 325 ILE cc_start: 0.9234 (mm) cc_final: 0.9019 (mm) REVERT: B 435 MET cc_start: 0.7917 (mmm) cc_final: 0.7510 (mmm) REVERT: B 449 LEU cc_start: 0.9010 (mm) cc_final: 0.8763 (mm) REVERT: B 638 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8450 (tmtt) REVERT: B 706 MET cc_start: 0.7104 (mtp) cc_final: 0.6841 (mtp) REVERT: B 834 GLU cc_start: 0.8193 (tp30) cc_final: 0.7985 (tm-30) REVERT: B 857 GLU cc_start: 0.8535 (tt0) cc_final: 0.8193 (tp30) REVERT: B 864 MET cc_start: 0.8563 (tpp) cc_final: 0.8326 (tpp) REVERT: B 942 MET cc_start: 0.7881 (mtp) cc_final: 0.7483 (mtt) REVERT: B 948 MET cc_start: 0.7832 (ttm) cc_final: 0.7567 (ttm) REVERT: C 8 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7292 (mtt-85) REVERT: C 68 GLU cc_start: 0.8245 (mp0) cc_final: 0.7861 (mp0) REVERT: C 89 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 130 GLU cc_start: 0.8160 (pp20) cc_final: 0.7696 (pp20) REVERT: C 346 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: C 474 MET cc_start: 0.8141 (mtm) cc_final: 0.7780 (mtm) REVERT: C 565 ASP cc_start: 0.6803 (t0) cc_final: 0.6551 (m-30) REVERT: C 723 ASP cc_start: 0.7502 (t0) cc_final: 0.7274 (t0) REVERT: C 770 SER cc_start: 0.9269 (m) cc_final: 0.8918 (t) REVERT: C 1018 PHE cc_start: 0.8495 (t80) cc_final: 0.8228 (t80) outliers start: 134 outliers final: 99 residues processed: 564 average time/residue: 0.1300 time to fit residues: 123.1728 Evaluate side-chains 526 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 424 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 772 MET Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 185 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN B 108 GLN B 109 ASN B 779 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 273 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095463 restraints weight = 41401.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.098022 restraints weight = 22051.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.099768 restraints weight = 14145.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100939 restraints weight = 10274.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101743 restraints weight = 8218.007| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 23595 Z= 0.190 Angle : 0.638 8.492 32004 Z= 0.321 Chirality : 0.043 0.204 3848 Planarity : 0.004 0.052 4027 Dihedral : 3.992 17.044 3178 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.69 % Allowed : 23.40 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.18 (0.16), residues: 3027 helix: 1.20 (0.13), residues: 1680 sheet: -1.48 (0.23), residues: 495 loop : -0.89 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 833 TYR 0.013 0.001 TYR A 524 PHE 0.028 0.002 PHE C 669 TRP 0.010 0.001 TRP A 187 HIS 0.008 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00448 (23595) covalent geometry : angle 0.63798 (32004) hydrogen bonds : bond 0.03998 ( 1490) hydrogen bonds : angle 4.72333 ( 4566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 447 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.8890 (mt) cc_final: 0.8542 (tt) REVERT: A 112 LYS cc_start: 0.7983 (tptt) cc_final: 0.7727 (tptp) REVERT: A 355 MET cc_start: 0.8155 (tpp) cc_final: 0.7944 (tpp) REVERT: A 383 MET cc_start: 0.8645 (ttm) cc_final: 0.8328 (mtt) REVERT: A 420 MET cc_start: 0.8175 (ptp) cc_final: 0.7911 (ptt) REVERT: A 477 SER cc_start: 0.8963 (t) cc_final: 0.8713 (m) REVERT: A 555 TYR cc_start: 0.6303 (t80) cc_final: 0.6093 (t80) REVERT: A 575 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 647 MET cc_start: 0.8396 (mmp) cc_final: 0.7243 (mmm) REVERT: B 20 ILE cc_start: 0.9257 (mm) cc_final: 0.9043 (mt) REVERT: B 66 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8135 (mm-30) REVERT: B 68 GLU cc_start: 0.7999 (mp0) cc_final: 0.7521 (mp0) REVERT: B 114 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8503 (m) REVERT: B 240 LEU cc_start: 0.8320 (mt) cc_final: 0.7620 (mp) REVERT: B 325 ILE cc_start: 0.9259 (mm) cc_final: 0.9043 (mm) REVERT: B 395 MET cc_start: 0.8489 (mmm) cc_final: 0.8170 (mmp) REVERT: B 435 MET cc_start: 0.8010 (mmm) cc_final: 0.7621 (mmm) REVERT: B 638 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8408 (tmtt) REVERT: B 857 GLU cc_start: 0.8607 (tt0) cc_final: 0.8321 (tt0) REVERT: B 864 MET cc_start: 0.8512 (tpp) cc_final: 0.8274 (tpp) REVERT: B 942 MET cc_start: 0.7959 (mtp) cc_final: 0.7669 (mtp) REVERT: B 948 MET cc_start: 0.7885 (ttm) cc_final: 0.7552 (ttm) REVERT: C 8 ARG cc_start: 0.7696 (mtt-85) cc_final: 0.7290 (mtt-85) REVERT: C 68 GLU cc_start: 0.8294 (mp0) cc_final: 0.7894 (mp0) REVERT: C 130 GLU cc_start: 0.8228 (pp20) cc_final: 0.7725 (pp20) REVERT: C 346 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: C 433 LYS cc_start: 0.8502 (tttt) cc_final: 0.8217 (tppt) REVERT: C 439 THR cc_start: 0.8785 (t) cc_final: 0.8482 (m) REVERT: C 474 MET cc_start: 0.8138 (mtm) cc_final: 0.7780 (mtm) REVERT: C 723 ASP cc_start: 0.7476 (t0) cc_final: 0.7257 (t0) REVERT: C 770 SER cc_start: 0.9303 (m) cc_final: 0.8938 (t) outliers start: 145 outliers final: 110 residues processed: 550 average time/residue: 0.1377 time to fit residues: 127.0936 Evaluate side-chains 534 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 421 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 772 MET Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1007 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 89 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 294 optimal weight: 0.9980 chunk 255 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.096510 restraints weight = 41287.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099112 restraints weight = 21936.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100875 restraints weight = 14030.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102010 restraints weight = 10189.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102832 restraints weight = 8137.657| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 23595 Z= 0.159 Angle : 0.625 9.084 32004 Z= 0.312 Chirality : 0.042 0.232 3848 Planarity : 0.004 0.051 4027 Dihedral : 3.977 18.824 3178 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.34 % Allowed : 23.56 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.30 (0.16), residues: 3027 helix: 1.29 (0.13), residues: 1680 sheet: -1.39 (0.23), residues: 487 loop : -0.85 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 168 TYR 0.015 0.001 TYR A 524 PHE 0.024 0.001 PHE C 669 TRP 0.011 0.001 TRP B 556 HIS 0.007 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00374 (23595) covalent geometry : angle 0.62460 (32004) hydrogen bonds : bond 0.03896 ( 1490) hydrogen bonds : angle 4.66349 ( 4566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 451 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7936 (tptt) cc_final: 0.7712 (tptp) REVERT: A 477 SER cc_start: 0.8934 (t) cc_final: 0.8647 (m) REVERT: A 539 MET cc_start: 0.7730 (mtp) cc_final: 0.7461 (mtp) REVERT: A 647 MET cc_start: 0.8375 (mmp) cc_final: 0.7252 (mmm) REVERT: A 948 MET cc_start: 0.7607 (tmm) cc_final: 0.7210 (ttt) REVERT: B 20 ILE cc_start: 0.9276 (mm) cc_final: 0.9041 (mt) REVERT: B 48 THR cc_start: 0.9118 (m) cc_final: 0.8672 (p) REVERT: B 66 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8114 (mm-30) REVERT: B 68 GLU cc_start: 0.7986 (mp0) cc_final: 0.7692 (mp0) REVERT: B 114 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8717 (m) REVERT: B 240 LEU cc_start: 0.8293 (mt) cc_final: 0.7680 (mp) REVERT: B 325 ILE cc_start: 0.9240 (mm) cc_final: 0.9022 (mm) REVERT: B 435 MET cc_start: 0.8046 (mmm) cc_final: 0.7685 (mmm) REVERT: B 479 LEU cc_start: 0.8999 (mp) cc_final: 0.8791 (mp) REVERT: B 638 LYS cc_start: 0.8974 (tmtt) cc_final: 0.8404 (tmtt) REVERT: B 695 MET cc_start: 0.9213 (mmm) cc_final: 0.8900 (mmm) REVERT: B 834 GLU cc_start: 0.8237 (tp30) cc_final: 0.7875 (tm-30) REVERT: B 857 GLU cc_start: 0.8571 (tt0) cc_final: 0.8242 (tt0) REVERT: B 864 MET cc_start: 0.8478 (tpp) cc_final: 0.8255 (tpp) REVERT: B 948 MET cc_start: 0.7838 (ttm) cc_final: 0.7305 (ttm) REVERT: B 952 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6367 (tp30) REVERT: B 1007 LEU cc_start: 0.9248 (tt) cc_final: 0.8991 (tt) REVERT: C 68 GLU cc_start: 0.8279 (mp0) cc_final: 0.7784 (mp0) REVERT: C 130 GLU cc_start: 0.8264 (pp20) cc_final: 0.7774 (pp20) REVERT: C 273 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8561 (tp40) REVERT: C 346 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: C 405 ILE cc_start: 0.9158 (mp) cc_final: 0.8942 (mp) REVERT: C 433 LYS cc_start: 0.8480 (tttt) cc_final: 0.8189 (tppt) REVERT: C 439 THR cc_start: 0.8818 (t) cc_final: 0.8517 (m) REVERT: C 474 MET cc_start: 0.8070 (mtm) cc_final: 0.7736 (mtm) REVERT: C 497 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7854 (mm) REVERT: C 565 ASP cc_start: 0.6857 (t0) cc_final: 0.6580 (m-30) REVERT: C 656 MET cc_start: 0.8388 (tpp) cc_final: 0.8115 (mmm) REVERT: C 723 ASP cc_start: 0.7471 (t0) cc_final: 0.7271 (t0) REVERT: C 770 SER cc_start: 0.9303 (m) cc_final: 0.8973 (t) REVERT: C 853 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8048 (mp) outliers start: 136 outliers final: 110 residues processed: 548 average time/residue: 0.1278 time to fit residues: 117.6727 Evaluate side-chains 540 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 425 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 436 LYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 772 MET Chi-restraints excluded: chain C residue 773 GLN Chi-restraints excluded: chain C residue 775 LYS Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1007 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 9 optimal weight: 5.9990 chunk 263 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN C 292 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.097740 restraints weight = 40853.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.100343 restraints weight = 21658.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102061 restraints weight = 13792.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103277 restraints weight = 9998.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103971 restraints weight = 7919.262| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23595 Z= 0.134 Angle : 0.626 11.555 32004 Z= 0.309 Chirality : 0.042 0.204 3848 Planarity : 0.004 0.056 4027 Dihedral : 3.940 19.214 3178 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.83 % Allowed : 24.42 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.16), residues: 3027 helix: 1.35 (0.13), residues: 1689 sheet: -1.20 (0.24), residues: 465 loop : -0.75 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.015 0.001 TYR A 524 PHE 0.022 0.001 PHE C 591 TRP 0.014 0.001 TRP B 556 HIS 0.007 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00310 (23595) covalent geometry : angle 0.62590 (32004) hydrogen bonds : bond 0.03770 ( 1490) hydrogen bonds : angle 4.60398 ( 4566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 467 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7894 (tptt) cc_final: 0.7667 (tptp) REVERT: A 165 GLU cc_start: 0.7602 (tp30) cc_final: 0.7394 (tp30) REVERT: A 364 TYR cc_start: 0.8159 (m-80) cc_final: 0.7787 (m-80) REVERT: A 383 MET cc_start: 0.8532 (ttm) cc_final: 0.8240 (mtt) REVERT: A 400 LEU cc_start: 0.9057 (mt) cc_final: 0.8850 (mt) REVERT: A 420 MET cc_start: 0.8226 (ptp) cc_final: 0.7926 (ptt) REVERT: A 477 SER cc_start: 0.8865 (t) cc_final: 0.8615 (m) REVERT: A 539 MET cc_start: 0.7882 (mtp) cc_final: 0.7513 (mtp) REVERT: A 647 MET cc_start: 0.8366 (mmp) cc_final: 0.7300 (mmm) REVERT: A 745 MET cc_start: 0.8325 (pmm) cc_final: 0.8112 (pmm) REVERT: A 948 MET cc_start: 0.7563 (tmm) cc_final: 0.7249 (ttt) REVERT: B 20 ILE cc_start: 0.9304 (mm) cc_final: 0.9048 (mt) REVERT: B 68 GLU cc_start: 0.7980 (mp0) cc_final: 0.7638 (mp0) REVERT: B 114 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8662 (m) REVERT: B 325 ILE cc_start: 0.9227 (mm) cc_final: 0.8980 (mm) REVERT: B 435 MET cc_start: 0.8082 (mmm) cc_final: 0.7782 (mmm) REVERT: B 479 LEU cc_start: 0.8992 (mp) cc_final: 0.8785 (mp) REVERT: B 553 MET cc_start: 0.8843 (mmm) cc_final: 0.8444 (mmt) REVERT: B 638 LYS cc_start: 0.8954 (tmtt) cc_final: 0.8400 (tmtt) REVERT: B 695 MET cc_start: 0.9185 (mmm) cc_final: 0.8887 (mmm) REVERT: B 710 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 857 GLU cc_start: 0.8519 (tt0) cc_final: 0.8097 (tp30) REVERT: B 864 MET cc_start: 0.8412 (tpp) cc_final: 0.8211 (tpp) REVERT: B 898 LEU cc_start: 0.8987 (mp) cc_final: 0.8771 (mt) REVERT: B 948 MET cc_start: 0.7811 (ttm) cc_final: 0.7306 (ttm) REVERT: B 952 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6317 (tp30) REVERT: B 1007 LEU cc_start: 0.9259 (tt) cc_final: 0.8880 (tt) REVERT: C 68 GLU cc_start: 0.8243 (mp0) cc_final: 0.7921 (mp0) REVERT: C 130 GLU cc_start: 0.8281 (pp20) cc_final: 0.7762 (pp20) REVERT: C 273 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: C 322 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: C 346 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: C 433 LYS cc_start: 0.8471 (tttt) cc_final: 0.8181 (tppt) REVERT: C 439 THR cc_start: 0.8739 (t) cc_final: 0.8412 (m) REVERT: C 472 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8645 (tp) REVERT: C 474 MET cc_start: 0.8093 (mtm) cc_final: 0.7809 (mtm) REVERT: C 497 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8029 (mm) REVERT: C 565 ASP cc_start: 0.6628 (t0) cc_final: 0.6295 (m-30) REVERT: C 761 GLN cc_start: 0.8472 (mt0) cc_final: 0.8219 (mt0) REVERT: C 770 SER cc_start: 0.9261 (m) cc_final: 0.8966 (t) REVERT: C 848 TYR cc_start: 0.8464 (p90) cc_final: 0.8026 (p90) REVERT: C 853 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7992 (mp) outliers start: 123 outliers final: 90 residues processed: 557 average time/residue: 0.1277 time to fit residues: 118.7428 Evaluate side-chains 519 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 422 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 772 MET Chi-restraints excluded: chain C residue 773 GLN Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1007 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 207 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 286 optimal weight: 0.6980 chunk 246 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 534 HIS C 211 ASN C 273 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.096206 restraints weight = 41436.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098799 restraints weight = 22007.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100545 restraints weight = 14040.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101744 restraints weight = 10159.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102414 restraints weight = 8052.557| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 23595 Z= 0.167 Angle : 0.652 13.231 32004 Z= 0.323 Chirality : 0.043 0.312 3848 Planarity : 0.004 0.053 4027 Dihedral : 4.011 27.783 3178 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.99 % Allowed : 24.66 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.48 (0.16), residues: 3027 helix: 1.37 (0.13), residues: 1680 sheet: -1.12 (0.24), residues: 466 loop : -0.78 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.022 0.001 TYR C 275 PHE 0.027 0.001 PHE C 4 TRP 0.019 0.001 TRP B 512 HIS 0.008 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00395 (23595) covalent geometry : angle 0.65157 (32004) hydrogen bonds : bond 0.03879 ( 1490) hydrogen bonds : angle 4.64481 ( 4566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 444 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 112 LYS cc_start: 0.7903 (tptt) cc_final: 0.7696 (tptp) REVERT: A 165 GLU cc_start: 0.7560 (tp30) cc_final: 0.7316 (tp30) REVERT: A 383 MET cc_start: 0.8584 (ttm) cc_final: 0.8232 (mtt) REVERT: A 400 LEU cc_start: 0.9109 (mt) cc_final: 0.8889 (mt) REVERT: A 477 SER cc_start: 0.8892 (t) cc_final: 0.8665 (m) REVERT: A 534 HIS cc_start: 0.6409 (OUTLIER) cc_final: 0.6139 (m90) REVERT: A 539 MET cc_start: 0.7873 (mtp) cc_final: 0.7671 (mtp) REVERT: A 647 MET cc_start: 0.8379 (mmp) cc_final: 0.7510 (mmm) REVERT: A 913 MET cc_start: 0.6940 (mmm) cc_final: 0.6485 (mmm) REVERT: A 948 MET cc_start: 0.7583 (tmm) cc_final: 0.7273 (ttt) REVERT: B 20 ILE cc_start: 0.9342 (mm) cc_final: 0.9093 (mt) REVERT: B 68 GLU cc_start: 0.7979 (mp0) cc_final: 0.7641 (mp0) REVERT: B 114 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8610 (m) REVERT: B 325 ILE cc_start: 0.9218 (mm) cc_final: 0.8982 (mm) REVERT: B 435 MET cc_start: 0.8159 (mmm) cc_final: 0.7897 (mmm) REVERT: B 553 MET cc_start: 0.8892 (mmm) cc_final: 0.8542 (mmt) REVERT: B 638 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8431 (tmtt) REVERT: B 695 MET cc_start: 0.9238 (mmm) cc_final: 0.8955 (mmm) REVERT: B 857 GLU cc_start: 0.8586 (tt0) cc_final: 0.8220 (tp30) REVERT: B 898 LEU cc_start: 0.9014 (mp) cc_final: 0.8759 (mt) REVERT: B 942 MET cc_start: 0.7966 (mtp) cc_final: 0.7686 (mtt) REVERT: B 948 MET cc_start: 0.7818 (ttm) cc_final: 0.7317 (ttm) REVERT: B 952 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6370 (tp30) REVERT: B 1007 LEU cc_start: 0.9265 (tt) cc_final: 0.8888 (tt) REVERT: B 1010 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7872 (m-10) REVERT: C 68 GLU cc_start: 0.8187 (mp0) cc_final: 0.7817 (mp0) REVERT: C 130 GLU cc_start: 0.8273 (pp20) cc_final: 0.7729 (pp20) REVERT: C 273 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: C 322 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6721 (mt-10) REVERT: C 346 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: C 433 LYS cc_start: 0.8536 (tttt) cc_final: 0.8243 (tppt) REVERT: C 439 THR cc_start: 0.8860 (t) cc_final: 0.8529 (m) REVERT: C 474 MET cc_start: 0.8105 (mtm) cc_final: 0.7815 (mtm) REVERT: C 497 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7959 (mm) REVERT: C 656 MET cc_start: 0.8295 (mmm) cc_final: 0.7867 (mmm) REVERT: C 761 GLN cc_start: 0.8543 (mt0) cc_final: 0.8270 (mt0) REVERT: C 770 SER cc_start: 0.9300 (m) cc_final: 0.8966 (t) REVERT: C 848 TYR cc_start: 0.8490 (p90) cc_final: 0.7993 (p90) REVERT: C 853 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8077 (mp) outliers start: 127 outliers final: 104 residues processed: 532 average time/residue: 0.1281 time to fit residues: 114.2015 Evaluate side-chains 530 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 418 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 PHE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 749 TYR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 772 MET Chi-restraints excluded: chain C residue 773 GLN Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1007 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 252 optimal weight: 0.3980 chunk 269 optimal weight: 0.9980 chunk 175 optimal weight: 0.1980 chunk 167 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.097779 restraints weight = 41183.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100404 restraints weight = 21760.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.102160 restraints weight = 13764.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103224 restraints weight = 9962.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104110 restraints weight = 8010.207| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 23595 Z= 0.136 Angle : 0.651 11.354 32004 Z= 0.320 Chirality : 0.043 0.351 3848 Planarity : 0.004 0.050 4027 Dihedral : 4.013 30.147 3178 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.36 % Allowed : 25.95 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.16), residues: 3027 helix: 1.42 (0.13), residues: 1679 sheet: -1.05 (0.24), residues: 458 loop : -0.75 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.019 0.001 TYR C 275 PHE 0.023 0.001 PHE C 591 TRP 0.017 0.001 TRP B 512 HIS 0.007 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00314 (23595) covalent geometry : angle 0.65146 (32004) hydrogen bonds : bond 0.03780 ( 1490) hydrogen bonds : angle 4.62420 ( 4566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 433 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 165 GLU cc_start: 0.7533 (tp30) cc_final: 0.7279 (tp30) REVERT: A 355 MET cc_start: 0.8438 (tpp) cc_final: 0.7861 (tpp) REVERT: A 383 MET cc_start: 0.8527 (ttm) cc_final: 0.8192 (mtt) REVERT: A 400 LEU cc_start: 0.9112 (mt) cc_final: 0.8902 (mt) REVERT: A 477 SER cc_start: 0.8873 (t) cc_final: 0.8649 (m) REVERT: A 539 MET cc_start: 0.7940 (mtp) cc_final: 0.7719 (mtp) REVERT: A 647 MET cc_start: 0.8366 (mmp) cc_final: 0.7595 (mmm) REVERT: A 745 MET cc_start: 0.8307 (pmm) cc_final: 0.8069 (pmm) REVERT: A 783 MET cc_start: 0.7399 (tpt) cc_final: 0.6932 (tpt) REVERT: A 913 MET cc_start: 0.6806 (mmm) cc_final: 0.6349 (mmm) REVERT: A 948 MET cc_start: 0.7536 (tmm) cc_final: 0.7235 (ttt) REVERT: B 20 ILE cc_start: 0.9371 (mm) cc_final: 0.9115 (mt) REVERT: B 68 GLU cc_start: 0.7871 (mp0) cc_final: 0.7129 (mm-30) REVERT: B 325 ILE cc_start: 0.9225 (mm) cc_final: 0.8982 (mm) REVERT: B 435 MET cc_start: 0.8124 (mmm) cc_final: 0.7892 (mmm) REVERT: B 553 MET cc_start: 0.8865 (mmm) cc_final: 0.8491 (mmt) REVERT: B 638 LYS cc_start: 0.8953 (tmtt) cc_final: 0.8411 (tmtt) REVERT: B 695 MET cc_start: 0.9206 (mmm) cc_final: 0.8910 (mmm) REVERT: B 857 GLU cc_start: 0.8526 (tt0) cc_final: 0.8129 (tp30) REVERT: B 864 MET cc_start: 0.8673 (tpp) cc_final: 0.8087 (tmm) REVERT: B 898 LEU cc_start: 0.9016 (mp) cc_final: 0.8760 (mt) REVERT: B 942 MET cc_start: 0.7999 (mtp) cc_final: 0.7654 (mtt) REVERT: B 948 MET cc_start: 0.7798 (ttm) cc_final: 0.7348 (ttm) REVERT: B 952 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6180 (tp30) REVERT: B 1007 LEU cc_start: 0.9231 (tt) cc_final: 0.8852 (tt) REVERT: C 130 GLU cc_start: 0.8254 (pp20) cc_final: 0.7749 (pp20) REVERT: C 273 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: C 346 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: C 433 LYS cc_start: 0.8501 (tttt) cc_final: 0.8211 (tppt) REVERT: C 439 THR cc_start: 0.8750 (t) cc_final: 0.8395 (m) REVERT: C 472 LEU cc_start: 0.8922 (tt) cc_final: 0.8541 (tp) REVERT: C 474 MET cc_start: 0.8063 (mtm) cc_final: 0.7751 (mtm) REVERT: C 497 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7912 (mm) REVERT: C 761 GLN cc_start: 0.8493 (mt0) cc_final: 0.7918 (mt0) REVERT: C 770 SER cc_start: 0.9268 (m) cc_final: 0.8961 (t) REVERT: C 848 TYR cc_start: 0.8446 (p90) cc_final: 0.7990 (p90) REVERT: C 853 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8019 (mp) REVERT: C 1018 PHE cc_start: 0.8292 (t80) cc_final: 0.8049 (t80) outliers start: 111 outliers final: 94 residues processed: 510 average time/residue: 0.1264 time to fit residues: 108.5998 Evaluate side-chains 517 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 419 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 749 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 969 SER Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 TRP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 749 TYR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 772 MET Chi-restraints excluded: chain C residue 773 GLN Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 885 SER Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1007 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.097325 restraints weight = 41095.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.099886 restraints weight = 21875.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101653 restraints weight = 13961.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102793 restraints weight = 10097.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103627 restraints weight = 8032.901| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 23595 Z= 0.149 Angle : 0.657 11.655 32004 Z= 0.324 Chirality : 0.043 0.359 3848 Planarity : 0.004 0.047 4027 Dihedral : 4.013 30.130 3178 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.52 % Allowed : 25.95 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 3027 helix: 1.46 (0.13), residues: 1670 sheet: -1.03 (0.24), residues: 458 loop : -0.73 (0.22), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.022 0.001 TYR C 275 PHE 0.024 0.001 PHE C 591 TRP 0.015 0.001 TRP B 556 HIS 0.007 0.001 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00356 (23595) covalent geometry : angle 0.65702 (32004) hydrogen bonds : bond 0.03788 ( 1490) hydrogen bonds : angle 4.64157 ( 4566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3642.06 seconds wall clock time: 63 minutes 53.61 seconds (3833.61 seconds total)