Starting phenix.real_space_refine on Sat Aug 8 20:57:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jje_61524/08_2026/9jje_61524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jje_61524/08_2026/9jje_61524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jje_61524/08_2026/9jje_61524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jje_61524/08_2026/9jje_61524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jje_61524/08_2026/9jje_61524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jje_61524/08_2026/9jje_61524.map" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 12 5.49 5 S 164 5.16 5 C 19748 2.51 5 N 5000 2.21 5 O 5544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30472 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7549 Classifications: {'peptide': 941} Link IDs: {'PTRANS': 35, 'TRANS': 905} Chain breaks: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {' CA': 1, 'A2R': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 9.59, per 1000 atoms: 0.31 Number of scatterers: 30472 At special positions: 0 Unit cell: (129.47, 129.47, 145.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 164 16.00 P 12 15.00 O 5544 8.00 N 5000 7.00 C 19748 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A1017 " " NAG F 1 " - " ASN B1017 " " NAG G 1 " - " ASN C1017 " " NAG H 1 " - " ASN D1017 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7096 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 4 sheets defined 70.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.984A pdb=" N VAL A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 171 Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.659A pdb=" N LEU A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 281 removed outlier: 3.781A pdb=" N ILE A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 374 through 386 removed outlier: 4.348A pdb=" N THR A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.640A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.539A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 4.712A pdb=" N ALA A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.598A pdb=" N VAL A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.565A pdb=" N TYR A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 545' Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'A' and resid 605 through 627 Processing helix chain 'A' and resid 633 through 657 Processing helix chain 'A' and resid 659 through 667 removed outlier: 3.600A pdb=" N SER A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 675 removed outlier: 3.889A pdb=" N SER A 675 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 694 through 706 Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.738A pdb=" N TYR A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 727 through 732 removed outlier: 4.070A pdb=" N ILE A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'A' and resid 836 through 861 Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 876 through 899 Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 915 through 934 removed outlier: 3.816A pdb=" N PHE A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 938 removed outlier: 4.595A pdb=" N THR A 938 " --> pdb=" O ARG A 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 935 through 938' Processing helix chain 'A' and resid 939 through 962 removed outlier: 4.933A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 970 through 1008 removed outlier: 3.948A pdb=" N LYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1034 Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1039 through 1044 Processing helix chain 'A' and resid 1057 through 1073 removed outlier: 3.690A pdb=" N LEU A1061 " --> pdb=" O ASP A1057 " (cutoff:3.500A) Proline residue: A1063 - end of helix Processing helix chain 'A' and resid 1076 through 1094 Processing helix chain 'A' and resid 1095 through 1113 removed outlier: 3.878A pdb=" N TYR A1105 " --> pdb=" O LYS A1101 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A1113 " --> pdb=" O GLN A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1131 Processing helix chain 'A' and resid 1154 through 1182 Processing helix chain 'A' and resid 1183 through 1206 Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.985A pdb=" N VAL B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 171 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.659A pdb=" N LEU B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 281 removed outlier: 3.781A pdb=" N ILE B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 374 through 386 removed outlier: 4.349A pdb=" N THR B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 386 " --> pdb=" O ILE B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.640A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.539A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.711A pdb=" N ALA B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 474 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 500 through 513 Processing helix chain 'B' and resid 518 through 531 removed outlier: 3.598A pdb=" N VAL B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 removed outlier: 3.565A pdb=" N TYR B 544 " --> pdb=" O ASP B 541 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 545 " --> pdb=" O GLY B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 545' Processing helix chain 'B' and resid 578 through 590 Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'B' and resid 605 through 627 Processing helix chain 'B' and resid 633 through 657 Processing helix chain 'B' and resid 659 through 667 removed outlier: 3.600A pdb=" N SER B 663 " --> pdb=" O ASN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 675 removed outlier: 3.889A pdb=" N SER B 675 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 686 Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 694 through 706 Processing helix chain 'B' and resid 714 through 723 removed outlier: 3.738A pdb=" N TYR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 727 through 732 removed outlier: 4.070A pdb=" N ILE B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 Processing helix chain 'B' and resid 836 through 861 Processing helix chain 'B' and resid 870 through 875 Processing helix chain 'B' and resid 876 through 899 Processing helix chain 'B' and resid 904 through 913 Processing helix chain 'B' and resid 915 through 934 removed outlier: 3.816A pdb=" N PHE B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 938 removed outlier: 4.595A pdb=" N THR B 938 " --> pdb=" O ARG B 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 935 through 938' Processing helix chain 'B' and resid 939 through 962 removed outlier: 4.933A pdb=" N ILE B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 968 Processing helix chain 'B' and resid 970 through 1008 removed outlier: 3.948A pdb=" N LYS B 974 " --> pdb=" O LEU B 970 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 990 " --> pdb=" O ALA B 986 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1034 Proline residue: B1030 - end of helix Processing helix chain 'B' and resid 1039 through 1044 Processing helix chain 'B' and resid 1057 through 1073 removed outlier: 3.690A pdb=" N LEU B1061 " --> pdb=" O ASP B1057 " (cutoff:3.500A) Proline residue: B1063 - end of helix Processing helix chain 'B' and resid 1076 through 1094 Processing helix chain 'B' and resid 1095 through 1113 removed outlier: 3.878A pdb=" N TYR B1105 " --> pdb=" O LYS B1101 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B1106 " --> pdb=" O PHE B1102 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER B1113 " --> pdb=" O GLN B1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1131 Processing helix chain 'B' and resid 1154 through 1182 Processing helix chain 'B' and resid 1183 through 1206 Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.984A pdb=" N VAL C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 171 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.658A pdb=" N LEU C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 281 removed outlier: 3.781A pdb=" N ILE C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 330 through 339 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'C' and resid 374 through 386 removed outlier: 4.349A pdb=" N THR C 378 " --> pdb=" O GLY C 374 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 386 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 417 removed outlier: 3.640A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.539A pdb=" N ALA C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 463 removed outlier: 4.711A pdb=" N ALA C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 474 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 500 through 513 Processing helix chain 'C' and resid 518 through 531 removed outlier: 3.598A pdb=" N VAL C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 545 removed outlier: 3.565A pdb=" N TYR C 544 " --> pdb=" O ASP C 541 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 545 " --> pdb=" O GLY C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 545' Processing helix chain 'C' and resid 578 through 590 Processing helix chain 'C' and resid 592 through 603 Processing helix chain 'C' and resid 605 through 627 Processing helix chain 'C' and resid 633 through 657 Processing helix chain 'C' and resid 659 through 667 removed outlier: 3.600A pdb=" N SER C 663 " --> pdb=" O ASN C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 675 removed outlier: 3.888A pdb=" N SER C 675 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 686 Processing helix chain 'C' and resid 688 through 693 Processing helix chain 'C' and resid 694 through 706 Processing helix chain 'C' and resid 714 through 723 removed outlier: 3.738A pdb=" N TYR C 723 " --> pdb=" O LEU C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 727 through 732 removed outlier: 4.070A pdb=" N ILE C 731 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 835 Processing helix chain 'C' and resid 836 through 861 Processing helix chain 'C' and resid 870 through 875 Processing helix chain 'C' and resid 876 through 899 Processing helix chain 'C' and resid 904 through 913 Processing helix chain 'C' and resid 915 through 934 removed outlier: 3.816A pdb=" N PHE C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 938 removed outlier: 4.596A pdb=" N THR C 938 " --> pdb=" O ARG C 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 935 through 938' Processing helix chain 'C' and resid 939 through 962 removed outlier: 4.932A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 968 Processing helix chain 'C' and resid 970 through 1008 removed outlier: 3.948A pdb=" N LYS C 974 " --> pdb=" O LEU C 970 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1034 Proline residue: C1030 - end of helix Processing helix chain 'C' and resid 1039 through 1044 Processing helix chain 'C' and resid 1057 through 1073 removed outlier: 3.690A pdb=" N LEU C1061 " --> pdb=" O ASP C1057 " (cutoff:3.500A) Proline residue: C1063 - end of helix Processing helix chain 'C' and resid 1076 through 1094 Processing helix chain 'C' and resid 1095 through 1113 removed outlier: 3.879A pdb=" N TYR C1105 " --> pdb=" O LYS C1101 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C1106 " --> pdb=" O PHE C1102 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C1113 " --> pdb=" O GLN C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1131 Processing helix chain 'C' and resid 1154 through 1182 Processing helix chain 'C' and resid 1183 through 1206 Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.984A pdb=" N VAL D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 171 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.659A pdb=" N LEU D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 281 removed outlier: 3.781A pdb=" N ILE D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 330 through 339 Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'D' and resid 374 through 386 removed outlier: 4.348A pdb=" N THR D 378 " --> pdb=" O GLY D 374 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 386 " --> pdb=" O ILE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 removed outlier: 3.640A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.538A pdb=" N ALA D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 removed outlier: 4.712A pdb=" N ALA D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 474 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 500 through 513 Processing helix chain 'D' and resid 518 through 531 removed outlier: 3.598A pdb=" N VAL D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 545 removed outlier: 3.565A pdb=" N TYR D 544 " --> pdb=" O ASP D 541 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 545 " --> pdb=" O GLY D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 545' Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 592 through 603 Processing helix chain 'D' and resid 605 through 627 Processing helix chain 'D' and resid 633 through 657 Processing helix chain 'D' and resid 659 through 667 removed outlier: 3.600A pdb=" N SER D 663 " --> pdb=" O ASN D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 675 removed outlier: 3.889A pdb=" N SER D 675 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 686 Processing helix chain 'D' and resid 688 through 693 Processing helix chain 'D' and resid 694 through 706 Processing helix chain 'D' and resid 714 through 723 removed outlier: 3.738A pdb=" N TYR D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'D' and resid 727 through 732 removed outlier: 4.070A pdb=" N ILE D 731 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 835 Processing helix chain 'D' and resid 836 through 861 Processing helix chain 'D' and resid 870 through 875 Processing helix chain 'D' and resid 876 through 899 Processing helix chain 'D' and resid 904 through 913 Processing helix chain 'D' and resid 915 through 934 removed outlier: 3.816A pdb=" N PHE D 919 " --> pdb=" O ASP D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 935 through 938 removed outlier: 4.595A pdb=" N THR D 938 " --> pdb=" O ARG D 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 935 through 938' Processing helix chain 'D' and resid 939 through 962 removed outlier: 4.934A pdb=" N ILE D 955 " --> pdb=" O SER D 951 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE D 956 " --> pdb=" O LEU D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 968 Processing helix chain 'D' and resid 970 through 1008 removed outlier: 3.947A pdb=" N LYS D 974 " --> pdb=" O LEU D 970 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE D 990 " --> pdb=" O ALA D 986 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1034 Proline residue: D1030 - end of helix Processing helix chain 'D' and resid 1039 through 1044 Processing helix chain 'D' and resid 1057 through 1073 removed outlier: 3.690A pdb=" N LEU D1061 " --> pdb=" O ASP D1057 " (cutoff:3.500A) Proline residue: D1063 - end of helix Processing helix chain 'D' and resid 1076 through 1094 Processing helix chain 'D' and resid 1095 through 1113 removed outlier: 3.879A pdb=" N TYR D1105 " --> pdb=" O LYS D1101 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP D1106 " --> pdb=" O PHE D1102 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER D1113 " --> pdb=" O GLN D1109 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1131 Processing helix chain 'D' and resid 1154 through 1182 Processing helix chain 'D' and resid 1183 through 1206 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 7.822A pdb=" N LEU A 255 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A 112 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 206 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE A 254 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY A 208 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 256 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 210 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 209 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 176 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR A 211 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 140 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A 139 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU A 299 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER A 141 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL A 322 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 298 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 324 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 300 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 95 through 98 removed outlier: 7.822A pdb=" N LEU B 255 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B 112 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 206 " --> pdb=" O HIS B 252 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE B 254 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 208 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL B 256 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 210 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE B 174 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE B 209 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR B 176 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N THR B 211 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 140 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 139 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 299 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER B 141 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL B 322 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 298 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE B 324 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 300 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 95 through 98 removed outlier: 7.822A pdb=" N LEU C 255 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 112 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 206 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE C 254 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY C 208 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL C 256 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 210 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE C 174 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE C 209 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR C 176 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N THR C 211 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 140 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 139 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU C 299 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER C 141 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL C 322 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU C 298 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE C 324 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL C 300 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 95 through 98 removed outlier: 7.822A pdb=" N LEU D 255 " --> pdb=" O PRO D 110 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU D 112 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D 206 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE D 254 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY D 208 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL D 256 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA D 210 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE D 174 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE D 209 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR D 176 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR D 211 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 140 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL D 139 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU D 299 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER D 141 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL D 322 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU D 298 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE D 324 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL D 300 " --> pdb=" O ILE D 324 " (cutoff:3.500A) 1816 hydrogen bonds defined for protein. 5352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8496 1.34 - 1.46: 5363 1.46 - 1.57: 16953 1.57 - 1.69: 24 1.69 - 1.81: 308 Bond restraints: 31144 Sorted by residual: bond pdb="C12' A2R A4001 " pdb="C13' A2R A4001 " ideal model delta sigma weight residual 1.524 1.308 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb="C12' A2R D4001 " pdb="C13' A2R D4001 " ideal model delta sigma weight residual 1.524 1.308 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb="C12' A2R B4001 " pdb="C13' A2R B4001 " ideal model delta sigma weight residual 1.524 1.308 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb="C12' A2R C4001 " pdb="C13' A2R C4001 " ideal model delta sigma weight residual 1.524 1.308 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2 A2R A4001 " pdb=" N3 A2R A4001 " ideal model delta sigma weight residual 1.321 1.475 -0.154 2.00e-02 2.50e+03 5.94e+01 ... (remaining 31139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 41241 2.60 - 5.19: 824 5.19 - 7.79: 123 7.79 - 10.39: 40 10.39 - 12.99: 20 Bond angle restraints: 42248 Sorted by residual: angle pdb=" N ILE C1129 " pdb=" CA ILE C1129 " pdb=" C ILE C1129 " ideal model delta sigma weight residual 111.58 106.61 4.97 1.06e+00 8.90e-01 2.20e+01 angle pdb=" N ILE B1129 " pdb=" CA ILE B1129 " pdb=" C ILE B1129 " ideal model delta sigma weight residual 111.58 106.65 4.93 1.06e+00 8.90e-01 2.16e+01 angle pdb=" N ILE A1129 " pdb=" CA ILE A1129 " pdb=" C ILE A1129 " ideal model delta sigma weight residual 111.58 106.65 4.93 1.06e+00 8.90e-01 2.16e+01 angle pdb=" N ILE D1129 " pdb=" CA ILE D1129 " pdb=" C ILE D1129 " ideal model delta sigma weight residual 111.58 106.65 4.93 1.06e+00 8.90e-01 2.16e+01 angle pdb=" O11 A2R A4001 " pdb=" P1 A2R A4001 " pdb=" O12 A2R A4001 " ideal model delta sigma weight residual 122.43 109.44 12.99 3.00e+00 1.11e-01 1.87e+01 ... (remaining 42243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 17550 15.08 - 30.16: 838 30.16 - 45.24: 236 45.24 - 60.32: 92 60.32 - 75.41: 68 Dihedral angle restraints: 18784 sinusoidal: 7808 harmonic: 10976 Sorted by residual: dihedral pdb=" CA ARG B 935 " pdb=" C ARG B 935 " pdb=" N PHE B 936 " pdb=" CA PHE B 936 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ARG A 935 " pdb=" C ARG A 935 " pdb=" N PHE A 936 " pdb=" CA PHE A 936 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ARG D 935 " pdb=" C ARG D 935 " pdb=" N PHE D 936 " pdb=" CA PHE D 936 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 18781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4623 0.117 - 0.235: 209 0.235 - 0.352: 4 0.352 - 0.469: 0 0.469 - 0.586: 4 Chirality restraints: 4840 Sorted by residual: chirality pdb=" C2' A2R D4001 " pdb=" C1' A2R D4001 " pdb=" C3' A2R D4001 " pdb=" O2' A2R D4001 " both_signs ideal model delta sigma weight residual False -2.42 -3.01 0.59 2.00e-01 2.50e+01 8.59e+00 chirality pdb=" C2' A2R B4001 " pdb=" C1' A2R B4001 " pdb=" C3' A2R B4001 " pdb=" O2' A2R B4001 " both_signs ideal model delta sigma weight residual False -2.42 -3.01 0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" C2' A2R A4001 " pdb=" C1' A2R A4001 " pdb=" C3' A2R A4001 " pdb=" O2' A2R A4001 " both_signs ideal model delta sigma weight residual False -2.42 -3.01 0.58 2.00e-01 2.50e+01 8.53e+00 ... (remaining 4837 not shown) Planarity restraints: 5276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1010 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO A1011 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO A1011 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1011 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B1010 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO B1011 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO B1011 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1011 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D1010 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO D1011 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO D1011 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D1011 " -0.062 5.00e-02 4.00e+02 ... (remaining 5273 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 7703 2.80 - 3.32: 29156 3.32 - 3.85: 52779 3.85 - 4.37: 63023 4.37 - 4.90: 104782 Nonbonded interactions: 257443 Sorted by model distance: nonbonded pdb=" O ILE D 958 " pdb=" OG SER D 961 " model vdw 2.273 3.040 nonbonded pdb=" O ILE A 958 " pdb=" OG SER A 961 " model vdw 2.273 3.040 nonbonded pdb=" O ILE B 958 " pdb=" OG SER B 961 " model vdw 2.273 3.040 nonbonded pdb=" O ILE C 958 " pdb=" OG SER C 961 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 484 " pdb=" OD1 ASP A 486 " model vdw 2.299 3.040 ... (remaining 257438 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.540 Find NCS groups from input model: 0.260 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:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 0.007 0.216 31152 Z= 0.364 Angle : 0.979 12.987 42272 Z= 0.506 Chirality : 0.057 0.586 4840 Planarity : 0.008 0.108 5272 Dihedral : 11.838 75.405 11688 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.45 (0.11), residues: 3716 helix: -2.04 (0.08), residues: 2424 sheet: -1.69 (0.28), residues: 232 loop : -2.54 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 592 TYR 0.031 0.003 TYR B 638 PHE 0.026 0.002 PHE C 957 TRP 0.020 0.002 TRP D 431 HIS 0.008 0.002 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.36 (31144) covalent geometry : angle 0.97807 / 0.51 (42248) hydrogen bonds : bond 0.12322 / 8.25 ( 1816) hydrogen bonds : angle 6.66157 / 4.62 ( 5352) link_BETA1-4 : bond 0.00115 / 0.05 ( 4) link_BETA1-4 : angle 2.20850 / 1.32 ( 12) link_NAG-ASN : bond 0.00029 / 0.01 ( 4) link_NAG-ASN : angle 1.78686 / 1.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 664 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.5828 (tpp) cc_final: 0.5237 (pmt) REVERT: A 714 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7583 (mmm160) REVERT: A 724 LEU cc_start: 0.7972 (mt) cc_final: 0.7677 (mm) REVERT: A 733 TYR cc_start: 0.7292 (m-10) cc_final: 0.6999 (m-10) REVERT: A 892 GLU cc_start: 0.7739 (tp30) cc_final: 0.7211 (tt0) REVERT: A 980 LYS cc_start: 0.8497 (mttm) cc_final: 0.8233 (mttp) REVERT: A 1007 MET cc_start: 0.8811 (mtm) cc_final: 0.8611 (mtm) REVERT: B 114 MET cc_start: 0.5891 (tpp) cc_final: 0.5262 (pmt) REVERT: B 714 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7597 (mmm160) REVERT: B 724 LEU cc_start: 0.7952 (mt) cc_final: 0.7670 (mm) REVERT: B 733 TYR cc_start: 0.7302 (m-10) cc_final: 0.7016 (m-10) REVERT: B 735 VAL cc_start: 0.8161 (m) cc_final: 0.7945 (t) REVERT: B 893 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7464 (mm-30) REVERT: B 980 LYS cc_start: 0.8502 (mttm) cc_final: 0.8257 (mttp) REVERT: B 1007 MET cc_start: 0.8819 (mtm) cc_final: 0.8590 (mtm) REVERT: C 114 MET cc_start: 0.5880 (tpp) cc_final: 0.5279 (pmt) REVERT: C 714 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7587 (mmm160) REVERT: C 724 LEU cc_start: 0.7952 (mt) cc_final: 0.7656 (mm) REVERT: C 733 TYR cc_start: 0.7293 (m-10) cc_final: 0.6999 (m-10) REVERT: C 892 GLU cc_start: 0.7708 (tp30) cc_final: 0.7178 (tt0) REVERT: C 980 LYS cc_start: 0.8495 (mttm) cc_final: 0.8234 (mttp) REVERT: D 114 MET cc_start: 0.5899 (tpp) cc_final: 0.5267 (pmt) REVERT: D 714 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7590 (mmm160) REVERT: D 724 LEU cc_start: 0.7945 (mt) cc_final: 0.7649 (mm) REVERT: D 733 TYR cc_start: 0.7295 (m-10) cc_final: 0.7006 (m-10) REVERT: D 893 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7571 (mm-30) REVERT: D 980 LYS cc_start: 0.8498 (mttm) cc_final: 0.8248 (mttp) REVERT: D 1007 MET cc_start: 0.8800 (mtm) cc_final: 0.8578 (mtm) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.7569 time to fit residues: 582.9698 Evaluate side-chains 440 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 GLN A 432 ASN A 968 ASN A1074 ASN A1103 GLN A1175 GLN B 403 GLN B 432 ASN B 832 HIS B 968 ASN B1074 ASN B1103 GLN B1175 GLN C 403 GLN C 432 ASN C 832 HIS C 968 ASN C1074 ASN C1103 GLN C1175 GLN D 403 GLN D 432 ASN D 832 HIS D 968 ASN D1074 ASN D1103 GLN D1175 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.221526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135529 restraints weight = 27901.714| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.18 r_work: 0.3186 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31152 Z= 0.172 Angle : 0.633 9.994 42272 Z= 0.326 Chirality : 0.044 0.151 4840 Planarity : 0.006 0.081 5272 Dihedral : 8.416 57.452 4472 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.14 % Allowed : 9.99 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 3716 helix: -0.17 (0.10), residues: 2452 sheet: -1.37 (0.32), residues: 200 loop : -2.05 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1016 TYR 0.023 0.002 TYR B 855 PHE 0.014 0.002 PHE C 838 TRP 0.016 0.002 TRP D1100 HIS 0.004 0.001 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (31144) covalent geometry : angle 0.63276 / 0.33 (42248) hydrogen bonds : bond 0.04629 / 3.10 ( 1816) hydrogen bonds : angle 4.73612 / 3.28 ( 5352) link_BETA1-4 : bond 0.00256 / 0.09 ( 4) link_BETA1-4 : angle 1.41867 / 0.84 ( 12) link_NAG-ASN : bond 0.00241 / 0.11 ( 4) link_NAG-ASN : angle 0.99427 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 448 time to evaluate : 0.998 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 114 MET cc_start: 0.7031 (tpp) cc_final: 0.5470 (pmt) REVERT: A 411 LYS cc_start: 0.7612 (mtmt) cc_final: 0.7140 (mttm) REVERT: A 471 LEU cc_start: 0.7626 (tp) cc_final: 0.7309 (tp) REVERT: A 507 LYS cc_start: 0.7905 (tttm) cc_final: 0.7683 (tttm) REVERT: A 528 GLU cc_start: 0.7723 (pt0) cc_final: 0.7213 (mm-30) REVERT: A 664 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7567 (mp-120) REVERT: A 665 THR cc_start: 0.8442 (p) cc_final: 0.8207 (t) REVERT: A 733 TYR cc_start: 0.7814 (m-10) cc_final: 0.7342 (m-10) REVERT: A 893 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 1157 GLU cc_start: 0.6914 (tp30) cc_final: 0.6353 (mp0) REVERT: A 1194 ARG cc_start: 0.6800 (mmm160) cc_final: 0.6319 (mmp-170) REVERT: B 114 MET cc_start: 0.7043 (tpp) cc_final: 0.5469 (pmt) REVERT: B 411 LYS cc_start: 0.7526 (mtmt) cc_final: 0.7073 (mttm) REVERT: B 508 GLU cc_start: 0.6524 (tp30) cc_final: 0.6159 (tp30) REVERT: B 528 GLU cc_start: 0.7713 (pt0) cc_final: 0.7250 (mm-30) REVERT: B 645 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: B 664 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7702 (mp-120) REVERT: B 665 THR cc_start: 0.8449 (p) cc_final: 0.8234 (t) REVERT: B 706 MET cc_start: 0.8758 (mmm) cc_final: 0.8506 (mmm) REVERT: B 733 TYR cc_start: 0.7735 (m-10) cc_final: 0.7266 (m-10) REVERT: B 735 VAL cc_start: 0.8101 (m) cc_final: 0.7732 (t) REVERT: B 893 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7743 (mm-30) REVERT: B 1193 ASP cc_start: 0.7304 (m-30) cc_final: 0.7086 (m-30) REVERT: C 114 MET cc_start: 0.7043 (tpp) cc_final: 0.5477 (pmt) REVERT: C 411 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7045 (mttm) REVERT: C 507 LYS cc_start: 0.7906 (tttm) cc_final: 0.7680 (tttm) REVERT: C 528 GLU cc_start: 0.7702 (pt0) cc_final: 0.7226 (mm-30) REVERT: C 664 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7723 (mp-120) REVERT: C 665 THR cc_start: 0.8459 (p) cc_final: 0.8233 (t) REVERT: C 709 MET cc_start: 0.7774 (ttp) cc_final: 0.7480 (ttp) REVERT: C 733 TYR cc_start: 0.7728 (m-10) cc_final: 0.7246 (m-10) REVERT: C 893 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8021 (mm-30) REVERT: C 1158 MET cc_start: 0.7063 (mtp) cc_final: 0.6845 (mtm) REVERT: C 1193 ASP cc_start: 0.7216 (m-30) cc_final: 0.6994 (m-30) REVERT: C 1194 ARG cc_start: 0.6843 (mmm160) cc_final: 0.6372 (mmp-170) REVERT: D 114 MET cc_start: 0.7036 (tpp) cc_final: 0.5466 (pmt) REVERT: D 411 LYS cc_start: 0.7458 (mtmt) cc_final: 0.7013 (mttm) REVERT: D 528 GLU cc_start: 0.7707 (pt0) cc_final: 0.7227 (mm-30) REVERT: D 664 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7626 (mp-120) REVERT: D 665 THR cc_start: 0.8465 (p) cc_final: 0.8240 (t) REVERT: D 709 MET cc_start: 0.7783 (ttp) cc_final: 0.7491 (ttp) REVERT: D 733 TYR cc_start: 0.7713 (m-10) cc_final: 0.7226 (m-10) REVERT: D 893 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8018 (mm-30) REVERT: D 1158 MET cc_start: 0.7103 (mtp) cc_final: 0.6898 (mtm) REVERT: D 1193 ASP cc_start: 0.7320 (m-30) cc_final: 0.7098 (m-30) REVERT: D 1194 ARG cc_start: 0.6834 (mmm160) cc_final: 0.6365 (mmp-170) outliers start: 70 outliers final: 18 residues processed: 477 average time/residue: 0.7043 time to fit residues: 391.7538 Evaluate side-chains 416 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 393 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1097 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1097 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 223 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 217 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN B 432 ASN B 832 HIS C 432 ASN D 432 ASN D 832 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.218780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128843 restraints weight = 27679.603| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.81 r_work: 0.3197 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31152 Z= 0.178 Angle : 0.617 9.676 42272 Z= 0.315 Chirality : 0.044 0.163 4840 Planarity : 0.005 0.079 5272 Dihedral : 6.828 57.280 4472 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.11 % Allowed : 11.28 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 3716 helix: 0.52 (0.10), residues: 2468 sheet: -1.09 (0.33), residues: 200 loop : -1.84 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1187 TYR 0.023 0.002 TYR D 855 PHE 0.012 0.002 PHE D 956 TRP 0.015 0.002 TRP A1100 HIS 0.005 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (31144) covalent geometry : angle 0.61588 / 0.32 (42248) hydrogen bonds : bond 0.04560 / 3.06 ( 1816) hydrogen bonds : angle 4.45349 / 3.08 ( 5352) link_BETA1-4 : bond 0.00124 / 0.06 ( 4) link_BETA1-4 : angle 1.50399 / 0.87 ( 12) link_NAG-ASN : bond 0.00073 / 0.03 ( 4) link_NAG-ASN : angle 1.13041 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 391 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7031 (tpp) cc_final: 0.5183 (pmt) REVERT: A 270 MET cc_start: 0.3317 (mmp) cc_final: 0.2804 (mtp) REVERT: A 426 ASN cc_start: 0.6629 (p0) cc_final: 0.6398 (m-40) REVERT: A 539 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7697 (mmm160) REVERT: A 664 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7742 (mp-120) REVERT: A 733 TYR cc_start: 0.7661 (m-10) cc_final: 0.7199 (m-10) REVERT: A 848 TYR cc_start: 0.7913 (t80) cc_final: 0.7672 (t80) REVERT: A 1157 GLU cc_start: 0.6978 (tp30) cc_final: 0.6435 (mp0) REVERT: A 1194 ARG cc_start: 0.6837 (mmm160) cc_final: 0.6334 (mmp-170) REVERT: B 114 MET cc_start: 0.7049 (tpp) cc_final: 0.5173 (pmt) REVERT: B 270 MET cc_start: 0.3237 (mmp) cc_final: 0.2813 (mtt) REVERT: B 426 ASN cc_start: 0.6662 (p0) cc_final: 0.6429 (m-40) REVERT: B 508 GLU cc_start: 0.6800 (tp30) cc_final: 0.6273 (tp30) REVERT: B 539 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7668 (mmm160) REVERT: B 664 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7667 (mp-120) REVERT: B 709 MET cc_start: 0.7816 (ttp) cc_final: 0.7528 (ttp) REVERT: B 733 TYR cc_start: 0.7731 (m-10) cc_final: 0.7247 (m-10) REVERT: B 735 VAL cc_start: 0.8107 (m) cc_final: 0.7731 (t) REVERT: B 848 TYR cc_start: 0.7930 (t80) cc_final: 0.7684 (t80) REVERT: B 1157 GLU cc_start: 0.6988 (tp30) cc_final: 0.6450 (mp0) REVERT: B 1193 ASP cc_start: 0.7230 (m-30) cc_final: 0.7007 (m-30) REVERT: C 114 MET cc_start: 0.7042 (tpp) cc_final: 0.5172 (pmt) REVERT: C 270 MET cc_start: 0.3175 (mmp) cc_final: 0.2769 (mtt) REVERT: C 539 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7705 (mmm160) REVERT: C 664 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7655 (mp-120) REVERT: C 733 TYR cc_start: 0.7660 (m-10) cc_final: 0.7194 (m-10) REVERT: C 848 TYR cc_start: 0.7925 (t80) cc_final: 0.7678 (t80) REVERT: C 1044 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: C 1157 GLU cc_start: 0.6974 (tp30) cc_final: 0.6447 (mp0) REVERT: C 1158 MET cc_start: 0.7345 (mtp) cc_final: 0.7124 (mtm) REVERT: C 1193 ASP cc_start: 0.7166 (m-30) cc_final: 0.6958 (m-30) REVERT: D 114 MET cc_start: 0.7041 (tpp) cc_final: 0.5179 (pmt) REVERT: D 270 MET cc_start: 0.3230 (mmp) cc_final: 0.2813 (mtp) REVERT: D 426 ASN cc_start: 0.6668 (p0) cc_final: 0.6435 (m-40) REVERT: D 539 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7704 (mmm160) REVERT: D 664 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7671 (mp-120) REVERT: D 733 TYR cc_start: 0.7637 (m-10) cc_final: 0.7160 (m-10) REVERT: D 848 TYR cc_start: 0.7882 (t80) cc_final: 0.7637 (t80) REVERT: D 1193 ASP cc_start: 0.7212 (m-30) cc_final: 0.6987 (m-30) outliers start: 69 outliers final: 21 residues processed: 422 average time/residue: 0.7616 time to fit residues: 373.5043 Evaluate side-chains 396 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 366 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1044 GLN Chi-restraints excluded: chain C residue 1097 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 297 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 284 optimal weight: 30.0000 chunk 287 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 GLN A 432 ASN A 979 GLN B 403 GLN B 432 ASN C 403 GLN C 426 ASN C 432 ASN C 979 GLN D 403 GLN D 432 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.217472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127603 restraints weight = 27531.326| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.88 r_work: 0.3163 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31152 Z= 0.194 Angle : 0.615 9.357 42272 Z= 0.314 Chirality : 0.045 0.166 4840 Planarity : 0.005 0.070 5272 Dihedral : 6.364 58.768 4472 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.41 % Allowed : 12.22 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3716 helix: 0.78 (0.10), residues: 2480 sheet: -1.03 (0.34), residues: 200 loop : -1.70 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1016 TYR 0.022 0.002 TYR B 855 PHE 0.014 0.002 PHE B 956 TRP 0.016 0.002 TRP A 716 HIS 0.005 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (31144) covalent geometry : angle 0.61453 / 0.31 (42248) hydrogen bonds : bond 0.04596 / 3.09 ( 1816) hydrogen bonds : angle 4.36879 / 3.01 ( 5352) link_BETA1-4 : bond 0.00181 / 0.08 ( 4) link_BETA1-4 : angle 1.54928 / 0.90 ( 12) link_NAG-ASN : bond 0.00179 / 0.08 ( 4) link_NAG-ASN : angle 1.24446 / 0.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 394 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6952 (tpp) cc_final: 0.5137 (pmt) REVERT: A 270 MET cc_start: 0.3282 (mmp) cc_final: 0.2888 (mtt) REVERT: A 480 ARG cc_start: 0.7124 (tpp-160) cc_final: 0.6606 (mmt90) REVERT: A 508 GLU cc_start: 0.7002 (tp30) cc_final: 0.6664 (tp30) REVERT: A 539 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7609 (mmm160) REVERT: A 733 TYR cc_start: 0.7656 (m-10) cc_final: 0.7197 (m-10) REVERT: A 1157 GLU cc_start: 0.7251 (tp30) cc_final: 0.6720 (mp0) REVERT: B 114 MET cc_start: 0.6965 (tpp) cc_final: 0.5396 (pmt) REVERT: B 508 GLU cc_start: 0.6960 (tp30) cc_final: 0.6417 (tp30) REVERT: B 539 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7553 (mmm160) REVERT: B 664 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7631 (mp-120) REVERT: B 733 TYR cc_start: 0.7688 (m-10) cc_final: 0.7266 (m-10) REVERT: B 735 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7787 (t) REVERT: B 1157 GLU cc_start: 0.7224 (tp30) cc_final: 0.6722 (mp0) REVERT: B 1193 ASP cc_start: 0.7139 (m-30) cc_final: 0.6923 (m-30) REVERT: C 114 MET cc_start: 0.6962 (tpp) cc_final: 0.5396 (pmt) REVERT: C 508 GLU cc_start: 0.7050 (tp30) cc_final: 0.6733 (tp30) REVERT: C 528 GLU cc_start: 0.7681 (pt0) cc_final: 0.7350 (mp0) REVERT: C 539 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7590 (mmm160) REVERT: C 664 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7619 (mp-120) REVERT: C 733 TYR cc_start: 0.7639 (m-10) cc_final: 0.7190 (m-10) REVERT: C 1157 GLU cc_start: 0.7111 (tp30) cc_final: 0.6616 (mp0) REVERT: C 1194 ARG cc_start: 0.6769 (mmm160) cc_final: 0.6277 (mmm160) REVERT: D 114 MET cc_start: 0.6958 (tpp) cc_final: 0.5133 (pmt) REVERT: D 270 MET cc_start: 0.3317 (mmp) cc_final: 0.2869 (mtt) REVERT: D 508 GLU cc_start: 0.7053 (tp30) cc_final: 0.6738 (tp30) REVERT: D 539 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7561 (mmm160) REVERT: D 664 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7618 (mp-120) REVERT: D 733 TYR cc_start: 0.7592 (m-10) cc_final: 0.7149 (m-10) REVERT: D 1157 GLU cc_start: 0.7096 (tp30) cc_final: 0.6649 (mp0) REVERT: D 1194 ARG cc_start: 0.6766 (mmm160) cc_final: 0.6271 (mmm160) outliers start: 79 outliers final: 32 residues processed: 432 average time/residue: 0.7511 time to fit residues: 377.4787 Evaluate side-chains 391 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 351 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1078 LEU Chi-restraints excluded: chain C residue 1097 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 280 optimal weight: 8.9990 chunk 274 optimal weight: 0.9980 chunk 265 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 250 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN A1175 GLN B 432 ASN B1175 GLN C 432 ASN C1175 GLN D 432 ASN D1175 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.218729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130525 restraints weight = 27704.355| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.14 r_work: 0.3135 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31152 Z= 0.140 Angle : 0.562 9.386 42272 Z= 0.286 Chirality : 0.042 0.143 4840 Planarity : 0.005 0.067 5272 Dihedral : 6.159 59.922 4472 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.57 % Allowed : 12.71 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3716 helix: 1.07 (0.10), residues: 2472 sheet: -0.91 (0.34), residues: 200 loop : -1.55 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1187 TYR 0.014 0.001 TYR D 855 PHE 0.011 0.001 PHE B 644 TRP 0.016 0.001 TRP D 716 HIS 0.004 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (31144) covalent geometry : angle 0.56186 / 0.29 (42248) hydrogen bonds : bond 0.04144 / 2.78 ( 1816) hydrogen bonds : angle 4.23367 / 2.91 ( 5352) link_BETA1-4 : bond 0.00023 / 0.01 ( 4) link_BETA1-4 : angle 1.32216 / 0.77 ( 12) link_NAG-ASN : bond 0.00049 / 0.02 ( 4) link_NAG-ASN : angle 0.88743 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 388 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6907 (tpp) cc_final: 0.5111 (pmt) REVERT: A 270 MET cc_start: 0.3439 (mmp) cc_final: 0.3048 (mtp) REVERT: A 381 MET cc_start: 0.4578 (tmm) cc_final: 0.4346 (pp-130) REVERT: A 508 GLU cc_start: 0.6948 (tp30) cc_final: 0.6570 (tp30) REVERT: A 539 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7557 (mmm160) REVERT: A 664 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7767 (mp-120) REVERT: A 733 TYR cc_start: 0.7630 (m-10) cc_final: 0.7144 (m-10) REVERT: A 1157 GLU cc_start: 0.7158 (tp30) cc_final: 0.6689 (mp0) REVERT: B 114 MET cc_start: 0.6924 (tpp) cc_final: 0.5081 (pmt) REVERT: B 270 MET cc_start: 0.3548 (mmp) cc_final: 0.3131 (mtt) REVERT: B 508 GLU cc_start: 0.6922 (tp30) cc_final: 0.6361 (tp30) REVERT: B 539 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7584 (mmm160) REVERT: B 664 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7750 (mp-120) REVERT: B 733 TYR cc_start: 0.7667 (m-10) cc_final: 0.7213 (m-10) REVERT: B 735 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7746 (t) REVERT: B 1157 GLU cc_start: 0.7037 (tp30) cc_final: 0.6542 (mp0) REVERT: B 1193 ASP cc_start: 0.7141 (m-30) cc_final: 0.6923 (m-30) REVERT: C 114 MET cc_start: 0.6941 (tpp) cc_final: 0.5282 (pmt) REVERT: C 270 MET cc_start: 0.3506 (mmp) cc_final: 0.3081 (mtp) REVERT: C 470 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6667 (pt0) REVERT: C 508 GLU cc_start: 0.6978 (tp30) cc_final: 0.6610 (tp30) REVERT: C 539 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7471 (mmm160) REVERT: C 664 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7750 (mp-120) REVERT: C 733 TYR cc_start: 0.7618 (m-10) cc_final: 0.7135 (m-10) REVERT: C 1044 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8474 (mt0) REVERT: C 1157 GLU cc_start: 0.7150 (tp30) cc_final: 0.6733 (mp0) REVERT: D 114 MET cc_start: 0.6920 (tpp) cc_final: 0.5087 (pmt) REVERT: D 270 MET cc_start: 0.3543 (mmp) cc_final: 0.3124 (mtt) REVERT: D 508 GLU cc_start: 0.6913 (tp30) cc_final: 0.6546 (tp30) REVERT: D 524 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: D 539 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7476 (mmm160) REVERT: D 664 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7756 (mp-120) REVERT: D 733 TYR cc_start: 0.7628 (m-10) cc_final: 0.7147 (m-10) REVERT: D 1157 GLU cc_start: 0.7045 (tp30) cc_final: 0.6555 (mp0) outliers start: 84 outliers final: 33 residues processed: 421 average time/residue: 0.7765 time to fit residues: 379.4514 Evaluate side-chains 399 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 354 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 994 VAL Chi-restraints excluded: chain C residue 1044 GLN Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1078 LEU Chi-restraints excluded: chain C residue 1097 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 8 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 331 optimal weight: 0.8980 chunk 181 optimal weight: 0.0070 chunk 270 optimal weight: 0.5980 chunk 286 optimal weight: 9.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN A 432 ASN A1199 ASN B 426 ASN B 432 ASN B 832 HIS B1175 GLN B1199 ASN C 432 ASN C1175 GLN D 432 ASN D 832 HIS D1175 GLN D1199 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.219564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.132290 restraints weight = 27672.873| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.06 r_work: 0.3162 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31152 Z= 0.124 Angle : 0.541 9.360 42272 Z= 0.276 Chirality : 0.041 0.149 4840 Planarity : 0.004 0.065 5272 Dihedral : 6.022 59.957 4472 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 12.99 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3716 helix: 1.26 (0.10), residues: 2472 sheet: -0.85 (0.34), residues: 200 loop : -1.47 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1187 TYR 0.013 0.001 TYR A 855 PHE 0.010 0.001 PHE B 644 TRP 0.018 0.001 TRP D 716 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (31144) covalent geometry : angle 0.54065 / 0.28 (42248) hydrogen bonds : bond 0.03921 / 2.63 ( 1816) hydrogen bonds : angle 4.14083 / 2.85 ( 5352) link_BETA1-4 : bond 0.00090 / 0.05 ( 4) link_BETA1-4 : angle 1.29369 / 0.75 ( 12) link_NAG-ASN : bond 0.00125 / 0.06 ( 4) link_NAG-ASN : angle 0.64835 / 0.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 374 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6876 (tpp) cc_final: 0.5056 (pmt) REVERT: A 270 MET cc_start: 0.3546 (mmp) cc_final: 0.3257 (mtt) REVERT: A 508 GLU cc_start: 0.6880 (tp30) cc_final: 0.6479 (tp30) REVERT: A 512 ARG cc_start: 0.7419 (mtm180) cc_final: 0.7099 (mtp180) REVERT: A 539 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7553 (mmm160) REVERT: A 664 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7696 (mp-120) REVERT: A 733 TYR cc_start: 0.7630 (m-10) cc_final: 0.7192 (m-10) REVERT: A 1157 GLU cc_start: 0.7396 (tp30) cc_final: 0.6662 (mp0) REVERT: B 114 MET cc_start: 0.6895 (tpp) cc_final: 0.5061 (pmt) REVERT: B 270 MET cc_start: 0.3602 (mmp) cc_final: 0.3267 (OUTLIER) REVERT: B 508 GLU cc_start: 0.6923 (tp30) cc_final: 0.6357 (tp30) REVERT: B 539 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7606 (mmm160) REVERT: B 664 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7533 (mp-120) REVERT: B 709 MET cc_start: 0.7740 (ttp) cc_final: 0.7536 (ttp) REVERT: B 733 TYR cc_start: 0.7634 (m-10) cc_final: 0.7154 (m-10) REVERT: B 735 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7708 (t) REVERT: B 1090 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 1157 GLU cc_start: 0.7363 (tp30) cc_final: 0.6807 (mp0) REVERT: B 1193 ASP cc_start: 0.7084 (m-30) cc_final: 0.6863 (m-30) REVERT: B 1194 ARG cc_start: 0.6700 (mmm160) cc_final: 0.6309 (mmp-170) REVERT: C 114 MET cc_start: 0.6836 (tpp) cc_final: 0.5152 (pmt) REVERT: C 270 MET cc_start: 0.3629 (mmp) cc_final: 0.3211 (mtp) REVERT: C 470 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6604 (pt0) REVERT: C 508 GLU cc_start: 0.6878 (tp30) cc_final: 0.6504 (tp30) REVERT: C 539 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7617 (mmm160) REVERT: C 664 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7607 (mp-120) REVERT: C 733 TYR cc_start: 0.7594 (m-10) cc_final: 0.7146 (m-10) REVERT: C 1044 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8452 (mt0) REVERT: C 1157 GLU cc_start: 0.7240 (tp30) cc_final: 0.6663 (mp0) REVERT: D 114 MET cc_start: 0.6895 (tpp) cc_final: 0.5061 (pmt) REVERT: D 270 MET cc_start: 0.3597 (mmp) cc_final: 0.3249 (OUTLIER) REVERT: D 508 GLU cc_start: 0.6888 (tp30) cc_final: 0.6520 (tp30) REVERT: D 524 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: D 539 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7412 (mmm160) REVERT: D 664 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7557 (mp-120) REVERT: D 733 TYR cc_start: 0.7596 (m-10) cc_final: 0.7145 (m-10) REVERT: D 1157 GLU cc_start: 0.7376 (tp30) cc_final: 0.6599 (mp0) outliers start: 78 outliers final: 38 residues processed: 412 average time/residue: 0.7736 time to fit residues: 369.9902 Evaluate side-chains 388 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 994 VAL Chi-restraints excluded: chain C residue 1044 GLN Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1078 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 916 THR Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 194 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 306 optimal weight: 0.4980 chunk 335 optimal weight: 0.7980 chunk 372 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 979 GLN A1175 GLN A1199 ASN B1175 GLN B1199 ASN C 432 ASN C 979 GLN C1175 GLN D 249 ASN D 426 ASN D1175 GLN D1199 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.219299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136152 restraints weight = 27711.827| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.45 r_work: 0.3130 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31152 Z= 0.135 Angle : 0.551 9.492 42272 Z= 0.279 Chirality : 0.042 0.185 4840 Planarity : 0.005 0.064 5272 Dihedral : 5.950 58.822 4472 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.60 % Allowed : 13.08 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.14), residues: 3716 helix: 1.33 (0.10), residues: 2472 sheet: -0.80 (0.35), residues: 200 loop : -1.43 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 935 TYR 0.014 0.001 TYR C 855 PHE 0.011 0.001 PHE B 644 TRP 0.019 0.001 TRP C 716 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (31144) covalent geometry : angle 0.55088 / 0.28 (42248) hydrogen bonds : bond 0.03966 / 2.66 ( 1816) hydrogen bonds : angle 4.11814 / 2.83 ( 5352) link_BETA1-4 : bond 0.00040 / 0.01 ( 4) link_BETA1-4 : angle 1.34139 / 0.78 ( 12) link_NAG-ASN : bond 0.00070 / 0.03 ( 4) link_NAG-ASN : angle 0.67563 / 0.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 354 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6832 (tpp) cc_final: 0.4963 (pmt) REVERT: A 270 MET cc_start: 0.3661 (mmp) cc_final: 0.3378 (OUTLIER) REVERT: A 381 MET cc_start: 0.4378 (tmm) cc_final: 0.4153 (pp-130) REVERT: A 470 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6805 (pt0) REVERT: A 508 GLU cc_start: 0.6949 (tp30) cc_final: 0.6557 (tp30) REVERT: A 539 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7585 (mmm160) REVERT: A 664 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7629 (mp-120) REVERT: A 733 TYR cc_start: 0.7673 (m-10) cc_final: 0.7236 (m-10) REVERT: A 1157 GLU cc_start: 0.7438 (tp30) cc_final: 0.6679 (mp0) REVERT: B 114 MET cc_start: 0.6894 (tpp) cc_final: 0.5083 (pmt) REVERT: B 270 MET cc_start: 0.3710 (mmp) cc_final: 0.3381 (mtt) REVERT: B 391 MET cc_start: 0.6080 (mmm) cc_final: 0.5803 (mmm) REVERT: B 508 GLU cc_start: 0.6952 (tp30) cc_final: 0.6373 (tp30) REVERT: B 539 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7600 (mmm160) REVERT: B 664 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7627 (mp-120) REVERT: B 709 MET cc_start: 0.7800 (ttp) cc_final: 0.7596 (ttp) REVERT: B 733 TYR cc_start: 0.7678 (m-10) cc_final: 0.7195 (m-10) REVERT: B 735 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7729 (t) REVERT: B 1157 GLU cc_start: 0.7411 (tp30) cc_final: 0.6636 (mp0) REVERT: B 1193 ASP cc_start: 0.7116 (m-30) cc_final: 0.6895 (m-30) REVERT: C 114 MET cc_start: 0.6840 (tpp) cc_final: 0.5153 (pmt) REVERT: C 270 MET cc_start: 0.3662 (mmp) cc_final: 0.3287 (mtp) REVERT: C 381 MET cc_start: 0.4392 (pp-130) cc_final: 0.3928 (ppp) REVERT: C 470 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6595 (pt0) REVERT: C 508 GLU cc_start: 0.6944 (tp30) cc_final: 0.6550 (tp30) REVERT: C 539 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7617 (mmm160) REVERT: C 664 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7629 (mp-120) REVERT: C 733 TYR cc_start: 0.7657 (m-10) cc_final: 0.7220 (m-10) REVERT: C 1044 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: C 1157 GLU cc_start: 0.7419 (tp30) cc_final: 0.6845 (mp0) REVERT: D 114 MET cc_start: 0.6849 (tpp) cc_final: 0.4999 (pmt) REVERT: D 270 MET cc_start: 0.3784 (mmp) cc_final: 0.3444 (mtt) REVERT: D 391 MET cc_start: 0.6067 (mmm) cc_final: 0.5793 (mmm) REVERT: D 502 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7621 (tppt) REVERT: D 508 GLU cc_start: 0.6963 (tp30) cc_final: 0.6570 (tp30) REVERT: D 524 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: D 539 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7475 (mmm160) REVERT: D 664 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7622 (mp-120) REVERT: D 733 TYR cc_start: 0.7645 (m-10) cc_final: 0.7197 (m-10) REVERT: D 1157 GLU cc_start: 0.7418 (tp30) cc_final: 0.6613 (mp0) outliers start: 85 outliers final: 39 residues processed: 392 average time/residue: 0.7494 time to fit residues: 342.6945 Evaluate side-chains 394 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 342 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 994 VAL Chi-restraints excluded: chain C residue 1044 GLN Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1078 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 916 THR Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 358 optimal weight: 0.0070 chunk 25 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 365 optimal weight: 0.6980 chunk 304 optimal weight: 0.3980 chunk 195 optimal weight: 9.9990 chunk 359 optimal weight: 0.9990 chunk 367 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 chunk 374 optimal weight: 5.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN A 979 GLN A1199 ASN B 249 ASN B 432 ASN B1175 GLN B1199 ASN C 432 ASN C 979 GLN C1175 GLN D 432 ASN D1175 GLN D1199 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.222560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139313 restraints weight = 29391.346| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.72 r_work: 0.3396 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31152 Z= 0.122 Angle : 0.541 10.935 42272 Z= 0.273 Chirality : 0.041 0.144 4840 Planarity : 0.004 0.063 5272 Dihedral : 5.812 55.756 4472 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.63 % Allowed : 13.39 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3716 helix: 1.42 (0.10), residues: 2472 sheet: -0.57 (0.35), residues: 208 loop : -1.40 (0.21), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 433 TYR 0.014 0.001 TYR B1111 PHE 0.010 0.001 PHE B1072 TRP 0.023 0.001 TRP C 716 HIS 0.003 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (31144) covalent geometry : angle 0.54017 / 0.27 (42248) hydrogen bonds : bond 0.03834 / 2.58 ( 1816) hydrogen bonds : angle 4.08381 / 2.81 ( 5352) link_BETA1-4 : bond 0.00096 / 0.04 ( 4) link_BETA1-4 : angle 1.29242 / 0.75 ( 12) link_NAG-ASN : bond 0.00105 / 0.05 ( 4) link_NAG-ASN : angle 0.59199 / 0.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 366 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6742 (tpp) cc_final: 0.5042 (pmt) REVERT: A 270 MET cc_start: 0.3621 (mmp) cc_final: 0.3412 (mtp) REVERT: A 381 MET cc_start: 0.4562 (tmm) cc_final: 0.4304 (pp-130) REVERT: A 470 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7115 (pt0) REVERT: A 508 GLU cc_start: 0.7315 (tp30) cc_final: 0.6873 (tp30) REVERT: A 524 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: A 539 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7414 (mmm160) REVERT: A 664 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7928 (mp-120) REVERT: A 733 TYR cc_start: 0.7849 (m-10) cc_final: 0.7466 (m-10) REVERT: A 1090 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8042 (mm-30) REVERT: A 1097 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8062 (t0) REVERT: A 1157 GLU cc_start: 0.7562 (tp30) cc_final: 0.6966 (mp0) REVERT: B 114 MET cc_start: 0.6751 (tpp) cc_final: 0.5042 (pmt) REVERT: B 270 MET cc_start: 0.3701 (mmp) cc_final: 0.3423 (mtp) REVERT: B 508 GLU cc_start: 0.7232 (tp30) cc_final: 0.6693 (tp30) REVERT: B 528 GLU cc_start: 0.8009 (pt0) cc_final: 0.7684 (tm-30) REVERT: B 539 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7580 (mmm160) REVERT: B 664 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7702 (mp-120) REVERT: B 733 TYR cc_start: 0.7827 (m-10) cc_final: 0.7441 (m-10) REVERT: B 735 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7914 (t) REVERT: B 1097 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8006 (t0) REVERT: B 1157 GLU cc_start: 0.7580 (tp30) cc_final: 0.6977 (mp0) REVERT: B 1193 ASP cc_start: 0.7432 (m-30) cc_final: 0.7231 (m-30) REVERT: B 1194 ARG cc_start: 0.7118 (mmm160) cc_final: 0.6742 (mmp-170) REVERT: C 114 MET cc_start: 0.6742 (tpp) cc_final: 0.5037 (pmt) REVERT: C 270 MET cc_start: 0.3706 (mmp) cc_final: 0.3442 (mtp) REVERT: C 470 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6972 (pt0) REVERT: C 508 GLU cc_start: 0.7242 (tp30) cc_final: 0.6874 (tp30) REVERT: C 539 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7562 (mmm160) REVERT: C 664 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7715 (mp-120) REVERT: C 733 TYR cc_start: 0.7831 (m-10) cc_final: 0.7454 (m-10) REVERT: C 1090 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8035 (mm-30) REVERT: C 1097 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8029 (t0) REVERT: C 1157 GLU cc_start: 0.7552 (tp30) cc_final: 0.6939 (mp0) REVERT: C 1194 ARG cc_start: 0.7257 (mmm160) cc_final: 0.6627 (mmm160) REVERT: D 114 MET cc_start: 0.6752 (tpp) cc_final: 0.5043 (pmt) REVERT: D 270 MET cc_start: 0.3748 (mmp) cc_final: 0.3473 (mtp) REVERT: D 508 GLU cc_start: 0.7258 (tp30) cc_final: 0.6921 (tp30) REVERT: D 539 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7600 (mmm160) REVERT: D 664 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7698 (mp-120) REVERT: D 733 TYR cc_start: 0.7763 (m-10) cc_final: 0.7359 (m-10) REVERT: D 1090 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8034 (mm-30) REVERT: D 1097 ASP cc_start: 0.8237 (m-30) cc_final: 0.7994 (t0) REVERT: D 1157 GLU cc_start: 0.7549 (tp30) cc_final: 0.6955 (mp0) outliers start: 86 outliers final: 39 residues processed: 407 average time/residue: 0.7233 time to fit residues: 345.1330 Evaluate side-chains 403 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 349 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 994 VAL Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1078 LEU Chi-restraints excluded: chain C residue 1097 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 916 THR Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 251 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 265 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN A 979 GLN A1175 GLN A1199 ASN B 432 ASN B1175 GLN B1199 ASN C 432 ASN C 979 GLN C1175 GLN D 432 ASN D1175 GLN D1199 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.222456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146744 restraints weight = 29499.586| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.19 r_work: 0.3422 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31152 Z= 0.167 Angle : 0.587 11.081 42272 Z= 0.296 Chirality : 0.043 0.145 4840 Planarity : 0.005 0.063 5272 Dihedral : 5.730 51.473 4472 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.29 % Allowed : 14.12 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3716 helix: 1.33 (0.10), residues: 2480 sheet: -0.59 (0.35), residues: 208 loop : -1.38 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 935 TYR 0.016 0.002 TYR D 855 PHE 0.013 0.002 PHE C 644 TRP 0.026 0.002 TRP C 716 HIS 0.004 0.001 HIS D 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (31144) covalent geometry : angle 0.58625 / 0.30 (42248) hydrogen bonds : bond 0.04210 / 2.83 ( 1816) hydrogen bonds : angle 4.14193 / 2.85 ( 5352) link_BETA1-4 : bond 0.00095 / 0.04 ( 4) link_BETA1-4 : angle 1.49058 / 0.86 ( 12) link_NAG-ASN : bond 0.00094 / 0.04 ( 4) link_NAG-ASN : angle 0.77012 / 0.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 360 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6763 (tpp) cc_final: 0.5067 (pmt) REVERT: A 381 MET cc_start: 0.4614 (tmm) cc_final: 0.4378 (pp-130) REVERT: A 470 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: A 508 GLU cc_start: 0.7549 (tp30) cc_final: 0.7180 (tp30) REVERT: A 539 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7575 (mmm160) REVERT: A 733 TYR cc_start: 0.7894 (m-10) cc_final: 0.7523 (m-10) REVERT: A 1157 GLU cc_start: 0.7615 (tp30) cc_final: 0.7041 (mp0) REVERT: B 114 MET cc_start: 0.6743 (tpp) cc_final: 0.5090 (pmt) REVERT: B 270 MET cc_start: 0.3602 (mmp) cc_final: 0.3366 (mtp) REVERT: B 508 GLU cc_start: 0.7430 (tp30) cc_final: 0.6904 (tp30) REVERT: B 539 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7636 (mmm160) REVERT: B 664 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7849 (mp-120) REVERT: B 733 TYR cc_start: 0.7913 (m-10) cc_final: 0.7559 (m-10) REVERT: B 735 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.7997 (t) REVERT: B 1157 GLU cc_start: 0.7632 (tp30) cc_final: 0.7055 (mp0) REVERT: B 1194 ARG cc_start: 0.7221 (mmm160) cc_final: 0.6826 (mmp-170) REVERT: C 114 MET cc_start: 0.6709 (tpp) cc_final: 0.5020 (pmt) REVERT: C 270 MET cc_start: 0.3740 (mmp) cc_final: 0.3503 (mtp) REVERT: C 470 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6988 (pt0) REVERT: C 508 GLU cc_start: 0.7376 (tp30) cc_final: 0.7011 (tp30) REVERT: C 539 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7711 (mmm160) REVERT: C 664 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7865 (mp-120) REVERT: C 733 TYR cc_start: 0.7855 (m-10) cc_final: 0.7484 (m-10) REVERT: C 1157 GLU cc_start: 0.7639 (tp30) cc_final: 0.7018 (mp0) REVERT: C 1194 ARG cc_start: 0.7360 (mmm160) cc_final: 0.6719 (mmm160) REVERT: D 114 MET cc_start: 0.6748 (tpp) cc_final: 0.5083 (pmt) REVERT: D 270 MET cc_start: 0.3762 (mmp) cc_final: 0.3491 (mtp) REVERT: D 508 GLU cc_start: 0.7378 (tp30) cc_final: 0.7022 (tp30) REVERT: D 524 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: D 539 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7590 (mmm160) REVERT: D 664 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7876 (mp-120) REVERT: D 733 TYR cc_start: 0.7972 (m-10) cc_final: 0.7612 (m-10) REVERT: D 1157 GLU cc_start: 0.7613 (tp30) cc_final: 0.7047 (mp0) outliers start: 75 outliers final: 40 residues processed: 397 average time/residue: 0.7484 time to fit residues: 346.9739 Evaluate side-chains 396 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 345 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1078 LEU Chi-restraints excluded: chain C residue 1097 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 916 THR Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 261 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 290 optimal weight: 0.0970 chunk 188 optimal weight: 20.0000 chunk 363 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 367 optimal weight: 0.5980 chunk 291 optimal weight: 6.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN A1175 GLN A1199 ASN B 432 ASN B1175 GLN B1199 ASN C 432 ASN C1175 GLN D 432 ASN D1175 GLN D1199 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.224021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.150482 restraints weight = 29476.778| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.09 r_work: 0.3500 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31152 Z= 0.122 Angle : 0.555 12.039 42272 Z= 0.279 Chirality : 0.041 0.145 4840 Planarity : 0.004 0.058 5272 Dihedral : 5.521 51.013 4472 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.99 % Allowed : 14.36 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3716 helix: 1.46 (0.10), residues: 2472 sheet: -0.71 (0.36), residues: 200 loop : -1.35 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 935 TYR 0.014 0.001 TYR C1111 PHE 0.010 0.001 PHE D1072 TRP 0.030 0.001 TRP B 716 HIS 0.003 0.001 HIS D 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (31144) covalent geometry : angle 0.55483 / 0.28 (42248) hydrogen bonds : bond 0.03847 / 2.59 ( 1816) hydrogen bonds : angle 4.09249 / 2.81 ( 5352) link_BETA1-4 : bond 0.00071 / 0.03 ( 4) link_BETA1-4 : angle 1.32707 / 0.77 ( 12) link_NAG-ASN : bond 0.00069 / 0.03 ( 4) link_NAG-ASN : angle 0.63309 / 0.39 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 346 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6260 (tpp) cc_final: 0.5108 (pmt) REVERT: A 381 MET cc_start: 0.4570 (tmm) cc_final: 0.4341 (pp-130) REVERT: A 470 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: A 508 GLU cc_start: 0.7414 (tp30) cc_final: 0.7013 (tp30) REVERT: A 528 GLU cc_start: 0.7914 (pt0) cc_final: 0.7630 (tm-30) REVERT: A 539 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7557 (mmm160) REVERT: A 664 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7872 (mp-120) REVERT: A 733 TYR cc_start: 0.7827 (m-10) cc_final: 0.7455 (m-10) REVERT: A 1097 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8045 (t0) REVERT: A 1157 GLU cc_start: 0.7585 (tp30) cc_final: 0.6978 (mp0) REVERT: B 114 MET cc_start: 0.6753 (tpp) cc_final: 0.5038 (pmt) REVERT: B 270 MET cc_start: 0.3687 (mmp) cc_final: 0.3474 (mtp) REVERT: B 508 GLU cc_start: 0.7290 (tp30) cc_final: 0.6739 (tp30) REVERT: B 528 GLU cc_start: 0.7870 (pt0) cc_final: 0.7649 (tm-30) REVERT: B 539 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7562 (mmm160) REVERT: B 664 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7891 (mp-120) REVERT: B 733 TYR cc_start: 0.7873 (m-10) cc_final: 0.7511 (m-10) REVERT: B 735 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7937 (t) REVERT: B 1097 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7999 (t0) REVERT: B 1157 GLU cc_start: 0.7573 (tp30) cc_final: 0.6998 (mp0) REVERT: B 1194 ARG cc_start: 0.7195 (mmm160) cc_final: 0.6799 (mmp-170) REVERT: C 114 MET cc_start: 0.6749 (tpp) cc_final: 0.5066 (pmt) REVERT: C 270 MET cc_start: 0.3727 (mmp) cc_final: 0.3482 (mtp) REVERT: C 279 MET cc_start: 0.5409 (mpp) cc_final: 0.4609 (mpp) REVERT: C 470 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6893 (pt0) REVERT: C 508 GLU cc_start: 0.7332 (tp30) cc_final: 0.6971 (tp30) REVERT: C 528 GLU cc_start: 0.7952 (pt0) cc_final: 0.7669 (tm-30) REVERT: C 539 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7611 (mmm160) REVERT: C 664 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7899 (mp-120) REVERT: C 733 TYR cc_start: 0.7786 (m-10) cc_final: 0.7417 (m-10) REVERT: C 1090 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8104 (mm-30) REVERT: C 1097 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8019 (t0) REVERT: C 1157 GLU cc_start: 0.7583 (tp30) cc_final: 0.6968 (mp0) REVERT: D 114 MET cc_start: 0.6759 (tpp) cc_final: 0.5056 (pmt) REVERT: D 270 MET cc_start: 0.3685 (mmp) cc_final: 0.3454 (mtp) REVERT: D 508 GLU cc_start: 0.7274 (tp30) cc_final: 0.6925 (tp30) REVERT: D 524 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: D 528 GLU cc_start: 0.7907 (pt0) cc_final: 0.7628 (tm-30) REVERT: D 539 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7483 (mmm160) REVERT: D 664 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7895 (mp-120) REVERT: D 709 MET cc_start: 0.7895 (ttp) cc_final: 0.7639 (ttp) REVERT: D 733 TYR cc_start: 0.7917 (m-10) cc_final: 0.7545 (m-10) REVERT: D 1090 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7993 (mm-30) REVERT: D 1157 GLU cc_start: 0.7558 (tp30) cc_final: 0.6988 (mp0) outliers start: 65 outliers final: 32 residues processed: 383 average time/residue: 0.7387 time to fit residues: 330.7650 Evaluate side-chains 388 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 916 THR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1078 LEU Chi-restraints excluded: chain C residue 1097 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 916 THR Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 198 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 311 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 319 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 320 optimal weight: 0.7980 chunk 351 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN A1175 GLN A1199 ASN B 432 ASN B1175 GLN B1199 ASN C 432 ASN C1175 GLN D 432 ASN D1175 GLN D1199 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.222758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146354 restraints weight = 29633.525| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.66 r_work: 0.3470 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31152 Z= 0.154 Angle : 0.585 11.657 42272 Z= 0.293 Chirality : 0.043 0.145 4840 Planarity : 0.004 0.059 5272 Dihedral : 5.385 50.712 4472 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.99 % Allowed : 14.36 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3716 helix: 1.41 (0.10), residues: 2480 sheet: -0.69 (0.36), residues: 200 loop : -1.33 (0.21), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 TYR 0.015 0.002 TYR C 855 PHE 0.012 0.001 PHE C 644 TRP 0.032 0.002 TRP D 716 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (31144) covalent geometry : angle 0.58491 / 0.29 (42248) hydrogen bonds : bond 0.04104 / 2.76 ( 1816) hydrogen bonds : angle 4.12011 / 2.83 ( 5352) link_BETA1-4 : bond 0.00073 / 0.03 ( 4) link_BETA1-4 : angle 1.51069 / 0.87 ( 12) link_NAG-ASN : bond 0.00090 / 0.04 ( 4) link_NAG-ASN : angle 0.82498 / 0.50 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15452.37 seconds wall clock time: 262 minutes 48.40 seconds (15768.40 seconds total)