Starting phenix.real_space_refine on Sun Jul 5 21:07:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jje_61524/07_2026/9jje_61524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jje_61524/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jje_61524/07_2026/9jje_61524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jje_61524/07_2026/9jje_61524.map" model { file = "/net/cci-nas-00/data/ceres_data/9jje_61524/07_2026/9jje_61524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jje_61524/07_2026/9jje_61524.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 40 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'A2R': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 7.05, per 1000 atoms: 0.23 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: 2.41 Conformation dependent library (CDL) restraints added in 1.2 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: 0.97 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: 5.93 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.110 Find NCS groups from input model: 0.300 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:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- 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 : 0.841 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: 0.6781 time to fit residues: 522.2070 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 : 1.009 ------------------------------------------------------------------------------- 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 968 ASN D1074 ASN D1103 GLN D1175 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.221401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133706 restraints weight = 27647.554| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.25 r_work: 0.3176 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31152 Z= 0.172 Angle : 0.631 10.038 42272 Z= 0.325 Chirality : 0.044 0.153 4840 Planarity : 0.006 0.080 5272 Dihedral : 8.152 57.957 4472 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.08 % Allowed : 10.12 % Favored : 87.81 % 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: -1.18 (0.13), residues: 3716 helix: -0.12 (0.10), residues: 2452 sheet: -1.34 (0.32), residues: 200 loop : -2.04 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 669 TYR 0.024 0.002 TYR D 855 PHE 0.015 0.002 PHE D 838 TRP 0.016 0.002 TRP D1100 HIS 0.004 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (31144) covalent geometry : angle 0.63015 / 0.32 (42248) hydrogen bonds : bond 0.04580 / 3.07 ( 1816) hydrogen bonds : angle 4.68483 / 3.24 ( 5352) link_BETA1-4 : bond 0.00132 / 0.07 ( 4) link_BETA1-4 : angle 1.40407 / 0.82 ( 12) link_NAG-ASN : bond 0.00052 / 0.03 ( 4) link_NAG-ASN : angle 0.93408 / 0.56 ( 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 515 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 447 time to evaluate : 0.960 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: 0.7030 (tpp) cc_final: 0.5465 (pmt) REVERT: A 411 LYS cc_start: 0.7543 (mtmt) cc_final: 0.7083 (mttm) REVERT: A 471 LEU cc_start: 0.7591 (tp) cc_final: 0.7284 (tp) REVERT: A 528 GLU cc_start: 0.7754 (pt0) cc_final: 0.7238 (mm-30) REVERT: A 664 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7595 (mp-120) REVERT: A 665 THR cc_start: 0.8465 (p) cc_final: 0.8245 (t) REVERT: A 709 MET cc_start: 0.7859 (ttp) cc_final: 0.7578 (ttp) REVERT: A 733 TYR cc_start: 0.7781 (m-10) cc_final: 0.7302 (m-10) REVERT: A 1157 GLU cc_start: 0.6935 (tp30) cc_final: 0.6367 (mp0) REVERT: A 1193 ASP cc_start: 0.7167 (m-30) cc_final: 0.6960 (m-30) REVERT: A 1194 ARG cc_start: 0.6760 (mmm160) cc_final: 0.6280 (mmp-170) REVERT: B 114 MET cc_start: 0.7037 (tpp) cc_final: 0.5463 (pmt) REVERT: B 411 LYS cc_start: 0.7519 (mtmt) cc_final: 0.7085 (mttm) REVERT: B 508 GLU cc_start: 0.6603 (tp30) cc_final: 0.6193 (tp30) REVERT: B 528 GLU cc_start: 0.7754 (pt0) cc_final: 0.7307 (mp0) REVERT: B 645 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: B 664 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7692 (mp-120) REVERT: B 733 TYR cc_start: 0.7718 (m-10) cc_final: 0.7242 (m-10) REVERT: B 735 VAL cc_start: 0.8093 (m) cc_final: 0.7729 (t) REVERT: B 1193 ASP cc_start: 0.7249 (m-30) cc_final: 0.7012 (m-30) REVERT: C 114 MET cc_start: 0.7037 (tpp) cc_final: 0.5473 (pmt) REVERT: C 411 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7105 (mttm) REVERT: C 507 LYS cc_start: 0.7886 (tttm) cc_final: 0.7645 (tttm) REVERT: C 528 GLU cc_start: 0.7734 (pt0) cc_final: 0.7207 (mm-30) REVERT: C 664 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7713 (mp-120) REVERT: C 665 THR cc_start: 0.8479 (p) cc_final: 0.8266 (t) REVERT: C 733 TYR cc_start: 0.7798 (m-10) cc_final: 0.7329 (m-10) REVERT: C 1158 MET cc_start: 0.7097 (mtp) cc_final: 0.6872 (mtm) REVERT: C 1193 ASP cc_start: 0.7186 (m-30) cc_final: 0.6973 (m-30) REVERT: C 1194 ARG cc_start: 0.6785 (mmm160) cc_final: 0.6313 (mmp-170) REVERT: D 114 MET cc_start: 0.7043 (tpp) cc_final: 0.5466 (pmt) REVERT: D 411 LYS cc_start: 0.7522 (mtmt) cc_final: 0.7071 (mttm) REVERT: D 528 GLU cc_start: 0.7757 (pt0) cc_final: 0.7217 (mm-30) REVERT: D 664 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7696 (mp-120) REVERT: D 665 THR cc_start: 0.8481 (p) cc_final: 0.8270 (t) REVERT: D 733 TYR cc_start: 0.7697 (m-10) cc_final: 0.7209 (m-10) REVERT: D 1193 ASP cc_start: 0.7233 (m-30) cc_final: 0.6991 (m-30) REVERT: D 1194 ARG cc_start: 0.6771 (mmm160) cc_final: 0.6301 (mmp-170) outliers start: 68 outliers final: 16 residues processed: 474 average time/residue: 0.7174 time to fit residues: 396.2898 Evaluate side-chains 402 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 381 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 166 optimal weight: 0.5980 chunk 217 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 311 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 340 optimal weight: 0.7980 chunk 304 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN A 979 GLN B 432 ASN B 832 HIS C 432 ASN C 979 GLN D 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.216607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.129912 restraints weight = 27556.223| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.39 r_work: 0.3089 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 31152 Z= 0.249 Angle : 0.680 9.700 42272 Z= 0.347 Chirality : 0.047 0.195 4840 Planarity : 0.006 0.081 5272 Dihedral : 6.912 58.183 4472 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.05 % Allowed : 11.89 % Favored : 86.06 % 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: -0.58 (0.13), residues: 3716 helix: 0.35 (0.10), residues: 2480 sheet: -1.06 (0.33), residues: 200 loop : -1.87 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1187 TYR 0.030 0.002 TYR B 855 PHE 0.014 0.002 PHE C 956 TRP 0.017 0.002 TRP B1100 HIS 0.006 0.002 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.25 (31144) covalent geometry : angle 0.67925 / 0.35 (42248) hydrogen bonds : bond 0.05049 / 3.39 ( 1816) hydrogen bonds : angle 4.57456 / 3.16 ( 5352) link_BETA1-4 : bond 0.00447 / 0.21 ( 4) link_BETA1-4 : angle 1.69331 / 0.98 ( 12) link_NAG-ASN : bond 0.00337 / 0.15 ( 4) link_NAG-ASN : angle 1.56436 / 0.94 ( 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 466 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 399 time to evaluate : 1.139 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: 0.7030 (tpp) cc_final: 0.5144 (pmt) REVERT: A 270 MET cc_start: 0.3407 (mmp) cc_final: 0.2957 (mtp) REVERT: A 480 ARG cc_start: 0.7166 (tpp-160) cc_final: 0.6798 (mmt180) REVERT: A 508 GLU cc_start: 0.6685 (tp30) cc_final: 0.6441 (tp30) REVERT: A 539 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7435 (mtm180) REVERT: A 733 TYR cc_start: 0.7605 (m-10) cc_final: 0.7129 (m-10) REVERT: A 848 TYR cc_start: 0.8085 (t80) cc_final: 0.7768 (t80) REVERT: A 1044 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8655 (mt0) REVERT: A 1157 GLU cc_start: 0.7021 (tp30) cc_final: 0.6436 (mp0) REVERT: B 114 MET cc_start: 0.7044 (tpp) cc_final: 0.5146 (pmt) REVERT: B 270 MET cc_start: 0.3432 (mmp) cc_final: 0.2928 (mtp) REVERT: B 508 GLU cc_start: 0.6890 (tp30) cc_final: 0.6343 (tp30) REVERT: B 539 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7742 (mmm160) REVERT: B 645 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7884 (tm-30) REVERT: B 733 TYR cc_start: 0.7703 (m-10) cc_final: 0.7235 (m-10) REVERT: B 735 VAL cc_start: 0.8118 (m) cc_final: 0.7724 (t) REVERT: B 848 TYR cc_start: 0.8114 (t80) cc_final: 0.7794 (t80) REVERT: B 1157 GLU cc_start: 0.6918 (tp30) cc_final: 0.6324 (mp0) REVERT: B 1193 ASP cc_start: 0.7178 (m-30) cc_final: 0.6951 (m-30) REVERT: C 114 MET cc_start: 0.7034 (tpp) cc_final: 0.5155 (pmt) REVERT: C 270 MET cc_start: 0.3320 (mmp) cc_final: 0.2820 (mtp) REVERT: C 508 GLU cc_start: 0.6857 (tp30) cc_final: 0.6638 (tp30) REVERT: C 539 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7614 (mmm160) REVERT: C 733 TYR cc_start: 0.7591 (m-10) cc_final: 0.7111 (m-10) REVERT: C 848 TYR cc_start: 0.8095 (t80) cc_final: 0.7771 (t80) REVERT: C 1044 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (mt0) REVERT: C 1157 GLU cc_start: 0.6909 (tp30) cc_final: 0.6364 (mp0) REVERT: C 1158 MET cc_start: 0.7222 (mtp) cc_final: 0.7002 (mtm) REVERT: C 1193 ASP cc_start: 0.7153 (m-30) cc_final: 0.6942 (m-30) REVERT: D 114 MET cc_start: 0.7040 (tpp) cc_final: 0.5157 (pmt) REVERT: D 270 MET cc_start: 0.3432 (mmp) cc_final: 0.2921 (mtp) REVERT: D 508 GLU cc_start: 0.6691 (tp30) cc_final: 0.6440 (tp30) REVERT: D 539 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7648 (mmm160) REVERT: D 733 TYR cc_start: 0.7574 (m-10) cc_final: 0.7094 (m-10) REVERT: D 848 TYR cc_start: 0.8087 (t80) cc_final: 0.7732 (t80) REVERT: D 1157 GLU cc_start: 0.6925 (tp30) cc_final: 0.6334 (mp0) outliers start: 67 outliers final: 33 residues processed: 434 average time/residue: 0.6864 time to fit residues: 347.2827 Evaluate side-chains 407 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 368 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 470 GLU 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 1044 GLN 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 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 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 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 1044 GLN 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 197 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 297 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 311 optimal weight: 7.9990 chunk 284 optimal weight: 30.0000 chunk 287 optimal weight: 7.9990 chunk 147 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 GLN A 426 ASN A 432 ASN A 979 GLN A1175 GLN B 403 GLN B 432 ASN B1175 GLN C 403 GLN C 426 ASN C 432 ASN C 979 GLN C1175 GLN D 403 GLN D 426 ASN D 432 ASN D1175 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.218806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130935 restraints weight = 27568.490| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.03 r_work: 0.3148 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31152 Z= 0.143 Angle : 0.572 9.407 42272 Z= 0.292 Chirality : 0.042 0.150 4840 Planarity : 0.005 0.068 5272 Dihedral : 6.434 59.428 4472 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.14 % Allowed : 12.41 % Favored : 85.45 % 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: -0.01 (0.14), residues: 3716 helix: 0.82 (0.10), residues: 2472 sheet: -0.98 (0.34), residues: 200 loop : -1.71 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1187 TYR 0.015 0.001 TYR B 855 PHE 0.011 0.001 PHE B 644 TRP 0.014 0.001 TRP B 716 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (31144) covalent geometry : angle 0.57117 / 0.29 (42248) hydrogen bonds : bond 0.04260 / 2.86 ( 1816) hydrogen bonds : angle 4.35871 / 3.01 ( 5352) link_BETA1-4 : bond 0.00097 / 0.04 ( 4) link_BETA1-4 : angle 1.33882 / 0.78 ( 12) link_NAG-ASN : bond 0.00041 / 0.02 ( 4) link_NAG-ASN : angle 1.02287 / 0.62 ( 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 458 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 388 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.6963 (tpp) cc_final: 0.5147 (pmt) REVERT: A 270 MET cc_start: 0.3320 (mmp) cc_final: 0.2843 (mtp) REVERT: A 508 GLU cc_start: 0.6824 (tp30) cc_final: 0.6522 (tp30) REVERT: A 528 GLU cc_start: 0.7668 (pt0) cc_final: 0.7258 (mp0) REVERT: A 539 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7669 (mmm160) REVERT: A 664 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7762 (mp-120) REVERT: A 733 TYR cc_start: 0.7649 (m-10) cc_final: 0.7185 (m-10) REVERT: A 848 TYR cc_start: 0.7978 (t80) cc_final: 0.7697 (t80) REVERT: A 1044 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: A 1157 GLU cc_start: 0.7015 (tp30) cc_final: 0.6514 (mp0) REVERT: B 114 MET cc_start: 0.7018 (tpp) cc_final: 0.5133 (pmt) REVERT: B 270 MET cc_start: 0.3280 (mmp) cc_final: 0.2841 (mtp) REVERT: B 508 GLU cc_start: 0.6903 (tp30) cc_final: 0.6333 (tp30) REVERT: B 528 GLU cc_start: 0.7743 (pt0) cc_final: 0.7285 (mp0) REVERT: B 539 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7526 (mmm160) REVERT: B 645 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: B 664 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7611 (mp-120) REVERT: B 733 TYR cc_start: 0.7701 (m-10) cc_final: 0.7220 (m-10) REVERT: B 735 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7711 (t) REVERT: B 848 TYR cc_start: 0.7933 (t80) cc_final: 0.7727 (t80) REVERT: B 1157 GLU cc_start: 0.7051 (tp30) cc_final: 0.6473 (mp0) REVERT: B 1193 ASP cc_start: 0.7130 (m-30) cc_final: 0.6917 (m-30) REVERT: C 114 MET cc_start: 0.6977 (tpp) cc_final: 0.5131 (pmt) REVERT: C 270 MET cc_start: 0.3361 (mmp) cc_final: 0.2824 (mtp) REVERT: C 508 GLU cc_start: 0.6920 (tp30) cc_final: 0.6615 (tp30) REVERT: C 528 GLU cc_start: 0.7706 (pt0) cc_final: 0.7276 (mp0) REVERT: C 539 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7518 (mmm160) REVERT: C 664 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7778 (mp-120) REVERT: C 733 TYR cc_start: 0.7648 (m-10) cc_final: 0.7186 (m-10) REVERT: C 848 TYR cc_start: 0.7990 (t80) cc_final: 0.7707 (t80) REVERT: C 1044 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: C 1157 GLU cc_start: 0.7018 (tp30) cc_final: 0.6483 (mp0) REVERT: D 114 MET cc_start: 0.7017 (tpp) cc_final: 0.5148 (pmt) REVERT: D 270 MET cc_start: 0.3284 (mmp) cc_final: 0.2833 (mtp) REVERT: D 508 GLU cc_start: 0.6841 (tp30) cc_final: 0.6571 (tp30) REVERT: D 528 GLU cc_start: 0.7723 (pt0) cc_final: 0.7292 (mp0) REVERT: D 539 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7513 (mmm160) REVERT: D 664 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7782 (mp-120) REVERT: D 709 MET cc_start: 0.7737 (ttp) cc_final: 0.7501 (ttp) REVERT: D 733 TYR cc_start: 0.7642 (m-10) cc_final: 0.7169 (m-10) REVERT: D 848 TYR cc_start: 0.7982 (t80) cc_final: 0.7704 (t80) REVERT: D 1157 GLU cc_start: 0.7045 (tp30) cc_final: 0.6479 (mp0) outliers start: 70 outliers final: 20 residues processed: 421 average time/residue: 0.7277 time to fit residues: 357.2468 Evaluate side-chains 388 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 356 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 992 LEU Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1097 ASP 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 645 GLU Chi-restraints excluded: chain B residue 664 GLN Chi-restraints excluded: chain B residue 735 VAL 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 458 LEU 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 1044 GLN Chi-restraints excluded: chain C residue 1097 ASP Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 635 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 280 optimal weight: 9.9990 chunk 274 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 289 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 234 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN A1199 ASN B 432 ASN B1199 ASN C 432 ASN C 979 GLN D 432 ASN D1199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.218331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132632 restraints weight = 27650.722| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.12 r_work: 0.3150 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2716 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= 0.156 Angle : 0.573 9.468 42272 Z= 0.292 Chirality : 0.043 0.144 4840 Planarity : 0.005 0.068 5272 Dihedral : 6.215 59.977 4472 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.69 % Allowed : 13.02 % Favored : 84.29 % 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: 0.29 (0.14), residues: 3716 helix: 1.03 (0.10), residues: 2472 sheet: -0.84 (0.35), residues: 200 loop : -1.55 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1187 TYR 0.016 0.002 TYR B 855 PHE 0.012 0.001 PHE C 644 TRP 0.016 0.002 TRP C 716 HIS 0.003 0.001 HIS C1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (31144) covalent geometry : angle 0.57251 / 0.29 (42248) hydrogen bonds : bond 0.04286 / 2.88 ( 1816) hydrogen bonds : angle 4.26195 / 2.94 ( 5352) link_BETA1-4 : bond 0.00101 / 0.05 ( 4) link_BETA1-4 : angle 1.41715 / 0.83 ( 12) link_NAG-ASN : bond 0.00018 / 0.01 ( 4) link_NAG-ASN : angle 0.95840 / 0.58 ( 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 469 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 381 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6910 (tpp) cc_final: 0.5123 (pmt) REVERT: A 270 MET cc_start: 0.3585 (mmp) cc_final: 0.3179 (mtp) REVERT: A 479 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8157 (mmm) REVERT: A 480 ARG cc_start: 0.7047 (tpp-160) cc_final: 0.6559 (mmt90) REVERT: A 508 GLU cc_start: 0.6889 (tp30) cc_final: 0.6541 (tp30) REVERT: A 539 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7556 (mmm160) REVERT: A 645 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: A 659 ASN cc_start: 0.7595 (t0) cc_final: 0.7349 (t0) REVERT: A 664 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7615 (mp-120) REVERT: A 733 TYR cc_start: 0.7645 (m-10) cc_final: 0.7179 (m-10) REVERT: A 1157 GLU cc_start: 0.7154 (tp30) cc_final: 0.6690 (mp0) REVERT: A 1194 ARG cc_start: 0.6795 (mmm160) cc_final: 0.6250 (mmm160) REVERT: B 114 MET cc_start: 0.6918 (tpp) cc_final: 0.5113 (pmt) REVERT: B 270 MET cc_start: 0.3310 (mmp) cc_final: 0.2867 (mtp) REVERT: B 508 GLU cc_start: 0.6988 (tp30) cc_final: 0.6424 (tp30) REVERT: B 539 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7657 (mmm160) REVERT: B 659 ASN cc_start: 0.7624 (t0) cc_final: 0.7404 (t0) REVERT: B 664 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7562 (mp-120) REVERT: B 733 TYR cc_start: 0.7671 (m-10) cc_final: 0.7227 (m-10) REVERT: B 735 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7744 (t) REVERT: B 848 TYR cc_start: 0.7903 (t80) cc_final: 0.7690 (t80) REVERT: B 1157 GLU cc_start: 0.7059 (tp30) cc_final: 0.6554 (mp0) REVERT: B 1193 ASP cc_start: 0.7144 (m-30) cc_final: 0.6925 (m-30) REVERT: C 114 MET cc_start: 0.6935 (tpp) cc_final: 0.5151 (pmt) REVERT: C 270 MET cc_start: 0.3362 (mmp) cc_final: 0.2901 (mtp) REVERT: C 508 GLU cc_start: 0.6822 (tp30) cc_final: 0.6484 (tp30) REVERT: C 539 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7642 (mmm160) REVERT: C 659 ASN cc_start: 0.7667 (t0) cc_final: 0.7414 (t0) REVERT: C 664 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7606 (mp-120) REVERT: C 733 TYR cc_start: 0.7630 (m-10) cc_final: 0.7158 (m-10) REVERT: C 1044 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: C 1157 GLU cc_start: 0.7017 (tp30) cc_final: 0.6583 (mp0) REVERT: C 1194 ARG cc_start: 0.6776 (mmm160) cc_final: 0.6236 (mmm160) REVERT: D 114 MET cc_start: 0.6918 (tpp) cc_final: 0.5110 (pmt) REVERT: D 270 MET cc_start: 0.3311 (mmp) cc_final: 0.2869 (mtp) REVERT: D 508 GLU cc_start: 0.6855 (tp30) cc_final: 0.6516 (tp30) REVERT: D 539 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7565 (mmm160) REVERT: D 659 ASN cc_start: 0.7601 (t0) cc_final: 0.7360 (t0) REVERT: D 664 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7618 (mp-120) REVERT: D 733 TYR cc_start: 0.7609 (m-10) cc_final: 0.7123 (m-10) REVERT: D 848 TYR cc_start: 0.7873 (t80) cc_final: 0.7659 (t80) REVERT: D 1157 GLU cc_start: 0.7043 (tp30) cc_final: 0.6556 (mp0) outliers start: 88 outliers final: 44 residues processed: 428 average time/residue: 0.6661 time to fit residues: 332.5240 Evaluate side-chains 404 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 348 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 479 MET Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 645 GLU 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 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 197 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 635 SER 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 158 MET 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 635 SER 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 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 539 ARG Chi-restraints excluded: chain D residue 635 SER 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: 3.9990 chunk 287 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 331 optimal weight: 0.9990 chunk 181 optimal weight: 0.0980 chunk 270 optimal weight: 0.6980 chunk 286 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.218878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133669 restraints weight = 27609.927| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.10 r_work: 0.3139 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31152 Z= 0.140 Angle : 0.556 9.457 42272 Z= 0.283 Chirality : 0.042 0.140 4840 Planarity : 0.004 0.064 5272 Dihedral : 6.031 57.802 4472 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.48 % Allowed : 13.08 % Favored : 84.44 % 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: 0.49 (0.14), residues: 3716 helix: 1.19 (0.10), residues: 2472 sheet: -0.83 (0.35), residues: 200 loop : -1.48 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1187 TYR 0.014 0.001 TYR C 855 PHE 0.011 0.001 PHE C 644 TRP 0.017 0.001 TRP B 716 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (31144) covalent geometry : angle 0.55566 / 0.28 (42248) hydrogen bonds : bond 0.04111 / 2.76 ( 1816) hydrogen bonds : angle 4.18647 / 2.88 ( 5352) link_BETA1-4 : bond 0.00037 / 0.02 ( 4) link_BETA1-4 : angle 1.34848 / 0.78 ( 12) link_NAG-ASN : bond 0.00042 / 0.02 ( 4) link_NAG-ASN : angle 0.80937 / 0.49 ( 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 446 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 365 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6911 (tpp) cc_final: 0.5107 (pmt) REVERT: A 270 MET cc_start: 0.3546 (mmp) cc_final: 0.3153 (mtp) REVERT: A 480 ARG cc_start: 0.7068 (tpp-160) cc_final: 0.6564 (mmt90) REVERT: A 508 GLU cc_start: 0.6906 (tp30) cc_final: 0.6410 (tp30) REVERT: A 539 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7512 (mmm160) REVERT: A 645 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: A 664 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7624 (mp-120) REVERT: A 733 TYR cc_start: 0.7639 (m-10) cc_final: 0.7169 (m-10) REVERT: A 1157 GLU cc_start: 0.7339 (tp30) cc_final: 0.6780 (mp0) REVERT: A 1194 ARG cc_start: 0.6703 (mmm160) cc_final: 0.6163 (mmm160) REVERT: B 114 MET cc_start: 0.6919 (tpp) cc_final: 0.5119 (pmt) REVERT: B 270 MET cc_start: 0.3609 (mmp) cc_final: 0.3178 (mtt) REVERT: B 451 GLU cc_start: 0.7540 (mp0) cc_final: 0.7026 (tt0) REVERT: B 508 GLU cc_start: 0.6978 (tp30) cc_final: 0.6342 (tp30) REVERT: B 539 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7647 (mmm160) REVERT: B 659 ASN cc_start: 0.7489 (t0) cc_final: 0.7056 (t0) REVERT: B 664 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7522 (mp-120) REVERT: B 733 TYR cc_start: 0.7670 (m-10) cc_final: 0.7214 (m-10) REVERT: B 735 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7756 (t) REVERT: B 1157 GLU cc_start: 0.7363 (tp30) cc_final: 0.6781 (mp0) REVERT: B 1193 ASP cc_start: 0.7099 (m-30) cc_final: 0.6883 (m-30) REVERT: C 114 MET cc_start: 0.6911 (tpp) cc_final: 0.5092 (pmt) REVERT: C 270 MET cc_start: 0.3642 (mmp) cc_final: 0.3195 (mtt) REVERT: C 391 MET cc_start: 0.6315 (mmm) cc_final: 0.5916 (mmm) REVERT: C 457 MET cc_start: 0.8297 (tpt) cc_final: 0.7513 (tpt) REVERT: C 470 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6738 (pt0) REVERT: C 508 GLU cc_start: 0.6947 (tp30) cc_final: 0.6461 (tp30) REVERT: C 539 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7583 (mmm160) REVERT: C 664 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7598 (mp-120) REVERT: C 733 TYR cc_start: 0.7627 (m-10) cc_final: 0.7138 (m-10) REVERT: C 1044 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: C 1157 GLU cc_start: 0.7146 (tp30) cc_final: 0.6702 (mp0) REVERT: C 1194 ARG cc_start: 0.6701 (mmm160) cc_final: 0.6159 (mmm160) REVERT: D 114 MET cc_start: 0.6917 (tpp) cc_final: 0.5087 (pmt) REVERT: D 270 MET cc_start: 0.3677 (mmp) cc_final: 0.3260 (mtt) REVERT: D 508 GLU cc_start: 0.6871 (tp30) cc_final: 0.6385 (tp30) REVERT: D 539 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7489 (mmm160) REVERT: D 664 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7612 (mp-120) REVERT: D 733 TYR cc_start: 0.7626 (m-10) cc_final: 0.7138 (m-10) REVERT: D 1157 GLU cc_start: 0.7354 (tp30) cc_final: 0.6783 (mp0) REVERT: D 1194 ARG cc_start: 0.6744 (mmm160) cc_final: 0.6207 (mmm160) outliers start: 81 outliers final: 39 residues processed: 406 average time/residue: 0.6719 time to fit residues: 318.4513 Evaluate side-chains 402 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 351 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 635 SER Chi-restraints excluded: chain A residue 645 GLU 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 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 635 SER 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 1097 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 635 SER 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 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 539 ARG Chi-restraints excluded: chain D residue 635 SER 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 1097 ASP 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: 3.9990 chunk 217 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 306 optimal weight: 4.9990 chunk 335 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.220035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143955 restraints weight = 29397.611| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.63 r_work: 0.3408 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 31152 Z= 0.251 Angle : 0.658 9.501 42272 Z= 0.334 Chirality : 0.047 0.198 4840 Planarity : 0.005 0.066 5272 Dihedral : 6.044 52.744 4472 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.60 % Allowed : 13.39 % Favored : 84.02 % 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: 0.24 (0.14), residues: 3716 helix: 0.91 (0.10), residues: 2500 sheet: -0.63 (0.35), residues: 208 loop : -1.46 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 593 TYR 0.022 0.002 TYR D 855 PHE 0.017 0.002 PHE D 644 TRP 0.019 0.002 TRP B 716 HIS 0.005 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (31144) covalent geometry : angle 0.65723 / 0.33 (42248) hydrogen bonds : bond 0.04908 / 3.30 ( 1816) hydrogen bonds : angle 4.38297 / 3.02 ( 5352) link_BETA1-4 : bond 0.00376 / 0.17 ( 4) link_BETA1-4 : angle 1.68980 / 0.97 ( 12) link_NAG-ASN : bond 0.00443 / 0.20 ( 4) link_NAG-ASN : angle 1.21305 / 0.73 ( 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 458 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 373 time to evaluate : 1.205 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: 0.6832 (tpp) cc_final: 0.5139 (pmt) REVERT: A 270 MET cc_start: 0.3543 (mmp) cc_final: 0.3190 (mtp) REVERT: A 508 GLU cc_start: 0.7353 (tp30) cc_final: 0.6925 (tp30) REVERT: A 539 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7592 (mtm180) REVERT: A 733 TYR cc_start: 0.7789 (m-10) cc_final: 0.7411 (m-10) REVERT: A 1157 GLU cc_start: 0.7405 (tp30) cc_final: 0.7079 (mp0) REVERT: A 1194 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6589 (mmm160) REVERT: B 114 MET cc_start: 0.6805 (tpp) cc_final: 0.5145 (pmt) REVERT: B 270 MET cc_start: 0.3605 (mmp) cc_final: 0.3202 (mtt) REVERT: B 486 ASP cc_start: 0.7934 (p0) cc_final: 0.7734 (p0) REVERT: B 508 GLU cc_start: 0.7376 (tp30) cc_final: 0.6806 (tp30) REVERT: B 539 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7586 (mtm180) REVERT: B 733 TYR cc_start: 0.7835 (m-10) cc_final: 0.7467 (m-10) REVERT: B 735 VAL cc_start: 0.8390 (m) cc_final: 0.7986 (t) REVERT: B 1157 GLU cc_start: 0.7411 (tp30) cc_final: 0.7062 (mp0) REVERT: C 114 MET cc_start: 0.6777 (tpp) cc_final: 0.5053 (pmt) REVERT: C 270 MET cc_start: 0.3537 (mmp) cc_final: 0.3155 (mtt) REVERT: C 486 ASP cc_start: 0.7900 (p0) cc_final: 0.7688 (p0) REVERT: C 508 GLU cc_start: 0.7357 (tp30) cc_final: 0.6925 (tp30) REVERT: C 539 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7589 (mtm180) REVERT: C 733 TYR cc_start: 0.7875 (m-10) cc_final: 0.7503 (m-10) REVERT: C 1157 GLU cc_start: 0.7467 (tp30) cc_final: 0.7094 (mp0) REVERT: D 114 MET cc_start: 0.6838 (tpp) cc_final: 0.5140 (pmt) REVERT: D 270 MET cc_start: 0.3582 (mmp) cc_final: 0.3178 (mtt) REVERT: D 508 GLU cc_start: 0.7304 (tp30) cc_final: 0.6893 (tp30) REVERT: D 539 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7581 (mtm180) REVERT: D 733 TYR cc_start: 0.7863 (m-10) cc_final: 0.7491 (m-10) REVERT: D 1157 GLU cc_start: 0.7466 (tp30) cc_final: 0.7102 (mp0) REVERT: D 1194 ARG cc_start: 0.7163 (mmm160) cc_final: 0.6615 (mmm160) outliers start: 85 outliers final: 50 residues processed: 424 average time/residue: 0.6468 time to fit residues: 320.9282 Evaluate side-chains 399 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 345 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 607 MET Chi-restraints excluded: chain A residue 635 SER 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 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 607 MET Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 664 GLN 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 1078 LEU Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 635 SER 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 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 607 MET Chi-restraints excluded: chain D residue 635 SER 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 1078 LEU Chi-restraints excluded: chain D residue 1097 ASP 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: 0.0770 chunk 25 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 chunk 365 optimal weight: 0.6980 chunk 304 optimal weight: 0.5980 chunk 195 optimal weight: 6.9990 chunk 359 optimal weight: 0.5980 chunk 367 optimal weight: 0.6980 chunk 286 optimal weight: 9.9990 chunk 374 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.223552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148549 restraints weight = 29617.596| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.02 r_work: 0.3475 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31152 Z= 0.117 Angle : 0.551 9.533 42272 Z= 0.279 Chirality : 0.041 0.144 4840 Planarity : 0.004 0.059 5272 Dihedral : 5.716 52.043 4472 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.41 % Allowed : 13.88 % Favored : 83.71 % 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: 0.65 (0.14), residues: 3716 helix: 1.28 (0.10), residues: 2480 sheet: -0.59 (0.35), residues: 208 loop : -1.40 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1187 TYR 0.014 0.001 TYR A1111 PHE 0.010 0.001 PHE A 644 TRP 0.021 0.001 TRP A 716 HIS 0.004 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (31144) covalent geometry : angle 0.55088 / 0.28 (42248) hydrogen bonds : bond 0.03943 / 2.64 ( 1816) hydrogen bonds : angle 4.19860 / 2.89 ( 5352) link_BETA1-4 : bond 0.00246 / 0.11 ( 4) link_BETA1-4 : angle 1.26949 / 0.75 ( 12) link_NAG-ASN : bond 0.00139 / 0.06 ( 4) link_NAG-ASN : angle 0.82169 / 0.50 ( 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: 79 poor density : 373 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6740 (tpp) cc_final: 0.5027 (pmt) REVERT: A 270 MET cc_start: 0.3559 (mmp) cc_final: 0.3257 (mtp) REVERT: A 470 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: A 508 GLU cc_start: 0.7349 (tp30) cc_final: 0.6822 (tp30) REVERT: A 528 GLU cc_start: 0.7889 (pt0) cc_final: 0.7618 (tm-30) REVERT: A 539 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7655 (mtm180) REVERT: A 664 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7913 (mp-120) REVERT: A 709 MET cc_start: 0.7874 (ttp) cc_final: 0.7671 (ttp) REVERT: A 733 TYR cc_start: 0.7833 (m-10) cc_final: 0.7421 (m-10) REVERT: A 1059 ARG cc_start: 0.8667 (mtt180) cc_final: 0.8299 (mtt180) REVERT: A 1157 GLU cc_start: 0.7486 (tp30) cc_final: 0.6876 (mp0) REVERT: A 1194 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6592 (mmm160) REVERT: B 114 MET cc_start: 0.6791 (tpp) cc_final: 0.5120 (pmt) REVERT: B 270 MET cc_start: 0.3688 (mmp) cc_final: 0.3334 (mtp) REVERT: B 486 ASP cc_start: 0.8131 (p0) cc_final: 0.7915 (p0) REVERT: B 508 GLU cc_start: 0.7421 (tp30) cc_final: 0.6878 (tp30) REVERT: B 528 GLU cc_start: 0.7871 (pt0) cc_final: 0.7594 (tm-30) REVERT: B 539 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7567 (mmm160) REVERT: B 659 ASN cc_start: 0.7534 (t0) cc_final: 0.7257 (t0) REVERT: B 664 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7763 (mp-120) REVERT: B 709 MET cc_start: 0.7906 (ttp) cc_final: 0.7684 (ttp) REVERT: B 733 TYR cc_start: 0.7840 (m-10) cc_final: 0.7454 (m-10) REVERT: B 735 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.7962 (t) REVERT: B 1059 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8269 (mtt180) REVERT: B 1157 GLU cc_start: 0.7435 (tp30) cc_final: 0.7034 (mp0) REVERT: B 1194 ARG cc_start: 0.7116 (mmm160) cc_final: 0.6742 (mmp-170) REVERT: C 114 MET cc_start: 0.6749 (tpp) cc_final: 0.5054 (pmt) REVERT: C 270 MET cc_start: 0.3535 (mmp) cc_final: 0.3250 (mtp) REVERT: C 470 GLU cc_start: 0.7502 (pt0) cc_final: 0.6936 (pt0) REVERT: C 486 ASP cc_start: 0.8097 (p0) cc_final: 0.7876 (p0) REVERT: C 508 GLU cc_start: 0.7302 (tp30) cc_final: 0.6810 (tp30) REVERT: C 528 GLU cc_start: 0.7875 (pt0) cc_final: 0.7622 (tm-30) REVERT: C 539 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7563 (mmm160) REVERT: C 664 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7789 (mp-120) REVERT: C 733 TYR cc_start: 0.7837 (m-10) cc_final: 0.7429 (m-10) REVERT: C 1059 ARG cc_start: 0.8653 (mtt180) cc_final: 0.8274 (mtt180) REVERT: C 1157 GLU cc_start: 0.7507 (tp30) cc_final: 0.6903 (mp0) REVERT: C 1194 ARG cc_start: 0.7144 (mmm160) cc_final: 0.6584 (mmm160) REVERT: D 114 MET cc_start: 0.6756 (tpp) cc_final: 0.5044 (pmt) REVERT: D 270 MET cc_start: 0.3690 (mmp) cc_final: 0.3336 (mtp) REVERT: D 508 GLU cc_start: 0.7269 (tp30) cc_final: 0.6788 (tp30) REVERT: D 528 GLU cc_start: 0.7894 (pt0) cc_final: 0.7646 (tm-30) REVERT: D 539 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7600 (mmm160) REVERT: D 659 ASN cc_start: 0.7551 (t0) cc_final: 0.7253 (t0) REVERT: D 664 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7802 (mp-120) REVERT: D 709 MET cc_start: 0.7882 (ttp) cc_final: 0.7670 (ttp) REVERT: D 733 TYR cc_start: 0.7822 (m-10) cc_final: 0.7402 (m-10) REVERT: D 1059 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8264 (mtt180) REVERT: D 1157 GLU cc_start: 0.7489 (tp30) cc_final: 0.6879 (mp0) REVERT: D 1194 ARG cc_start: 0.7173 (mmm160) cc_final: 0.6619 (mmm160) outliers start: 79 outliers final: 31 residues processed: 416 average time/residue: 0.7036 time to fit residues: 340.8378 Evaluate side-chains 393 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 352 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 470 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 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 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 158 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 994 VAL 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 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 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: 0.8980 chunk 88 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 265 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 290 optimal weight: 0.0040 chunk 215 optimal weight: 7.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.221473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.143859 restraints weight = 29502.997| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.01 r_work: 0.3437 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31152 Z= 0.178 Angle : 0.601 11.348 42272 Z= 0.303 Chirality : 0.044 0.149 4840 Planarity : 0.005 0.061 5272 Dihedral : 5.618 51.896 4472 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.11 % Allowed : 14.30 % 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: 0.63 (0.14), residues: 3716 helix: 1.25 (0.10), residues: 2480 sheet: -0.53 (0.35), residues: 208 loop : -1.39 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 480 TYR 0.016 0.002 TYR C 855 PHE 0.014 0.002 PHE D 644 TRP 0.026 0.002 TRP D 716 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (31144) covalent geometry : angle 0.60028 / 0.30 (42248) hydrogen bonds : bond 0.04356 / 2.93 ( 1816) hydrogen bonds : angle 4.22613 / 2.91 ( 5352) link_BETA1-4 : bond 0.00211 / 0.10 ( 4) link_BETA1-4 : angle 1.53118 / 0.88 ( 12) link_NAG-ASN : bond 0.00132 / 0.06 ( 4) link_NAG-ASN : angle 0.96057 / 0.58 ( 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 422 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 353 time to evaluate : 1.027 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: 0.5078 (pmt) REVERT: A 270 MET cc_start: 0.3578 (mmp) cc_final: 0.3288 (mtt) REVERT: A 470 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: A 508 GLU cc_start: 0.7323 (tp30) cc_final: 0.6818 (tp30) REVERT: A 539 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7561 (mtm180) REVERT: A 733 TYR cc_start: 0.7820 (m-10) cc_final: 0.7426 (m-10) REVERT: A 885 TRP cc_start: 0.7064 (t-100) cc_final: 0.6774 (t60) REVERT: A 1157 GLU cc_start: 0.7463 (tp30) cc_final: 0.7098 (mp0) REVERT: A 1194 ARG cc_start: 0.7106 (mmm160) cc_final: 0.6538 (mmm160) REVERT: B 114 MET cc_start: 0.6787 (tpp) cc_final: 0.5160 (pmt) REVERT: B 270 MET cc_start: 0.3630 (mmp) cc_final: 0.3285 (mtp) REVERT: B 451 GLU cc_start: 0.7652 (mp0) cc_final: 0.7220 (tt0) REVERT: B 486 ASP cc_start: 0.8065 (p0) cc_final: 0.7863 (p0) REVERT: B 508 GLU cc_start: 0.7480 (tp30) cc_final: 0.6937 (tp30) REVERT: B 539 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7553 (mmm160) REVERT: B 664 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7822 (mp-120) REVERT: B 733 TYR cc_start: 0.7807 (m-10) cc_final: 0.7437 (m-10) REVERT: B 735 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.7977 (t) REVERT: B 885 TRP cc_start: 0.7034 (t-100) cc_final: 0.6738 (t60) REVERT: B 1157 GLU cc_start: 0.7486 (tp30) cc_final: 0.7096 (mp0) REVERT: B 1194 ARG cc_start: 0.7107 (mmm160) cc_final: 0.6722 (mmp-170) REVERT: C 114 MET cc_start: 0.6722 (tpp) cc_final: 0.5052 (pmt) REVERT: C 270 MET cc_start: 0.3529 (mmp) cc_final: 0.3241 (mtp) REVERT: C 470 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6899 (pt0) REVERT: C 486 ASP cc_start: 0.8028 (p0) cc_final: 0.7815 (p0) REVERT: C 508 GLU cc_start: 0.7331 (tp30) cc_final: 0.6804 (tp30) REVERT: C 539 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7593 (mmm160) REVERT: C 660 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6931 (mt-10) REVERT: C 664 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7902 (mp-120) REVERT: C 733 TYR cc_start: 0.7756 (m-10) cc_final: 0.7359 (m-10) REVERT: C 885 TRP cc_start: 0.7048 (t-100) cc_final: 0.6765 (t60) REVERT: C 1157 GLU cc_start: 0.7527 (tp30) cc_final: 0.7132 (mp0) REVERT: D 114 MET cc_start: 0.6733 (tpp) cc_final: 0.5031 (pmt) REVERT: D 270 MET cc_start: 0.3617 (mmp) cc_final: 0.3274 (mtp) REVERT: D 508 GLU cc_start: 0.7284 (tp30) cc_final: 0.6777 (tp30) REVERT: D 539 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7543 (mmm160) REVERT: D 664 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7819 (mp-120) REVERT: D 733 TYR cc_start: 0.7792 (m-10) cc_final: 0.7394 (m-10) REVERT: D 885 TRP cc_start: 0.7016 (t-100) cc_final: 0.6716 (t60) REVERT: D 1157 GLU cc_start: 0.7517 (tp30) cc_final: 0.7130 (mp0) REVERT: D 1194 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6600 (mmm160) outliers start: 69 outliers final: 37 residues processed: 395 average time/residue: 0.6767 time to fit residues: 312.0615 Evaluate side-chains 393 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 346 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 385 VAL 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 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 385 VAL 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 1071 VAL Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 158 MET 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 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 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 385 VAL 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 1071 VAL Chi-restraints excluded: chain D residue 1078 LEU 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: 1.9990 chunk 161 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 290 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 363 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 367 optimal weight: 0.5980 chunk 291 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.221924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145820 restraints weight = 29417.979| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.04 r_work: 0.3449 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31152 Z= 0.156 Angle : 0.590 11.792 42272 Z= 0.297 Chirality : 0.043 0.145 4840 Planarity : 0.004 0.059 5272 Dihedral : 5.460 51.598 4472 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.05 % Allowed : 14.64 % Favored : 83.31 % 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: 0.69 (0.14), residues: 3716 helix: 1.29 (0.10), residues: 2480 sheet: -0.49 (0.35), residues: 208 loop : -1.35 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 480 TYR 0.015 0.002 TYR B1111 PHE 0.013 0.001 PHE A 644 TRP 0.026 0.002 TRP D 716 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (31144) covalent geometry : angle 0.58929 / 0.30 (42248) hydrogen bonds : bond 0.04216 / 2.83 ( 1816) hydrogen bonds : angle 4.21079 / 2.90 ( 5352) link_BETA1-4 : bond 0.00098 / 0.04 ( 4) link_BETA1-4 : angle 1.49479 / 0.87 ( 12) link_NAG-ASN : bond 0.00080 / 0.04 ( 4) link_NAG-ASN : angle 0.91012 / 0.55 ( 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 420 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6742 (tpp) cc_final: 0.5096 (pmt) REVERT: A 270 MET cc_start: 0.3622 (mmp) cc_final: 0.3378 (mtp) REVERT: A 463 ASP cc_start: 0.7483 (m-30) cc_final: 0.7280 (m-30) REVERT: A 470 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6976 (pt0) REVERT: A 508 GLU cc_start: 0.7320 (tp30) cc_final: 0.6808 (tp30) REVERT: A 539 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7550 (mtm180) REVERT: A 664 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7870 (mp-120) REVERT: A 709 MET cc_start: 0.7917 (ttp) cc_final: 0.7697 (ttp) REVERT: A 733 TYR cc_start: 0.7813 (m-10) cc_final: 0.7458 (m-10) REVERT: A 885 TRP cc_start: 0.7140 (t-100) cc_final: 0.6850 (t60) REVERT: A 1157 GLU cc_start: 0.7431 (tp30) cc_final: 0.7082 (mp0) REVERT: A 1194 ARG cc_start: 0.7096 (mmm160) cc_final: 0.6518 (mmm160) REVERT: B 114 MET cc_start: 0.6723 (tpp) cc_final: 0.5050 (pmt) REVERT: B 270 MET cc_start: 0.3693 (mmp) cc_final: 0.3391 (OUTLIER) REVERT: B 451 GLU cc_start: 0.7634 (mp0) cc_final: 0.7203 (tt0) REVERT: B 486 ASP cc_start: 0.8090 (p0) cc_final: 0.7886 (p0) REVERT: B 508 GLU cc_start: 0.7472 (tp30) cc_final: 0.6956 (tp30) REVERT: B 539 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7512 (mmm160) REVERT: B 664 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7798 (mp-120) REVERT: B 709 MET cc_start: 0.7894 (ttp) cc_final: 0.7629 (ttp) REVERT: B 733 TYR cc_start: 0.7806 (m-10) cc_final: 0.7429 (m-10) REVERT: B 735 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.7979 (t) REVERT: B 885 TRP cc_start: 0.7136 (t-100) cc_final: 0.6800 (t60) REVERT: B 1157 GLU cc_start: 0.7459 (tp30) cc_final: 0.7074 (mp0) REVERT: B 1194 ARG cc_start: 0.7126 (mmm160) cc_final: 0.6724 (mmp-170) REVERT: C 114 MET cc_start: 0.6725 (tpp) cc_final: 0.5070 (pmt) REVERT: C 270 MET cc_start: 0.3609 (mmp) cc_final: 0.3378 (mtp) REVERT: C 279 MET cc_start: 0.5615 (mpp) cc_final: 0.4826 (mpp) REVERT: C 470 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: C 486 ASP cc_start: 0.8023 (p0) cc_final: 0.7808 (p0) REVERT: C 508 GLU cc_start: 0.7348 (tp30) cc_final: 0.6832 (tp30) REVERT: C 539 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7583 (mmm160) REVERT: C 664 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7824 (mp-120) REVERT: C 709 MET cc_start: 0.7932 (ttp) cc_final: 0.7646 (ttp) REVERT: C 733 TYR cc_start: 0.7761 (m-10) cc_final: 0.7405 (m-10) REVERT: C 885 TRP cc_start: 0.7139 (t-100) cc_final: 0.6836 (t60) REVERT: C 1157 GLU cc_start: 0.7501 (tp30) cc_final: 0.6904 (mp0) REVERT: D 114 MET cc_start: 0.6737 (tpp) cc_final: 0.5058 (pmt) REVERT: D 270 MET cc_start: 0.3689 (mmp) cc_final: 0.3379 (OUTLIER) REVERT: D 451 GLU cc_start: 0.7649 (mp0) cc_final: 0.7232 (tt0) REVERT: D 508 GLU cc_start: 0.7291 (tp30) cc_final: 0.6787 (tp30) REVERT: D 539 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7566 (mtm180) REVERT: D 660 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6940 (mt-10) REVERT: D 664 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7880 (mp-120) REVERT: D 709 MET cc_start: 0.7887 (ttp) cc_final: 0.7661 (ttp) REVERT: D 733 TYR cc_start: 0.7779 (m-10) cc_final: 0.7422 (m-10) REVERT: D 885 TRP cc_start: 0.7120 (t-100) cc_final: 0.6809 (t60) REVERT: D 1157 GLU cc_start: 0.7474 (tp30) cc_final: 0.7095 (mp0) REVERT: D 1194 ARG cc_start: 0.7111 (mmm160) cc_final: 0.6546 (mmm160) outliers start: 67 outliers final: 43 residues processed: 392 average time/residue: 0.6862 time to fit residues: 313.3566 Evaluate side-chains 402 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 350 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 385 VAL 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 848 TYR 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 1122 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 385 VAL 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 848 TYR 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 158 MET 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 848 TYR 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 1122 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 385 VAL 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 848 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 198 optimal weight: 0.0030 chunk 264 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 283 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 319 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4388 r_free = 0.4388 target = 0.220282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143986 restraints weight = 29530.303| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.17 r_work: 0.3409 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31152 Z= 0.215 Angle : 0.638 11.704 42272 Z= 0.322 Chirality : 0.045 0.176 4840 Planarity : 0.005 0.060 5272 Dihedral : 5.471 51.367 4472 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.51 % Allowed : 14.36 % Favored : 83.13 % 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: 0.52 (0.14), residues: 3716 helix: 1.11 (0.10), residues: 2504 sheet: -0.46 (0.35), residues: 208 loop : -1.34 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 935 TYR 0.019 0.002 TYR B 855 PHE 0.014 0.002 PHE D 644 TRP 0.028 0.002 TRP C 716 HIS 0.005 0.001 HIS D 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (31144) covalent geometry : angle 0.63754 / 0.32 (42248) hydrogen bonds : bond 0.04632 / 3.11 ( 1816) hydrogen bonds : angle 4.29223 / 2.96 ( 5352) link_BETA1-4 : bond 0.00314 / 0.14 ( 4) link_BETA1-4 : angle 1.64819 / 0.95 ( 12) link_NAG-ASN : bond 0.00359 / 0.16 ( 4) link_NAG-ASN : angle 1.16894 / 0.71 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14044.73 seconds wall clock time: 238 minutes 50.55 seconds (14330.55 seconds total)