Starting phenix.real_space_refine on Wed Mar 4 11:28:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3f_23653/03_2026/7m3f_23653_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3f_23653/03_2026/7m3f_23653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m3f_23653/03_2026/7m3f_23653_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3f_23653/03_2026/7m3f_23653_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m3f_23653/03_2026/7m3f_23653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3f_23653/03_2026/7m3f_23653.map" } resolution = 2.8 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= 0.006 sd= 0.135 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 71 5.16 5 C 8470 2.51 5 N 2113 2.21 5 O 2418 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13084 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6395 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 31, 'TRANS': 786} Chain breaks: 3 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 8, 'HIS:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6383 Classifications: {'peptide': 811} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 31, 'TRANS': 779} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" 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: "D" 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 105 Unusual residues: {' CA': 3, 'NAG': 4, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 906 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {' CA': 1, 'NAG': 5, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B 907 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.96, per 1000 atoms: 0.23 Number of scatterers: 13084 At special positions: 0 Unit cell: (95.46, 92.13, 190.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 71 16.00 P 2 15.00 F 6 9.00 O 2418 8.00 N 2113 7.00 C 8470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.04 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.04 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.04 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.04 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 901 " - " ASN A 261 " " NAG A 902 " - " ASN A 287 " " NAG A 903 " - " ASN A 468 " " NAG A 904 " - " ASN A 594 " " NAG B 901 " - " ASN B 261 " " NAG B 902 " - " ASN B 287 " " NAG B 903 " - " ASN B 488 " " NAG B 904 " - " ASN B 468 " " NAG B 905 " - " ASN B 594 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 541 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 603.1 milliseconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 48.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.690A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.608A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.514A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.611A pdb=" N ALA A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.658A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.720A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.884A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.657A pdb=" N ILE A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.553A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.623A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.505A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 removed outlier: 3.542A pdb=" N ILE A 528 " --> pdb=" O GLU A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 525 through 528' Processing helix chain 'A' and resid 610 through 637 removed outlier: 4.024A pdb=" N PHE A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 646 removed outlier: 3.633A pdb=" N THR A 646 " --> pdb=" O VAL A 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 643 through 646' Processing helix chain 'A' and resid 647 through 664 removed outlier: 3.758A pdb=" N SER A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.542A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 673 through 678 Processing helix chain 'A' and resid 680 through 698 removed outlier: 3.984A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 744 removed outlier: 4.045A pdb=" N VAL A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 738 " --> pdb=" O MET A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 793 removed outlier: 3.960A pdb=" N LEU A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.708A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 832 through 854 removed outlier: 4.072A pdb=" N VAL A 836 " --> pdb=" O PHE A 832 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 862 removed outlier: 4.411A pdb=" N TYR A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 874 removed outlier: 4.085A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 887 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.514A pdb=" N SER B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.756A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.737A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.920A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.542A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.841A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 removed outlier: 3.580A pdb=" N ILE B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.635A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.713A pdb=" N ASN B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.913A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.529A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 612 through 637 removed outlier: 3.512A pdb=" N PHE B 637 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.772A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.538A pdb=" N SER B 651 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 668 removed outlier: 3.655A pdb=" N PHE B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 673 through 678 removed outlier: 3.602A pdb=" N CYS B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 678' Processing helix chain 'B' and resid 679 through 698 removed outlier: 3.586A pdb=" N ALA B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 4.007A pdb=" N VAL B 728 " --> pdb=" O GLN B 724 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 793 removed outlier: 4.112A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 removed outlier: 3.650A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.192A pdb=" N TYR B 825 " --> pdb=" O PHE B 821 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 826 " --> pdb=" O ILE B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 831 through 861 removed outlier: 3.578A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 875 removed outlier: 4.154A pdb=" N SER B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.479A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.045A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AA5, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.629A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 762 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.356A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.955A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 320 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.071A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N CYS B 765 " --> pdb=" O GLU B 604 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1575 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: 2.28 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3637 1.34 - 1.46: 3268 1.46 - 1.58: 6410 1.58 - 1.70: 0 1.70 - 1.83: 84 Bond restraints: 13399 Sorted by residual: bond pdb=" N YP4 A 905 " pdb=" C3 YP4 A 905 " ideal model delta sigma weight residual 1.452 1.538 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" N YP4 B 906 " pdb=" C3 YP4 B 906 " ideal model delta sigma weight residual 1.452 1.538 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" N YP4 A 905 " pdb=" CA YP4 A 905 " ideal model delta sigma weight residual 1.457 1.539 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N YP4 B 906 " pdb=" CA YP4 B 906 " ideal model delta sigma weight residual 1.457 1.537 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O3 PO4 B 909 " pdb=" P PO4 B 909 " ideal model delta sigma weight residual 1.569 1.495 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 13394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 17461 2.30 - 4.61: 636 4.61 - 6.91: 76 6.91 - 9.21: 19 9.21 - 11.51: 7 Bond angle restraints: 18199 Sorted by residual: angle pdb=" N LYS A 882 " pdb=" CA LYS A 882 " pdb=" C LYS A 882 " ideal model delta sigma weight residual 113.23 106.69 6.54 1.22e+00 6.72e-01 2.87e+01 angle pdb=" C PRO B 89 " pdb=" N ASN B 90 " pdb=" CA ASN B 90 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" CA PHE A 881 " pdb=" CB PHE A 881 " pdb=" CG PHE A 881 " ideal model delta sigma weight residual 113.80 118.60 -4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" CB LYS B 119 " pdb=" CG LYS B 119 " pdb=" CD LYS B 119 " ideal model delta sigma weight residual 111.30 100.67 10.63 2.30e+00 1.89e-01 2.13e+01 angle pdb=" N PHE B 862 " pdb=" CA PHE B 862 " pdb=" CB PHE B 862 " ideal model delta sigma weight residual 110.45 117.06 -6.61 1.44e+00 4.82e-01 2.10e+01 ... (remaining 18194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7511 17.87 - 35.75: 467 35.75 - 53.62: 72 53.62 - 71.49: 20 71.49 - 89.37: 9 Dihedral angle restraints: 8079 sinusoidal: 3334 harmonic: 4745 Sorted by residual: dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual 93.00 173.61 -80.61 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 154.65 -61.65 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CA VAL A 142 " pdb=" C VAL A 142 " pdb=" N GLY A 143 " pdb=" CA GLY A 143 " ideal model delta harmonic sigma weight residual -180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 8076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1722 0.080 - 0.160: 317 0.160 - 0.240: 33 0.240 - 0.320: 6 0.320 - 0.400: 1 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CB VAL B 702 " pdb=" CA VAL B 702 " pdb=" CG1 VAL B 702 " pdb=" CG2 VAL B 702 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA CYS B 598 " pdb=" N CYS B 598 " pdb=" C CYS B 598 " pdb=" CB CYS B 598 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB THR B 445 " pdb=" CA THR B 445 " pdb=" OG1 THR B 445 " pdb=" CG2 THR B 445 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2076 not shown) Planarity restraints: 2297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 287 " 0.039 2.00e-02 2.50e+03 4.00e-02 2.00e+01 pdb=" CG ASN A 287 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 287 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 287 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 640 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO A 641 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA YP4 A 905 " 0.047 2.00e-02 2.50e+03 2.24e-02 1.38e+01 pdb=" CB YP4 A 905 " -0.011 2.00e-02 2.50e+03 pdb=" CG YP4 A 905 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 YP4 A 905 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 YP4 A 905 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 YP4 A 905 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 YP4 A 905 " -0.024 2.00e-02 2.50e+03 pdb=" CZ YP4 A 905 " -0.001 2.00e-02 2.50e+03 pdb=" C14 YP4 A 905 " -0.027 2.00e-02 2.50e+03 pdb=" C15 YP4 A 905 " -0.016 2.00e-02 2.50e+03 pdb=" C16 YP4 A 905 " 0.013 2.00e-02 2.50e+03 ... (remaining 2294 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2673 2.78 - 3.31: 11229 3.31 - 3.84: 20365 3.84 - 4.37: 24116 4.37 - 4.90: 42042 Nonbonded interactions: 100425 Sorted by model distance: nonbonded pdb=" O LYS A 805 " pdb=" OG1 THR A 808 " model vdw 2.245 3.040 nonbonded pdb=" O ALA A 548 " pdb=" OG SER A 574 " model vdw 2.262 3.040 nonbonded pdb=" O PHE A 846 " pdb=" O GLY A 847 " model vdw 2.311 3.040 nonbonded pdb=" O ALA B 824 " pdb=" OG1 THR B 828 " model vdw 2.317 3.040 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.321 3.040 ... (remaining 100420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 131 or (resid 132 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 635 or (resid 636 through 637 and (name N \ or name CA or name C or name O or name CB )) or resid 638 through 700 or (resid \ 701 and (name N or name CA or name C or name O or name CB )) or resid 702 throug \ h 831 or (resid 832 and (name N or name CA or name C or name O or name CB )) or \ resid 833 through 861 or (resid 862 through 863 and (name N or name CA or name C \ or name O or name CB )) or resid 864 through 865 or (resid 866 through 867 and \ (name N or name CA or name C or name O or name CB )) or resid 868 through 876 or \ resid 901 through 907)) selection = (chain 'B' and (resid 20 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 124 or (re \ sid 125 and (name N or name CA or name C or name O or name CB )) or (resid 131 t \ hrough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 \ through 361 or (resid 362 and (name N or name CA or name C or name O or name CB \ )) or resid 392 through 480 or (resid 481 and (name N or name CA or name C or n \ ame O or name CB )) or resid 482 through 498 or (resid 499 through 500 and (name \ N or name CA or name C or name O or name CB )) or resid 501 through 591 or (res \ id 592 through 593 and (name N or name CA or name C or name O or name CB )) or r \ esid 594 through 650 or (resid 651 and (name N or name CA or name C or name O or \ name CB )) or resid 652 through 663 or (resid 664 through 665 and (name N or na \ me CA or name C or name O or name CB )) or resid 666 through 670 or (resid 671 a \ nd (name N or name CA or name C or name O or name CB )) or resid 672 through 698 \ or (resid 699 and (name N or name CA or name C or name O or name CB )) or resid \ 700 through 703 or (resid 704 and (name N or name CA or name C or name O or nam \ e CB )) or resid 722 through 728 or (resid 729 and (name N or name CA or name C \ or name O or name CB )) or resid 730 through 733 or (resid 734 and (name N or na \ me CA or name C or name O or name CB )) or resid 735 through 758 or (resid 759 a \ nd (name N or name CA or name C or name O or name CB )) or resid 760 through 853 \ or (resid 854 and (name N or name CA or name C or name O or name CB )) or resid \ 855 through 870 or (resid 871 and (name N or name CA or name C or name O or nam \ e CB )) or resid 872 through 876 or resid 902 through 908)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 3.300 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.270 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.008 0.086 13432 Z= 0.374 Angle : 1.053 18.988 18280 Z= 0.578 Chirality : 0.063 0.400 2079 Planarity : 0.008 0.109 2285 Dihedral : 12.467 89.365 4955 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.18), residues: 1613 helix: -1.41 (0.17), residues: 675 sheet: -1.53 (0.33), residues: 212 loop : -1.92 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 648 TYR 0.037 0.003 TYR B 425 PHE 0.036 0.003 PHE B 846 TRP 0.049 0.003 TRP A 818 HIS 0.025 0.002 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00818 (13399) covalent geometry : angle 1.01186 (18199) SS BOND : bond 0.00681 ( 18) SS BOND : angle 2.19181 ( 36) hydrogen bonds : bond 0.15809 ( 549) hydrogen bonds : angle 6.24870 ( 1575) link_BETA1-4 : bond 0.00994 ( 3) link_BETA1-4 : angle 3.75274 ( 9) link_NAG-ASN : bond 0.00793 ( 12) link_NAG-ASN : angle 6.08098 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 751 TYR cc_start: 0.8128 (t80) cc_final: 0.7921 (t80) REVERT: A 792 PHE cc_start: 0.8874 (t80) cc_final: 0.8628 (t80) REVERT: A 796 LYS cc_start: 0.8749 (mttm) cc_final: 0.8050 (pmtt) outliers start: 0 outliers final: 3 residues processed: 193 average time/residue: 0.4062 time to fit residues: 88.1619 Evaluate side-chains 161 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain B residue 695 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS A 753 ASN B 463 HIS B 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.081861 restraints weight = 20952.164| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.70 r_work: 0.2841 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13432 Z= 0.162 Angle : 0.638 13.296 18280 Z= 0.330 Chirality : 0.046 0.239 2079 Planarity : 0.005 0.079 2285 Dihedral : 7.225 59.441 2084 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.90 % Allowed : 7.37 % Favored : 90.74 % 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: -1.38 (0.20), residues: 1613 helix: 0.11 (0.19), residues: 706 sheet: -1.42 (0.33), residues: 218 loop : -1.79 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.019 0.002 TYR B 425 PHE 0.015 0.002 PHE A 469 TRP 0.020 0.002 TRP A 675 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00373 (13399) covalent geometry : angle 0.60845 (18199) SS BOND : bond 0.00475 ( 18) SS BOND : angle 1.62087 ( 36) hydrogen bonds : bond 0.05952 ( 549) hydrogen bonds : angle 4.48996 ( 1575) link_BETA1-4 : bond 0.00143 ( 3) link_BETA1-4 : angle 1.91122 ( 9) link_NAG-ASN : bond 0.00448 ( 12) link_NAG-ASN : angle 3.97268 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.531 Fit side-chains REVERT: A 340 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7820 (mtp180) REVERT: A 751 TYR cc_start: 0.8258 (t80) cc_final: 0.7880 (t80) REVERT: A 753 ASN cc_start: 0.8988 (t0) cc_final: 0.8734 (t0) REVERT: A 792 PHE cc_start: 0.8905 (t80) cc_final: 0.8559 (t80) REVERT: A 796 LYS cc_start: 0.8965 (mttm) cc_final: 0.8038 (pmtt) REVERT: A 855 ASN cc_start: 0.9092 (t0) cc_final: 0.8662 (t0) REVERT: B 50 ASP cc_start: 0.8236 (p0) cc_final: 0.7965 (p0) REVERT: B 205 ARG cc_start: 0.8609 (mtp-110) cc_final: 0.8356 (mtt180) REVERT: B 771 MET cc_start: 0.3203 (OUTLIER) cc_final: 0.2399 (ttp) outliers start: 26 outliers final: 12 residues processed: 182 average time/residue: 0.3757 time to fit residues: 78.0742 Evaluate side-chains 176 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 2 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 0.0010 chunk 76 optimal weight: 6.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 673 GLN B 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.083182 restraints weight = 21098.322| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.71 r_work: 0.2849 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13432 Z= 0.145 Angle : 0.588 11.176 18280 Z= 0.300 Chirality : 0.045 0.225 2079 Planarity : 0.004 0.069 2285 Dihedral : 6.361 54.996 2080 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.33 % Allowed : 9.04 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1613 helix: 0.78 (0.20), residues: 707 sheet: -1.31 (0.34), residues: 214 loop : -1.66 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.022 0.002 TYR B 573 PHE 0.023 0.001 PHE A 788 TRP 0.015 0.001 TRP A 675 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00340 (13399) covalent geometry : angle 0.56372 (18199) SS BOND : bond 0.00332 ( 18) SS BOND : angle 1.37283 ( 36) hydrogen bonds : bond 0.05134 ( 549) hydrogen bonds : angle 4.15089 ( 1575) link_BETA1-4 : bond 0.00304 ( 3) link_BETA1-4 : angle 1.77675 ( 9) link_NAG-ASN : bond 0.00459 ( 12) link_NAG-ASN : angle 3.53665 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.533 Fit side-chains REVERT: A 119 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6952 (ttmt) REVERT: A 340 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: A 608 TRP cc_start: 0.8924 (m100) cc_final: 0.8576 (m100) REVERT: A 701 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6621 (mmp-170) REVERT: A 751 TYR cc_start: 0.8220 (t80) cc_final: 0.7817 (t80) REVERT: A 753 ASN cc_start: 0.8896 (t0) cc_final: 0.8677 (t0) REVERT: A 792 PHE cc_start: 0.8912 (t80) cc_final: 0.8539 (t80) REVERT: A 796 LYS cc_start: 0.8991 (mttm) cc_final: 0.8053 (pmtt) REVERT: A 855 ASN cc_start: 0.9072 (t0) cc_final: 0.8486 (t0) REVERT: A 881 PHE cc_start: 0.5274 (OUTLIER) cc_final: 0.2020 (t80) REVERT: B 50 ASP cc_start: 0.8184 (p0) cc_final: 0.7936 (p0) REVERT: B 189 ASN cc_start: 0.9033 (p0) cc_final: 0.8815 (p0) REVERT: B 588 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8490 (t0) REVERT: B 688 PHE cc_start: 0.8507 (t80) cc_final: 0.8267 (t80) outliers start: 32 outliers final: 14 residues processed: 180 average time/residue: 0.3553 time to fit residues: 73.0792 Evaluate side-chains 183 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN B 463 HIS B 673 GLN B 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.082083 restraints weight = 21107.259| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.71 r_work: 0.2816 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13432 Z= 0.209 Angle : 0.629 10.752 18280 Z= 0.324 Chirality : 0.047 0.238 2079 Planarity : 0.005 0.066 2285 Dihedral : 6.275 57.678 2080 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 2.55 % Allowed : 10.80 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1613 helix: 0.96 (0.20), residues: 701 sheet: -1.34 (0.34), residues: 214 loop : -1.69 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.028 0.002 TYR A 744 PHE 0.016 0.002 PHE A 469 TRP 0.013 0.002 TRP A 299 HIS 0.006 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00509 (13399) covalent geometry : angle 0.60484 (18199) SS BOND : bond 0.00486 ( 18) SS BOND : angle 1.60392 ( 36) hydrogen bonds : bond 0.05865 ( 549) hydrogen bonds : angle 4.21643 ( 1575) link_BETA1-4 : bond 0.00210 ( 3) link_BETA1-4 : angle 1.90453 ( 9) link_NAG-ASN : bond 0.00490 ( 12) link_NAG-ASN : angle 3.51679 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.531 Fit side-chains REVERT: A 340 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7812 (mtp180) REVERT: A 701 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6665 (mmp-170) REVERT: A 751 TYR cc_start: 0.8236 (t80) cc_final: 0.7809 (t80) REVERT: A 753 ASN cc_start: 0.8871 (t0) cc_final: 0.8622 (t0) REVERT: A 792 PHE cc_start: 0.8921 (t80) cc_final: 0.8553 (t80) REVERT: A 796 LYS cc_start: 0.9049 (mttm) cc_final: 0.8078 (pmtt) REVERT: A 855 ASN cc_start: 0.9090 (t0) cc_final: 0.8546 (t0) REVERT: A 881 PHE cc_start: 0.5338 (OUTLIER) cc_final: 0.1977 (t80) REVERT: B 50 ASP cc_start: 0.8197 (p0) cc_final: 0.7939 (p0) REVERT: B 189 ASN cc_start: 0.9124 (p0) cc_final: 0.8886 (p0) outliers start: 35 outliers final: 20 residues processed: 183 average time/residue: 0.3643 time to fit residues: 76.2715 Evaluate side-chains 181 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 860 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 146 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 673 GLN B 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.083130 restraints weight = 21324.726| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.72 r_work: 0.2836 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13432 Z= 0.152 Angle : 0.581 9.609 18280 Z= 0.296 Chirality : 0.045 0.263 2079 Planarity : 0.004 0.063 2285 Dihedral : 5.916 55.263 2080 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 3.06 % Allowed : 11.52 % Favored : 85.41 % 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: -0.60 (0.21), residues: 1613 helix: 1.09 (0.20), residues: 703 sheet: -1.32 (0.34), residues: 212 loop : -1.66 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.028 0.002 TYR A 744 PHE 0.025 0.001 PHE B 789 TRP 0.013 0.001 TRP A 675 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00361 (13399) covalent geometry : angle 0.55805 (18199) SS BOND : bond 0.00361 ( 18) SS BOND : angle 1.21800 ( 36) hydrogen bonds : bond 0.05050 ( 549) hydrogen bonds : angle 4.09927 ( 1575) link_BETA1-4 : bond 0.00311 ( 3) link_BETA1-4 : angle 1.65059 ( 9) link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 3.39753 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.425 Fit side-chains REVERT: A 340 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7819 (mtp180) REVERT: A 608 TRP cc_start: 0.8918 (m100) cc_final: 0.8578 (m100) REVERT: A 659 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7848 (mt) REVERT: A 701 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6513 (mmp-170) REVERT: A 751 TYR cc_start: 0.8267 (t80) cc_final: 0.7819 (t80) REVERT: A 753 ASN cc_start: 0.8854 (t0) cc_final: 0.8625 (t0) REVERT: A 796 LYS cc_start: 0.9031 (mttm) cc_final: 0.8068 (pmtt) REVERT: A 799 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7191 (pt0) REVERT: A 855 ASN cc_start: 0.9055 (t0) cc_final: 0.8545 (t0) REVERT: A 881 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.2182 (t80) REVERT: B 50 ASP cc_start: 0.8194 (p0) cc_final: 0.7941 (p0) REVERT: B 189 ASN cc_start: 0.9014 (p0) cc_final: 0.8799 (p0) outliers start: 42 outliers final: 20 residues processed: 181 average time/residue: 0.3774 time to fit residues: 77.8528 Evaluate side-chains 185 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 860 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 23 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 HIS B 673 GLN B 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.083603 restraints weight = 21091.938| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.62 r_work: 0.2853 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13432 Z= 0.144 Angle : 0.601 20.851 18280 Z= 0.300 Chirality : 0.053 1.315 2079 Planarity : 0.004 0.060 2285 Dihedral : 5.934 55.488 2080 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.70 % Allowed : 12.62 % Favored : 84.68 % 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 (0.21), residues: 1613 helix: 1.15 (0.20), residues: 703 sheet: -1.29 (0.34), residues: 212 loop : -1.61 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 286 TYR 0.027 0.002 TYR A 744 PHE 0.024 0.001 PHE A 814 TRP 0.012 0.001 TRP A 530 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00340 (13399) covalent geometry : angle 0.55873 (18199) SS BOND : bond 0.00329 ( 18) SS BOND : angle 1.15509 ( 36) hydrogen bonds : bond 0.04899 ( 549) hydrogen bonds : angle 4.06102 ( 1575) link_BETA1-4 : bond 0.00251 ( 3) link_BETA1-4 : angle 1.61821 ( 9) link_NAG-ASN : bond 0.00795 ( 12) link_NAG-ASN : angle 4.86235 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.373 Fit side-chains REVERT: A 340 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7775 (mtp180) REVERT: A 608 TRP cc_start: 0.8941 (m100) cc_final: 0.8623 (m100) REVERT: A 625 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 701 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6524 (mmp-170) REVERT: A 751 TYR cc_start: 0.8268 (t80) cc_final: 0.7839 (t80) REVERT: A 753 ASN cc_start: 0.8850 (t0) cc_final: 0.8626 (t0) REVERT: A 796 LYS cc_start: 0.9066 (mttm) cc_final: 0.8072 (pmtt) REVERT: A 799 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7168 (pt0) REVERT: A 881 PHE cc_start: 0.5408 (OUTLIER) cc_final: 0.2174 (t80) REVERT: B 50 ASP cc_start: 0.8165 (p0) cc_final: 0.7913 (p0) outliers start: 37 outliers final: 20 residues processed: 179 average time/residue: 0.3734 time to fit residues: 76.5400 Evaluate side-chains 180 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 860 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 60 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 42 optimal weight: 0.0070 chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 19 optimal weight: 0.4980 chunk 131 optimal weight: 0.0870 chunk 116 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS A 855 ASN B 673 GLN ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.084809 restraints weight = 21118.515| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.71 r_work: 0.2873 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13432 Z= 0.109 Angle : 0.548 10.697 18280 Z= 0.276 Chirality : 0.043 0.220 2079 Planarity : 0.004 0.057 2285 Dihedral : 5.398 53.646 2080 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 2.19 % Allowed : 13.20 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1613 helix: 1.31 (0.20), residues: 701 sheet: -1.20 (0.35), residues: 212 loop : -1.53 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.025 0.001 TYR A 744 PHE 0.025 0.001 PHE A 814 TRP 0.011 0.001 TRP A 530 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00240 (13399) covalent geometry : angle 0.53253 (18199) SS BOND : bond 0.00227 ( 18) SS BOND : angle 0.91874 ( 36) hydrogen bonds : bond 0.04171 ( 549) hydrogen bonds : angle 3.94173 ( 1575) link_BETA1-4 : bond 0.00378 ( 3) link_BETA1-4 : angle 1.39218 ( 9) link_NAG-ASN : bond 0.00579 ( 12) link_NAG-ASN : angle 2.75471 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.506 Fit side-chains REVERT: A 340 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7817 (mtp180) REVERT: A 608 TRP cc_start: 0.8915 (m100) cc_final: 0.8591 (m100) REVERT: A 701 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6612 (mmp-170) REVERT: A 751 TYR cc_start: 0.8205 (t80) cc_final: 0.7707 (t80) REVERT: A 753 ASN cc_start: 0.8789 (t0) cc_final: 0.8552 (t0) REVERT: A 796 LYS cc_start: 0.9074 (mttm) cc_final: 0.8059 (pmtt) REVERT: A 799 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7160 (pt0) REVERT: B 50 ASP cc_start: 0.8185 (p0) cc_final: 0.7949 (p0) REVERT: B 753 ASN cc_start: 0.8280 (t0) cc_final: 0.7956 (t0) REVERT: B 756 LEU cc_start: 0.9110 (mp) cc_final: 0.8742 (mp) REVERT: B 760 ILE cc_start: 0.8444 (pt) cc_final: 0.8145 (pp) outliers start: 30 outliers final: 16 residues processed: 176 average time/residue: 0.3836 time to fit residues: 76.7449 Evaluate side-chains 172 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 860 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 0.7980 chunk 30 optimal weight: 0.0370 chunk 153 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 0.0470 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS A 855 ASN B 463 HIS B 673 GLN ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.084989 restraints weight = 20979.630| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.70 r_work: 0.2875 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13432 Z= 0.112 Angle : 0.542 12.212 18280 Z= 0.275 Chirality : 0.043 0.199 2079 Planarity : 0.004 0.057 2285 Dihedral : 5.242 54.544 2080 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 1.97 % Allowed : 14.00 % Favored : 84.03 % 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: -0.25 (0.21), residues: 1613 helix: 1.40 (0.20), residues: 700 sheet: -1.13 (0.35), residues: 212 loop : -1.49 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.022 0.001 TYR A 744 PHE 0.027 0.001 PHE A 814 TRP 0.013 0.001 TRP A 818 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00251 (13399) covalent geometry : angle 0.52846 (18199) SS BOND : bond 0.00235 ( 18) SS BOND : angle 0.92676 ( 36) hydrogen bonds : bond 0.04197 ( 549) hydrogen bonds : angle 3.91414 ( 1575) link_BETA1-4 : bond 0.00376 ( 3) link_BETA1-4 : angle 1.38627 ( 9) link_NAG-ASN : bond 0.00487 ( 12) link_NAG-ASN : angle 2.62312 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.380 Fit side-chains REVERT: A 340 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7790 (mtp180) REVERT: A 608 TRP cc_start: 0.8908 (m100) cc_final: 0.8558 (m100) REVERT: A 701 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6616 (mmp-170) REVERT: A 751 TYR cc_start: 0.8184 (t80) cc_final: 0.7692 (t80) REVERT: A 753 ASN cc_start: 0.8784 (t0) cc_final: 0.8545 (t0) REVERT: A 796 LYS cc_start: 0.9115 (mttm) cc_final: 0.8073 (pmtt) REVERT: A 881 PHE cc_start: 0.5233 (OUTLIER) cc_final: 0.2155 (t80) REVERT: B 50 ASP cc_start: 0.8187 (p0) cc_final: 0.7950 (p0) REVERT: B 753 ASN cc_start: 0.8267 (t0) cc_final: 0.7946 (t0) REVERT: B 756 LEU cc_start: 0.9112 (mp) cc_final: 0.8727 (mp) REVERT: B 760 ILE cc_start: 0.8430 (pt) cc_final: 0.8119 (pp) outliers start: 27 outliers final: 19 residues processed: 171 average time/residue: 0.3559 time to fit residues: 69.7072 Evaluate side-chains 175 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 860 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 31 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS A 583 ASN A 855 ASN B 673 GLN ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.081975 restraints weight = 21056.333| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.70 r_work: 0.2820 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13432 Z= 0.217 Angle : 0.633 11.577 18280 Z= 0.324 Chirality : 0.048 0.215 2079 Planarity : 0.004 0.058 2285 Dihedral : 5.734 58.158 2080 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 1.97 % Allowed : 14.44 % 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: -0.44 (0.21), residues: 1613 helix: 1.20 (0.20), residues: 700 sheet: -1.22 (0.35), residues: 213 loop : -1.55 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.018 0.002 TYR A 425 PHE 0.024 0.002 PHE A 814 TRP 0.015 0.002 TRP A 818 HIS 0.010 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00534 (13399) covalent geometry : angle 0.61778 (18199) SS BOND : bond 0.00484 ( 18) SS BOND : angle 1.39229 ( 36) hydrogen bonds : bond 0.05580 ( 549) hydrogen bonds : angle 4.11982 ( 1575) link_BETA1-4 : bond 0.00190 ( 3) link_BETA1-4 : angle 1.80441 ( 9) link_NAG-ASN : bond 0.00433 ( 12) link_NAG-ASN : angle 2.78233 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.474 Fit side-chains REVERT: A 340 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7781 (mtp180) REVERT: A 608 TRP cc_start: 0.8942 (m100) cc_final: 0.8608 (m100) REVERT: A 625 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 701 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6620 (mmp-170) REVERT: A 751 TYR cc_start: 0.8249 (t80) cc_final: 0.7808 (t80) REVERT: A 753 ASN cc_start: 0.8826 (t0) cc_final: 0.8587 (t0) REVERT: A 793 LYS cc_start: 0.8506 (ttmt) cc_final: 0.7899 (tptm) REVERT: A 796 LYS cc_start: 0.9128 (mttm) cc_final: 0.8104 (pmtt) REVERT: A 799 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7193 (pt0) REVERT: A 881 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.2144 (t80) REVERT: B 50 ASP cc_start: 0.8204 (p0) cc_final: 0.7945 (p0) REVERT: B 644 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7840 (tptm) REVERT: B 753 ASN cc_start: 0.8284 (t0) cc_final: 0.7947 (t0) REVERT: B 756 LEU cc_start: 0.9125 (mp) cc_final: 0.8730 (mp) REVERT: B 760 ILE cc_start: 0.8441 (pt) cc_final: 0.8127 (pp) outliers start: 27 outliers final: 16 residues processed: 172 average time/residue: 0.3803 time to fit residues: 74.4301 Evaluate side-chains 178 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 860 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 141 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS A 583 ASN A 855 ASN B 463 HIS B 673 GLN B 724 GLN ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.082821 restraints weight = 20928.311| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.70 r_work: 0.2840 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13432 Z= 0.160 Angle : 0.592 14.372 18280 Z= 0.302 Chirality : 0.045 0.252 2079 Planarity : 0.004 0.058 2285 Dihedral : 5.568 55.803 2078 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 1.60 % Allowed : 14.59 % Favored : 83.81 % 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: -0.42 (0.21), residues: 1613 helix: 1.21 (0.20), residues: 701 sheet: -1.22 (0.34), residues: 213 loop : -1.53 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.018 0.002 TYR A 744 PHE 0.029 0.001 PHE A 814 TRP 0.017 0.001 TRP A 818 HIS 0.010 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00384 (13399) covalent geometry : angle 0.57692 (18199) SS BOND : bond 0.00346 ( 18) SS BOND : angle 1.14057 ( 36) hydrogen bonds : bond 0.04988 ( 549) hydrogen bonds : angle 4.06675 ( 1575) link_BETA1-4 : bond 0.00239 ( 3) link_BETA1-4 : angle 1.64349 ( 9) link_NAG-ASN : bond 0.00439 ( 12) link_NAG-ASN : angle 2.76185 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.483 Fit side-chains REVERT: A 340 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7764 (mtp180) REVERT: A 608 TRP cc_start: 0.8934 (m100) cc_final: 0.8598 (m100) REVERT: A 701 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6611 (mmp-170) REVERT: A 751 TYR cc_start: 0.8194 (t80) cc_final: 0.7751 (t80) REVERT: A 753 ASN cc_start: 0.8809 (t0) cc_final: 0.8569 (t0) REVERT: A 796 LYS cc_start: 0.9129 (mttm) cc_final: 0.8128 (pmtt) REVERT: A 799 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7224 (pt0) REVERT: A 811 MET cc_start: 0.8374 (mmm) cc_final: 0.8084 (tpp) REVERT: A 881 PHE cc_start: 0.5290 (OUTLIER) cc_final: 0.2067 (t80) REVERT: B 50 ASP cc_start: 0.8192 (p0) cc_final: 0.7946 (p0) REVERT: B 644 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7852 (tptm) REVERT: B 724 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: B 753 ASN cc_start: 0.8212 (t0) cc_final: 0.7886 (t0) REVERT: B 756 LEU cc_start: 0.9138 (mp) cc_final: 0.8747 (mp) REVERT: B 760 ILE cc_start: 0.8412 (pt) cc_final: 0.8116 (pp) REVERT: B 811 MET cc_start: 0.8946 (mpt) cc_final: 0.8509 (mmm) outliers start: 22 outliers final: 16 residues processed: 169 average time/residue: 0.3878 time to fit residues: 74.5177 Evaluate side-chains 172 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 724 GLN Chi-restraints excluded: chain B residue 852 ILE Chi-restraints excluded: chain B residue 860 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 149 optimal weight: 0.0970 chunk 38 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 HIS A 583 ASN A 855 ASN B 673 GLN B 724 GLN B 753 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.084087 restraints weight = 21001.742| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.69 r_work: 0.2859 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13432 Z= 0.123 Angle : 0.570 13.834 18280 Z= 0.289 Chirality : 0.044 0.296 2079 Planarity : 0.004 0.057 2285 Dihedral : 5.391 54.730 2078 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 1.53 % Allowed : 14.88 % 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: -0.33 (0.21), residues: 1613 helix: 1.31 (0.20), residues: 701 sheet: -1.19 (0.35), residues: 212 loop : -1.49 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.020 0.001 TYR A 744 PHE 0.027 0.001 PHE A 814 TRP 0.019 0.001 TRP A 818 HIS 0.009 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00282 (13399) covalent geometry : angle 0.55653 (18199) SS BOND : bond 0.00248 ( 18) SS BOND : angle 0.96423 ( 36) hydrogen bonds : bond 0.04544 ( 549) hydrogen bonds : angle 4.00847 ( 1575) link_BETA1-4 : bond 0.00381 ( 3) link_BETA1-4 : angle 1.50300 ( 9) link_NAG-ASN : bond 0.00426 ( 12) link_NAG-ASN : angle 2.65502 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.56 seconds wall clock time: 70 minutes 24.29 seconds (4224.29 seconds total)