Starting phenix.real_space_refine on Thu Jul 31 08:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3f_23653/07_2025/7m3f_23653_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3f_23653/07_2025/7m3f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m3f_23653/07_2025/7m3f_23653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3f_23653/07_2025/7m3f_23653.map" model { file = "/net/cci-nas-00/data/ceres_data/7m3f_23653/07_2025/7m3f_23653_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3f_23653/07_2025/7m3f_23653_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 8, 'ASP:plan': 2} 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: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 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: 8.95, per 1000 atoms: 0.68 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: 3.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.39 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: 4.36 Time building geometry restraints manager: 3.99 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: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.070 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.710 ------------------------------------------------------------------------------- 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 : 2.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.049 0.003 TRP A 818 HIS 0.025 0.002 HIS A 463 PHE 0.036 0.003 PHE B 846 TYR 0.037 0.003 TYR B 425 ARG 0.008 0.001 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00793 ( 12) link_NAG-ASN : angle 6.08098 ( 36) link_BETA1-4 : bond 0.00994 ( 3) link_BETA1-4 : angle 3.75274 ( 9) hydrogen bonds : bond 0.15809 ( 549) hydrogen bonds : angle 6.24870 ( 1575) SS BOND : bond 0.00681 ( 18) SS BOND : angle 2.19181 ( 36) covalent geometry : bond 0.00818 (13399) covalent geometry : angle 1.01186 (18199) *********************** 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 : 1.520 Fit side-chains revert: symmetry clash REVERT: A 751 TYR cc_start: 0.8128 (t80) cc_final: 0.7895 (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: 0.8671 time to fit residues: 189.8558 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 : 1.397 ------------------------------------------------------------------------------- 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 136 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.113048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.082735 restraints weight = 20804.225| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.61 r_work: 0.2855 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13432 Z= 0.156 Angle : 0.620 13.123 18280 Z= 0.321 Chirality : 0.045 0.238 2079 Planarity : 0.005 0.075 2285 Dihedral : 7.171 58.523 2084 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.97 % Allowed : 7.37 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1613 helix: 0.20 (0.19), residues: 706 sheet: -1.40 (0.33), residues: 218 loop : -1.77 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 675 HIS 0.007 0.001 HIS A 463 PHE 0.014 0.002 PHE B 688 TYR 0.025 0.002 TYR A 744 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 12) link_NAG-ASN : angle 3.80096 ( 36) link_BETA1-4 : bond 0.00439 ( 3) link_BETA1-4 : angle 1.73627 ( 9) hydrogen bonds : bond 0.05630 ( 549) hydrogen bonds : angle 4.43618 ( 1575) SS BOND : bond 0.00769 ( 18) SS BOND : angle 1.44079 ( 36) covalent geometry : bond 0.00359 (13399) covalent geometry : angle 0.59279 (18199) *********************** 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 201 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.514 Fit side-chains REVERT: A 340 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7800 (mtp180) REVERT: A 751 TYR cc_start: 0.8261 (t80) cc_final: 0.7853 (t80) REVERT: A 753 ASN cc_start: 0.8989 (t0) cc_final: 0.8738 (t0) REVERT: A 792 PHE cc_start: 0.8913 (t80) cc_final: 0.8587 (t80) REVERT: A 796 LYS cc_start: 0.8962 (mttm) cc_final: 0.8038 (pmtt) REVERT: A 855 ASN cc_start: 0.9105 (t0) cc_final: 0.8647 (t0) REVERT: B 50 ASP cc_start: 0.8214 (p0) cc_final: 0.7951 (p0) REVERT: B 205 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.8393 (mtt180) REVERT: B 771 MET cc_start: 0.3292 (OUTLIER) cc_final: 0.2520 (ttp) outliers start: 27 outliers final: 13 residues processed: 184 average time/residue: 0.7873 time to fit residues: 167.3649 Evaluate side-chains 176 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 770 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 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 55 optimal weight: 0.0470 chunk 89 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 B 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083628 restraints weight = 21003.658| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.63 r_work: 0.2864 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13432 Z= 0.135 Angle : 0.581 11.253 18280 Z= 0.297 Chirality : 0.044 0.222 2079 Planarity : 0.004 0.068 2285 Dihedral : 6.458 54.595 2080 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.97 % Allowed : 9.77 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1613 helix: 0.77 (0.20), residues: 709 sheet: -1.31 (0.34), residues: 214 loop : -1.69 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 675 HIS 0.003 0.001 HIS B 312 PHE 0.021 0.001 PHE A 788 TYR 0.022 0.002 TYR A 744 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 12) link_NAG-ASN : angle 3.48826 ( 36) link_BETA1-4 : bond 0.00242 ( 3) link_BETA1-4 : angle 1.73824 ( 9) hydrogen bonds : bond 0.04998 ( 549) hydrogen bonds : angle 4.15219 ( 1575) SS BOND : bond 0.00390 ( 18) SS BOND : angle 1.37316 ( 36) covalent geometry : bond 0.00312 (13399) covalent geometry : angle 0.55680 (18199) *********************** 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 194 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.663 Fit side-chains REVERT: A 340 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7741 (mtp180) REVERT: A 590 TRP cc_start: 0.8624 (t-100) cc_final: 0.8271 (t-100) REVERT: A 608 TRP cc_start: 0.8936 (m100) cc_final: 0.8589 (m100) REVERT: A 701 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6646 (mmp-170) REVERT: A 751 TYR cc_start: 0.8228 (t80) cc_final: 0.7810 (t80) REVERT: A 753 ASN cc_start: 0.8909 (t0) cc_final: 0.8695 (t0) REVERT: A 792 PHE cc_start: 0.8911 (t80) cc_final: 0.8583 (t80) REVERT: A 796 LYS cc_start: 0.8909 (mttm) cc_final: 0.8020 (pmtt) REVERT: A 855 ASN cc_start: 0.9094 (t0) cc_final: 0.8544 (t0) REVERT: B 50 ASP cc_start: 0.8168 (p0) cc_final: 0.7929 (p0) REVERT: B 189 ASN cc_start: 0.8995 (p0) cc_final: 0.8789 (p0) REVERT: B 205 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8349 (mtt180) REVERT: B 771 MET cc_start: 0.2986 (OUTLIER) cc_final: 0.2201 (ttp) outliers start: 27 outliers final: 10 residues processed: 176 average time/residue: 0.8948 time to fit residues: 181.2038 Evaluate side-chains 171 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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 B residue 83 SER Chi-restraints excluded: chain B residue 270 PHE 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 776 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 127 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 132 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.113930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.083574 restraints weight = 20833.554| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.70 r_work: 0.2853 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13432 Z= 0.135 Angle : 0.558 10.314 18280 Z= 0.287 Chirality : 0.044 0.217 2079 Planarity : 0.004 0.062 2285 Dihedral : 6.042 55.601 2080 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.26 % Allowed : 10.94 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1613 helix: 1.06 (0.20), residues: 707 sheet: -1.24 (0.34), residues: 214 loop : -1.65 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 530 HIS 0.004 0.001 HIS B 429 PHE 0.013 0.001 PHE A 469 TYR 0.027 0.001 TYR A 744 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 12) link_NAG-ASN : angle 3.25335 ( 36) link_BETA1-4 : bond 0.00302 ( 3) link_BETA1-4 : angle 1.58541 ( 9) hydrogen bonds : bond 0.04816 ( 549) hydrogen bonds : angle 4.03261 ( 1575) SS BOND : bond 0.00311 ( 18) SS BOND : angle 1.25246 ( 36) covalent geometry : bond 0.00316 (13399) covalent geometry : angle 0.53649 (18199) *********************** 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 198 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.237 Fit side-chains REVERT: A 340 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7772 (mtp180) REVERT: A 590 TRP cc_start: 0.8598 (t-100) cc_final: 0.8249 (t-100) REVERT: A 608 TRP cc_start: 0.8909 (m100) cc_final: 0.8556 (m100) REVERT: A 701 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6559 (mmp-170) REVERT: A 751 TYR cc_start: 0.8218 (t80) cc_final: 0.7796 (t80) REVERT: A 753 ASN cc_start: 0.8834 (t0) cc_final: 0.8595 (t0) REVERT: A 792 PHE cc_start: 0.8922 (t80) cc_final: 0.8578 (t80) REVERT: A 796 LYS cc_start: 0.8929 (mttm) cc_final: 0.7981 (pmtt) REVERT: A 855 ASN cc_start: 0.9074 (t0) cc_final: 0.8512 (t0) REVERT: A 881 PHE cc_start: 0.5201 (OUTLIER) cc_final: 0.2024 (t80) REVERT: B 50 ASP cc_start: 0.8188 (p0) cc_final: 0.7930 (p0) outliers start: 31 outliers final: 18 residues processed: 179 average time/residue: 0.9462 time to fit residues: 193.4681 Evaluate side-chains 180 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 846 PHE 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 587 ASP Chi-restraints excluded: chain B residue 664 SER 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 70 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN 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 = 0.3527 r_free = 0.3527 target = 0.113943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.083763 restraints weight = 21133.505| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.62 r_work: 0.2857 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13432 Z= 0.150 Angle : 0.572 9.673 18280 Z= 0.292 Chirality : 0.044 0.213 2079 Planarity : 0.004 0.060 2285 Dihedral : 5.847 55.850 2078 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 2.63 % Allowed : 11.67 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.21), residues: 1613 helix: 1.12 (0.20), residues: 706 sheet: -1.18 (0.34), residues: 210 loop : -1.61 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 530 HIS 0.004 0.001 HIS B 429 PHE 0.023 0.001 PHE B 789 TYR 0.019 0.002 TYR A 744 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 12) link_NAG-ASN : angle 3.21125 ( 36) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 1.62801 ( 9) hydrogen bonds : bond 0.04898 ( 549) hydrogen bonds : angle 4.03108 ( 1575) SS BOND : bond 0.00363 ( 18) SS BOND : angle 1.15626 ( 36) covalent geometry : bond 0.00358 (13399) covalent geometry : angle 0.55146 (18199) *********************** 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 199 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.727 Fit side-chains REVERT: A 340 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7763 (mtp180) REVERT: A 608 TRP cc_start: 0.8927 (m100) cc_final: 0.8600 (m100) REVERT: A 701 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6560 (mmp-170) REVERT: A 751 TYR cc_start: 0.8272 (t80) cc_final: 0.7829 (t80) REVERT: A 753 ASN cc_start: 0.8850 (t0) cc_final: 0.8617 (t0) REVERT: A 796 LYS cc_start: 0.8940 (mttm) cc_final: 0.8035 (pmtt) REVERT: A 799 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7183 (pt0) REVERT: A 855 ASN cc_start: 0.9067 (t0) cc_final: 0.8529 (t0) REVERT: A 881 PHE cc_start: 0.5217 (OUTLIER) cc_final: 0.2019 (t80) REVERT: B 50 ASP cc_start: 0.8176 (p0) cc_final: 0.7925 (p0) outliers start: 36 outliers final: 20 residues processed: 179 average time/residue: 0.8807 time to fit residues: 180.6658 Evaluate side-chains 177 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER 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 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 587 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 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 95 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 54 optimal weight: 0.0570 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 122 optimal weight: 0.0870 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.115395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.085069 restraints weight = 21367.078| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.72 r_work: 0.2874 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13432 Z= 0.105 Angle : 0.523 9.819 18280 Z= 0.268 Chirality : 0.042 0.195 2079 Planarity : 0.004 0.057 2285 Dihedral : 5.462 53.898 2078 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 2.63 % Allowed : 12.11 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1613 helix: 1.29 (0.20), residues: 702 sheet: -1.15 (0.35), residues: 212 loop : -1.56 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 530 HIS 0.004 0.001 HIS B 463 PHE 0.023 0.001 PHE A 814 TYR 0.018 0.001 TYR A 744 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 12) link_NAG-ASN : angle 2.92946 ( 36) link_BETA1-4 : bond 0.00334 ( 3) link_BETA1-4 : angle 1.44117 ( 9) hydrogen bonds : bond 0.04184 ( 549) hydrogen bonds : angle 3.92140 ( 1575) SS BOND : bond 0.00250 ( 18) SS BOND : angle 0.89269 ( 36) covalent geometry : bond 0.00232 (13399) covalent geometry : angle 0.50557 (18199) *********************** 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 198 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.309 Fit side-chains REVERT: A 340 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7788 (mtp180) REVERT: A 590 TRP cc_start: 0.8601 (t-100) cc_final: 0.8247 (t-100) REVERT: A 608 TRP cc_start: 0.8896 (m100) cc_final: 0.8548 (m100) REVERT: A 701 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6548 (mmp-170) REVERT: A 751 TYR cc_start: 0.8224 (t80) cc_final: 0.7747 (t80) REVERT: A 753 ASN cc_start: 0.8801 (t0) cc_final: 0.8550 (t0) REVERT: A 799 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7053 (pt0) REVERT: A 881 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.2124 (t80) REVERT: B 50 ASP cc_start: 0.8195 (p0) cc_final: 0.7958 (p0) outliers start: 36 outliers final: 17 residues processed: 178 average time/residue: 0.8304 time to fit residues: 169.5275 Evaluate side-chains 173 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 340 ARG 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 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 587 ASP Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE 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 110 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 123 optimal weight: 0.0570 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN 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 = 0.3533 r_free = 0.3533 target = 0.114145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.083652 restraints weight = 21095.410| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.71 r_work: 0.2856 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13432 Z= 0.143 Angle : 0.603 21.600 18280 Z= 0.297 Chirality : 0.051 1.158 2079 Planarity : 0.004 0.057 2285 Dihedral : 5.700 55.844 2078 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 2.12 % Allowed : 12.84 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1613 helix: 1.27 (0.20), residues: 703 sheet: -1.14 (0.35), residues: 212 loop : -1.52 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 530 HIS 0.004 0.001 HIS B 429 PHE 0.020 0.001 PHE B 789 TYR 0.014 0.001 TYR A 744 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00846 ( 12) link_NAG-ASN : angle 4.81409 ( 36) link_BETA1-4 : bond 0.00311 ( 3) link_BETA1-4 : angle 1.58159 ( 9) hydrogen bonds : bond 0.04655 ( 549) hydrogen bonds : angle 3.97690 ( 1575) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.01106 ( 36) covalent geometry : bond 0.00337 (13399) covalent geometry : angle 0.56213 (18199) *********************** 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 185 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 1.550 Fit side-chains REVERT: A 340 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7826 (mtp180) REVERT: A 608 TRP cc_start: 0.8912 (m100) cc_final: 0.8582 (m100) REVERT: A 701 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6504 (mmp-170) REVERT: A 751 TYR cc_start: 0.8235 (t80) cc_final: 0.7764 (t80) REVERT: A 753 ASN cc_start: 0.8790 (t0) cc_final: 0.8549 (t0) REVERT: A 881 PHE cc_start: 0.5275 (OUTLIER) cc_final: 0.2175 (t80) REVERT: B 50 ASP cc_start: 0.8187 (p0) cc_final: 0.7930 (p0) REVERT: B 753 ASN cc_start: 0.8252 (t0) cc_final: 0.7926 (t0) REVERT: B 756 LEU cc_start: 0.9127 (mp) cc_final: 0.8737 (mp) REVERT: B 760 ILE cc_start: 0.8423 (pt) cc_final: 0.8116 (pp) outliers start: 29 outliers final: 20 residues processed: 172 average time/residue: 0.8178 time to fit residues: 162.3642 Evaluate side-chains 172 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 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 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 664 SER 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 140 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.084390 restraints weight = 21011.469| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.70 r_work: 0.2861 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13432 Z= 0.132 Angle : 0.564 11.446 18280 Z= 0.285 Chirality : 0.044 0.260 2079 Planarity : 0.004 0.056 2285 Dihedral : 5.432 55.258 2078 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 2.33 % Allowed : 13.20 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1613 helix: 1.30 (0.20), residues: 704 sheet: -1.13 (0.35), residues: 212 loop : -1.50 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 818 HIS 0.004 0.001 HIS B 463 PHE 0.025 0.001 PHE A 814 TYR 0.014 0.001 TYR A 779 ARG 0.002 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 12) link_NAG-ASN : angle 3.22882 ( 36) link_BETA1-4 : bond 0.00300 ( 3) link_BETA1-4 : angle 1.53497 ( 9) hydrogen bonds : bond 0.04504 ( 549) hydrogen bonds : angle 3.95821 ( 1575) SS BOND : bond 0.00283 ( 18) SS BOND : angle 0.98842 ( 36) covalent geometry : bond 0.00309 (13399) covalent geometry : angle 0.54358 (18199) *********************** 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 184 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.374 Fit side-chains REVERT: A 340 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7825 (mtp180) REVERT: A 608 TRP cc_start: 0.8920 (m100) cc_final: 0.8594 (m100) REVERT: A 701 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6597 (mmp-170) REVERT: A 751 TYR cc_start: 0.8217 (t80) cc_final: 0.7747 (t80) REVERT: A 753 ASN cc_start: 0.8751 (t0) cc_final: 0.8517 (t0) REVERT: A 799 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7076 (pt0) REVERT: A 881 PHE cc_start: 0.5210 (OUTLIER) cc_final: 0.2160 (t80) REVERT: B 50 ASP cc_start: 0.8191 (p0) cc_final: 0.7943 (p0) REVERT: B 753 ASN cc_start: 0.8260 (t0) cc_final: 0.7937 (t0) REVERT: B 756 LEU cc_start: 0.9116 (mp) cc_final: 0.8737 (mp) REVERT: B 760 ILE cc_start: 0.8389 (pt) cc_final: 0.8098 (pp) outliers start: 32 outliers final: 22 residues processed: 169 average time/residue: 0.9663 time to fit residues: 187.5652 Evaluate side-chains 176 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 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 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 587 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.083680 restraints weight = 21087.534| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.71 r_work: 0.2853 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1858 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= 0.148 Angle : 0.576 13.000 18280 Z= 0.292 Chirality : 0.045 0.235 2079 Planarity : 0.004 0.056 2285 Dihedral : 5.447 55.799 2078 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.26 % Allowed : 13.64 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1613 helix: 1.26 (0.20), residues: 706 sheet: -1.13 (0.35), residues: 212 loop : -1.48 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 818 HIS 0.009 0.001 HIS A 463 PHE 0.023 0.001 PHE A 814 TYR 0.013 0.001 TYR A 744 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 12) link_NAG-ASN : angle 2.93077 ( 36) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 1.57777 ( 9) hydrogen bonds : bond 0.04682 ( 549) hydrogen bonds : angle 3.97750 ( 1575) SS BOND : bond 0.00313 ( 18) SS BOND : angle 1.06057 ( 36) covalent geometry : bond 0.00352 (13399) covalent geometry : angle 0.55948 (18199) *********************** 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 183 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.513 Fit side-chains REVERT: A 340 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7826 (mtp180) REVERT: A 608 TRP cc_start: 0.8928 (m100) cc_final: 0.8606 (m100) REVERT: A 701 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6608 (mmp-170) REVERT: A 751 TYR cc_start: 0.8221 (t80) cc_final: 0.7750 (t80) REVERT: A 753 ASN cc_start: 0.8734 (t0) cc_final: 0.8507 (t0) REVERT: A 799 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7084 (pt0) REVERT: A 881 PHE cc_start: 0.5229 (OUTLIER) cc_final: 0.2165 (t80) REVERT: B 50 ASP cc_start: 0.8195 (p0) cc_final: 0.7946 (p0) REVERT: B 753 ASN cc_start: 0.8257 (t0) cc_final: 0.7942 (t0) REVERT: B 756 LEU cc_start: 0.9116 (mp) cc_final: 0.8738 (mp) REVERT: B 760 ILE cc_start: 0.8385 (pt) cc_final: 0.8072 (pp) outliers start: 31 outliers final: 23 residues processed: 167 average time/residue: 0.8638 time to fit residues: 164.6150 Evaluate side-chains 174 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 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 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 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 842 LEU 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 139 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 115 optimal weight: 0.0980 chunk 150 optimal weight: 4.9990 chunk 46 optimal weight: 0.0670 chunk 110 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 137 optimal weight: 0.0010 overall best weight: 0.2724 ------------------------------------------------------------------------------- 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 753 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.086104 restraints weight = 20921.106| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.69 r_work: 0.2894 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13432 Z= 0.101 Angle : 0.534 13.339 18280 Z= 0.270 Chirality : 0.043 0.212 2079 Planarity : 0.004 0.055 2285 Dihedral : 5.107 53.009 2078 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.71 % Rotamer: Outliers : 1.53 % Allowed : 14.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1613 helix: 1.45 (0.20), residues: 702 sheet: -1.06 (0.35), residues: 212 loop : -1.43 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 818 HIS 0.005 0.001 HIS A 463 PHE 0.022 0.001 PHE A 814 TYR 0.016 0.001 TYR A 744 ARG 0.008 0.000 ARG A 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 2.71752 ( 36) link_BETA1-4 : bond 0.00413 ( 3) link_BETA1-4 : angle 1.33272 ( 9) hydrogen bonds : bond 0.03855 ( 549) hydrogen bonds : angle 3.85914 ( 1575) SS BOND : bond 0.00193 ( 18) SS BOND : angle 0.77640 ( 36) covalent geometry : bond 0.00220 (13399) covalent geometry : angle 0.51897 (18199) ********************** 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 177 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.520 Fit side-chains REVERT: A 340 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7787 (mtp180) REVERT: A 608 TRP cc_start: 0.8894 (m100) cc_final: 0.8569 (m100) REVERT: A 701 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6605 (mmp-170) REVERT: A 751 TYR cc_start: 0.8180 (t80) cc_final: 0.7649 (t80) REVERT: A 753 ASN cc_start: 0.8717 (t0) cc_final: 0.8494 (t0) REVERT: A 799 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7149 (pt0) REVERT: A 811 MET cc_start: 0.8425 (mmm) cc_final: 0.8062 (mmt) REVERT: A 881 PHE cc_start: 0.5053 (OUTLIER) cc_final: 0.2093 (t80) REVERT: B 50 ASP cc_start: 0.8179 (p0) cc_final: 0.7945 (p0) REVERT: B 753 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7894 (t0) REVERT: B 756 LEU cc_start: 0.9086 (mp) cc_final: 0.8732 (mp) REVERT: B 760 ILE cc_start: 0.8347 (pt) cc_final: 0.8050 (pp) REVERT: B 811 MET cc_start: 0.8843 (mpt) cc_final: 0.8495 (mmm) outliers start: 21 outliers final: 15 residues processed: 168 average time/residue: 0.8165 time to fit residues: 157.7019 Evaluate side-chains 169 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 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 695 ILE Chi-restraints excluded: chain B residue 753 ASN 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 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 753 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.084080 restraints weight = 21096.083| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.70 r_work: 0.2856 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13432 Z= 0.155 Angle : 0.587 12.888 18280 Z= 0.295 Chirality : 0.045 0.238 2079 Planarity : 0.004 0.055 2285 Dihedral : 5.294 56.097 2078 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 1.82 % Allowed : 14.51 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1613 helix: 1.34 (0.20), residues: 707 sheet: -1.07 (0.35), residues: 212 loop : -1.42 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 818 HIS 0.009 0.001 HIS A 463 PHE 0.021 0.001 PHE A 814 TYR 0.014 0.002 TYR A 425 ARG 0.003 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 12) link_NAG-ASN : angle 2.71948 ( 36) link_BETA1-4 : bond 0.00277 ( 3) link_BETA1-4 : angle 1.55227 ( 9) hydrogen bonds : bond 0.04659 ( 549) hydrogen bonds : angle 3.94470 ( 1575) SS BOND : bond 0.00330 ( 18) SS BOND : angle 1.04831 ( 36) covalent geometry : bond 0.00372 (13399) covalent geometry : angle 0.57279 (18199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9707.91 seconds wall clock time: 172 minutes 29.51 seconds (10349.51 seconds total)