Starting phenix.real_space_refine on Sat Sep 12 02:21:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3e_23652/09_2026/7m3e_23652_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3e_23652/09_2026/7m3e_23652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m3e_23652/09_2026/7m3e_23652_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3e_23652/09_2026/7m3e_23652_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m3e_23652/09_2026/7m3e_23652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3e_23652/09_2026/7m3e_23652.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 0.628 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 74 5.16 5 Cl 2 4.86 5 C 8477 2.51 5 N 2111 2.21 5 O 2421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13091 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6410 Classifications: {'peptide': 810} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 31, 'TRANS': 778} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 6425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6425 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 31, 'TRANS': 780} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 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: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 108 Unusual residues: {' CA': 3, 'NAG': 4, 'PO4': 1, 'YP1': 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: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 120 Unusual residues: {' CA': 1, 'NAG': 5, 'PO4': 1, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B 907 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.96, per 1000 atoms: 0.23 Number of scatterers: 13091 At special positions: 0 Unit cell: (103.194, 99.0108, 192.443, 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 Cl 2 17.00 S 74 16.00 P 2 15.00 O 2421 8.00 N 2111 7.00 C 8477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.02 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=2.03 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=2.03 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=2.03 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-ASN " NAG A 902 " - " ASN A 261 " " NAG A 903 " - " ASN A 287 " " NAG A 904 " - " ASN A 488 " " NAG A 905 " - " ASN A 468 " " NAG B 902 " - " ASN B 541 " " NAG B 903 " - " ASN B 261 " " NAG B 904 " - " ASN B 287 " " NAG B 905 " - " ASN B 488 " " NAG B 906 " - " ASN B 468 " " NAG C 1 " - " ASN A 541 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 579.5 milliseconds 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3058 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 46.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.539A pdb=" N PHE A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.685A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.610A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 removed outlier: 3.638A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.816A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.521A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.822A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.763A pdb=" N ILE A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 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 Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.538A pdb=" N PHE A 356 " --> pdb=" O TRP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.551A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.708A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.907A pdb=" N GLY A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 4.038A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.749A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 697 removed outlier: 5.244A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.645A pdb=" N ILE A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 746 removed outlier: 3.981A pdb=" N LEU A 730 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 738 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 743 " --> pdb=" O CYS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 removed outlier: 3.853A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 828 removed outlier: 3.845A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 815 " --> pdb=" O MET A 811 " (cutoff:3.500A) Proline residue: A 823 - end of helix removed outlier: 4.056A pdb=" N ALA A 826 " --> pdb=" O ILE A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.987A pdb=" N ILE A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 862 Processing helix chain 'A' and resid 863 through 866 removed outlier: 3.587A pdb=" N ARG A 866 " --> pdb=" O LYS A 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 863 through 866' Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.563A pdb=" N PHE B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET B 74 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.674A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.598A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.784A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.742A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.520A 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 233 removed outlier: 4.117A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 removed outlier: 3.503A 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 336 removed outlier: 3.701A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.715A pdb=" N SER B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'B' and resid 416 through 436 removed outlier: 4.123A pdb=" N ILE B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.529A pdb=" N VAL B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 removed outlier: 3.501A pdb=" N ILE B 528 " --> pdb=" O GLU B 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 525 through 528' Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 593 through 596 removed outlier: 4.241A pdb=" N THR B 596 " --> pdb=" O GLU B 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 593 through 596' Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.650A pdb=" N LEU B 618 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 620 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 623 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.914A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.635A pdb=" N SER B 651 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 679 Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.604A pdb=" N ALA B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 746 removed outlier: 3.739A pdb=" N PHE B 729 " --> pdb=" O PHE B 725 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 730 " --> pdb=" O LEU B 726 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 743 " --> pdb=" O CYS B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 793 removed outlier: 3.582A pdb=" N LEU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 826 removed outlier: 3.890A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 815 " --> pdb=" O MET B 811 " (cutoff:3.500A) Proline residue: B 823 - end of helix removed outlier: 4.383A pdb=" N ALA B 826 " --> pdb=" O ILE B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 840 removed outlier: 4.047A pdb=" N ILE B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 862 removed outlier: 3.734A pdb=" N ALA B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE B 846 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 866 removed outlier: 3.610A pdb=" N ARG B 866 " --> pdb=" O LYS B 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 863 through 866' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.196A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.088A 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: 7.906A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 552 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: 3.720A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.386A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.914A 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: 8.057A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 320 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.676A 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 551 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: 6.493A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N CYS B 765 " --> pdb=" O GLU B 604 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2109 1.29 - 1.43: 3683 1.43 - 1.56: 7525 1.56 - 1.69: 4 1.69 - 1.83: 90 Bond restraints: 13411 Sorted by residual: bond pdb=" O4 PO4 B 909 " pdb=" P PO4 B 909 " ideal model delta sigma weight residual 1.568 1.495 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O2 PO4 B 909 " pdb=" P PO4 B 909 " ideal model delta sigma weight residual 1.567 1.501 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O4 PO4 A 910 " pdb=" P PO4 A 910 " ideal model delta sigma weight residual 1.568 1.503 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3 PO4 A 910 " pdb=" P PO4 A 910 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O1 PO4 A 910 " pdb=" P PO4 A 910 " ideal model delta sigma weight residual 1.565 1.500 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 13406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 17592 2.32 - 4.64: 510 4.64 - 6.96: 70 6.96 - 9.27: 20 9.27 - 11.59: 7 Bond angle restraints: 18199 Sorted by residual: angle pdb=" C TYR A 411 " pdb=" N THR A 412 " pdb=" CA THR A 412 " ideal model delta sigma weight residual 121.54 133.13 -11.59 1.91e+00 2.74e-01 3.68e+01 angle pdb=" CA PRO B 823 " pdb=" N PRO B 823 " pdb=" CD PRO B 823 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" CA PRO A 823 " pdb=" N PRO A 823 " pdb=" CD PRO A 823 " ideal model delta sigma weight residual 112.00 104.77 7.23 1.40e+00 5.10e-01 2.67e+01 angle pdb=" C ARG B 638 " pdb=" N ASN B 639 " pdb=" CA ASN B 639 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C ARG A 638 " pdb=" N ASN A 639 " pdb=" CA ASN A 639 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 ... (remaining 18194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.17: 7612 22.17 - 44.33: 351 44.33 - 66.50: 50 66.50 - 88.66: 22 88.66 - 110.83: 9 Dihedral angle restraints: 8044 sinusoidal: 3320 harmonic: 4724 Sorted by residual: dihedral pdb=" CA ARG A 54 " pdb=" C ARG A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA GLN A 260 " pdb=" C GLN A 260 " pdb=" N ASN A 261 " pdb=" CA ASN A 261 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA SER A 53 " pdb=" C SER A 53 " pdb=" N ARG A 54 " pdb=" CA ARG A 54 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 8041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1974 0.127 - 0.254: 72 0.254 - 0.381: 0 0.381 - 0.508: 3 0.508 - 0.635: 3 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CB ILE A 822 " pdb=" CA ILE A 822 " pdb=" CG1 ILE A 822 " pdb=" CG2 ILE A 822 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CB ILE B 822 " pdb=" CA ILE B 822 " pdb=" CG1 ILE B 822 " pdb=" CG2 ILE B 822 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" CB ILE A 869 " pdb=" CA ILE A 869 " pdb=" CG1 ILE A 869 " pdb=" CG2 ILE A 869 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 2049 not shown) Planarity restraints: 2301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 YP1 B 901 " -0.050 2.00e-02 2.50e+03 1.00e-01 2.52e+02 pdb=" C19 YP1 B 901 " -0.007 2.00e-02 2.50e+03 pdb=" C20 YP1 B 901 " -0.021 2.00e-02 2.50e+03 pdb=" C21 YP1 B 901 " 0.066 2.00e-02 2.50e+03 pdb=" C22 YP1 B 901 " 0.108 2.00e-02 2.50e+03 pdb=" C23 YP1 B 901 " 0.028 2.00e-02 2.50e+03 pdb=" C24 YP1 B 901 " 0.070 2.00e-02 2.50e+03 pdb=" N1 YP1 B 901 " 0.141 2.00e-02 2.50e+03 pdb=" O1 YP1 B 901 " -0.163 2.00e-02 2.50e+03 pdb="CL1 YP1 B 901 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 YP1 A 901 " 0.049 2.00e-02 2.50e+03 1.00e-01 2.51e+02 pdb=" C19 YP1 A 901 " 0.007 2.00e-02 2.50e+03 pdb=" C20 YP1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C21 YP1 A 901 " -0.066 2.00e-02 2.50e+03 pdb=" C22 YP1 A 901 " -0.108 2.00e-02 2.50e+03 pdb=" C23 YP1 A 901 " -0.028 2.00e-02 2.50e+03 pdb=" C24 YP1 A 901 " -0.069 2.00e-02 2.50e+03 pdb=" N1 YP1 A 901 " -0.142 2.00e-02 2.50e+03 pdb=" O1 YP1 A 901 " 0.163 2.00e-02 2.50e+03 pdb="CL1 YP1 A 901 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 822 " -0.090 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO A 823 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 823 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 823 " -0.072 5.00e-02 4.00e+02 ... (remaining 2298 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3010 2.79 - 3.32: 10963 3.32 - 3.85: 19929 3.85 - 4.37: 23710 4.37 - 4.90: 42497 Nonbonded interactions: 100109 Sorted by model distance: nonbonded pdb=" O PHE B 351 " pdb=" OG1 THR B 355 " model vdw 2.265 3.040 nonbonded pdb=" OD2 ASP B 238 " pdb=" OG SER B 262 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR B 203 " pdb=" OE2 GLU B 525 " model vdw 2.302 3.040 nonbonded pdb=" NH1 ARG A 69 " pdb=" O PRO A 407 " model vdw 2.309 3.120 nonbonded pdb=" NH1 ARG B 69 " pdb=" O PRO B 407 " model vdw 2.316 3.120 ... (remaining 100104 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 905 or resid 909 through 910)) selection = (chain 'B' and (resid 20 through 361 or resid 391 through 553 or (resid 554 and \ (name N or name CA or name C or name O or name CB )) or resid 555 through 706 or \ (resid 721 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 2 through 905 or resid 908 through 909)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.006 0.073 13439 Z= 0.284 Angle : 0.958 11.593 18266 Z= 0.520 Chirality : 0.062 0.635 2052 Planarity : 0.009 0.132 2291 Dihedral : 13.866 110.828 4935 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.18), residues: 1606 helix: -1.87 (0.16), residues: 690 sheet: -1.29 (0.36), residues: 212 loop : -1.76 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 54 TYR 0.057 0.003 TYR A 573 PHE 0.043 0.003 PHE B 788 TRP 0.023 0.002 TRP B 299 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.28 (13411) covalent geometry : angle 0.94203 / 0.52 (18199) SS BOND : bond 0.00370 / 0.26 ( 17) SS BOND : angle 1.99189 / 1.42 ( 34) hydrogen bonds : bond 0.16887 / 11.72 ( 497) hydrogen bonds : angle 6.36947 / 4.40 ( 1449) link_BETA1-4 : bond 0.00192 / 0.10 ( 1) link_BETA1-4 : angle 2.79646 / 1.44 ( 3) link_NAG-ASN : bond 0.00537 / 0.36 ( 10) link_NAG-ASN : angle 3.96418 / 2.67 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 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: 0 poor density : 185 time to evaluate : 0.508 Fit side-chains REVERT: A 729 PHE cc_start: 0.8120 (t80) cc_final: 0.7910 (t80) REVERT: B 205 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6524 (mtp180) REVERT: B 575 ASP cc_start: 0.7395 (p0) cc_final: 0.6956 (p0) REVERT: B 577 THR cc_start: 0.8757 (m) cc_final: 0.8536 (m) REVERT: B 729 PHE cc_start: 0.7855 (t80) cc_final: 0.7651 (t80) REVERT: B 858 TYR cc_start: 0.8237 (t80) cc_final: 0.7949 (t80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1211 time to fit residues: 32.3232 Evaluate side-chains 164 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN B 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102999 restraints weight = 19603.122| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.26 r_work: 0.2970 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13439 Z= 0.163 Angle : 0.618 9.891 18266 Z= 0.321 Chirality : 0.046 0.297 2052 Planarity : 0.006 0.085 2291 Dihedral : 9.010 77.067 1995 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.72 % Allowed : 5.29 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1606 helix: -0.57 (0.19), residues: 687 sheet: -1.01 (0.37), residues: 196 loop : -1.71 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.015 0.002 TYR A 435 PHE 0.027 0.002 PHE B 330 TRP 0.017 0.002 TRP B 299 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (13411) covalent geometry : angle 0.60549 / 0.32 (18199) SS BOND : bond 0.00347 / 0.24 ( 17) SS BOND : angle 1.06961 / 0.76 ( 34) hydrogen bonds : bond 0.05619 / 3.71 ( 497) hydrogen bonds : angle 4.55375 / 3.10 ( 1449) link_BETA1-4 : bond 0.00246 / 0.13 ( 1) link_BETA1-4 : angle 1.78019 / 0.94 ( 3) link_NAG-ASN : bond 0.00449 / 0.30 ( 10) link_NAG-ASN : angle 2.87258 / 2.02 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 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: 10 poor density : 167 time to evaluate : 0.357 Fit side-chains REVERT: A 253 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7977 (mp10) REVERT: B 205 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7690 (mmm160) REVERT: B 602 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7416 (mm-30) outliers start: 10 outliers final: 8 residues processed: 173 average time/residue: 0.1058 time to fit residues: 27.3358 Evaluate side-chains 171 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 36 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 0.0000 chunk 126 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN B 724 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.101931 restraints weight = 19866.996| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.21 r_work: 0.2914 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13439 Z= 0.185 Angle : 0.626 9.803 18266 Z= 0.323 Chirality : 0.047 0.284 2052 Planarity : 0.005 0.070 2291 Dihedral : 8.556 74.501 1995 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.93 % Allowed : 7.73 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.20), residues: 1606 helix: -0.10 (0.19), residues: 701 sheet: -1.09 (0.37), residues: 196 loop : -1.78 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.018 0.002 TYR A 411 PHE 0.025 0.002 PHE B 330 TRP 0.015 0.002 TRP B 299 HIS 0.004 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (13411) covalent geometry : angle 0.61410 / 0.32 (18199) SS BOND : bond 0.00387 / 0.26 ( 17) SS BOND : angle 1.09077 / 0.77 ( 34) hydrogen bonds : bond 0.05710 / 3.78 ( 497) hydrogen bonds : angle 4.35106 / 2.97 ( 1449) link_BETA1-4 : bond 0.00272 / 0.14 ( 1) link_BETA1-4 : angle 1.86730 / 0.99 ( 3) link_NAG-ASN : bond 0.00403 / 0.27 ( 10) link_NAG-ASN : angle 2.82850 / 2.01 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 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: 13 poor density : 164 time to evaluate : 0.537 Fit side-chains REVERT: A 573 TYR cc_start: 0.7083 (p90) cc_final: 0.6761 (p90) REVERT: A 625 PHE cc_start: 0.8095 (m-80) cc_final: 0.7844 (m-80) REVERT: A 635 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8702 (mt) REVERT: B 575 ASP cc_start: 0.7825 (p0) cc_final: 0.7487 (p0) REVERT: B 635 ILE cc_start: 0.8987 (mt) cc_final: 0.8642 (mt) outliers start: 13 outliers final: 12 residues processed: 170 average time/residue: 0.1154 time to fit residues: 28.5453 Evaluate side-chains 173 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 chunk 6 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN B 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102993 restraints weight = 19754.737| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.30 r_work: 0.2932 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13439 Z= 0.120 Angle : 0.544 9.660 18266 Z= 0.283 Chirality : 0.044 0.275 2052 Planarity : 0.004 0.057 2291 Dihedral : 8.163 75.294 1995 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.86 % Allowed : 9.01 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1606 helix: 0.29 (0.20), residues: 695 sheet: -1.13 (0.36), residues: 208 loop : -1.70 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.013 0.001 TYR B 421 PHE 0.013 0.001 PHE B 330 TRP 0.014 0.001 TRP B 299 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13411) covalent geometry : angle 0.53328 / 0.28 (18199) SS BOND : bond 0.00262 / 0.18 ( 17) SS BOND : angle 0.80454 / 0.57 ( 34) hydrogen bonds : bond 0.04433 / 2.93 ( 497) hydrogen bonds : angle 4.10207 / 2.80 ( 1449) link_BETA1-4 : bond 0.00409 / 0.22 ( 1) link_BETA1-4 : angle 1.46811 / 0.75 ( 3) link_NAG-ASN : bond 0.00376 / 0.25 ( 10) link_NAG-ASN : angle 2.62339 / 1.86 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.488 Fit side-chains REVERT: A 573 TYR cc_start: 0.6998 (p90) cc_final: 0.6662 (p90) REVERT: A 625 PHE cc_start: 0.8109 (m-80) cc_final: 0.7868 (m-80) REVERT: B 635 ILE cc_start: 0.8949 (mt) cc_final: 0.8614 (mt) outliers start: 12 outliers final: 9 residues processed: 167 average time/residue: 0.1179 time to fit residues: 28.8582 Evaluate side-chains 167 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 59 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 65 optimal weight: 0.0470 chunk 85 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN B 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102532 restraints weight = 19842.708| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.25 r_work: 0.2920 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 0.036 13439 Z= 0.143 Angle : 0.561 9.698 18266 Z= 0.290 Chirality : 0.045 0.281 2052 Planarity : 0.004 0.050 2291 Dihedral : 8.121 73.720 1995 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.07 % Allowed : 9.23 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1606 helix: 0.51 (0.20), residues: 688 sheet: -1.01 (0.37), residues: 194 loop : -1.70 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.013 0.002 TYR A 411 PHE 0.011 0.001 PHE B 330 TRP 0.013 0.001 TRP B 299 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (13411) covalent geometry : angle 0.55086 / 0.29 (18199) SS BOND : bond 0.00296 / 0.20 ( 17) SS BOND : angle 0.85737 / 0.61 ( 34) hydrogen bonds : bond 0.04740 / 3.13 ( 497) hydrogen bonds : angle 4.06162 / 2.77 ( 1449) link_BETA1-4 : bond 0.00237 / 0.12 ( 1) link_BETA1-4 : angle 1.60584 / 0.84 ( 3) link_NAG-ASN : bond 0.00377 / 0.25 ( 10) link_NAG-ASN : angle 2.57031 / 1.82 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.411 Fit side-chains REVERT: A 270 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8003 (t80) REVERT: A 573 TYR cc_start: 0.7035 (p90) cc_final: 0.6617 (p90) REVERT: A 578 ASP cc_start: 0.7742 (t0) cc_final: 0.7348 (t70) REVERT: B 635 ILE cc_start: 0.8971 (mt) cc_final: 0.8612 (mt) REVERT: B 641 PRO cc_start: 0.8174 (Cg_exo) cc_final: 0.7875 (Cg_endo) outliers start: 15 outliers final: 11 residues processed: 161 average time/residue: 0.1116 time to fit residues: 26.5624 Evaluate side-chains 164 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101638 restraints weight = 19724.862| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.34 r_work: 0.2868 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13439 Z= 0.162 Angle : 0.583 9.925 18266 Z= 0.301 Chirality : 0.046 0.291 2052 Planarity : 0.004 0.051 2291 Dihedral : 8.059 71.077 1995 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.57 % Allowed : 9.08 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1606 helix: 0.55 (0.20), residues: 701 sheet: -1.03 (0.38), residues: 194 loop : -1.73 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.016 0.002 TYR A 411 PHE 0.013 0.001 PHE B 330 TRP 0.012 0.002 TRP B 299 HIS 0.004 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (13411) covalent geometry : angle 0.57191 / 0.30 (18199) SS BOND : bond 0.00329 / 0.22 ( 17) SS BOND : angle 0.93210 / 0.66 ( 34) hydrogen bonds : bond 0.05126 / 3.38 ( 497) hydrogen bonds : angle 4.07967 / 2.79 ( 1449) link_BETA1-4 : bond 0.00197 / 0.10 ( 1) link_BETA1-4 : angle 1.73487 / 0.91 ( 3) link_NAG-ASN : bond 0.00403 / 0.27 ( 10) link_NAG-ASN : angle 2.67202 / 1.90 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.496 Fit side-chains REVERT: A 270 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8031 (t80) REVERT: A 635 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8740 (mt) REVERT: B 635 ILE cc_start: 0.8986 (mt) cc_final: 0.8626 (mt) REVERT: B 641 PRO cc_start: 0.8025 (Cg_exo) cc_final: 0.7796 (Cg_endo) outliers start: 22 outliers final: 17 residues processed: 165 average time/residue: 0.1136 time to fit residues: 28.0935 Evaluate side-chains 173 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN B 90 ASN B 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102312 restraints weight = 19773.682| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.29 r_work: 0.2892 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13439 Z= 0.137 Angle : 0.554 8.775 18266 Z= 0.286 Chirality : 0.045 0.247 2052 Planarity : 0.004 0.047 2291 Dihedral : 7.964 71.813 1995 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.86 % Allowed : 9.23 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1606 helix: 0.70 (0.20), residues: 700 sheet: -1.13 (0.37), residues: 208 loop : -1.65 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.015 0.002 TYR A 573 PHE 0.011 0.001 PHE B 311 TRP 0.013 0.001 TRP B 299 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13411) covalent geometry : angle 0.54350 / 0.28 (18199) SS BOND : bond 0.00290 / 0.19 ( 17) SS BOND : angle 0.85169 / 0.60 ( 34) hydrogen bonds : bond 0.04696 / 3.10 ( 497) hydrogen bonds : angle 4.01632 / 2.74 ( 1449) link_BETA1-4 : bond 0.00286 / 0.15 ( 1) link_BETA1-4 : angle 1.60968 / 0.84 ( 3) link_NAG-ASN : bond 0.00413 / 0.29 ( 10) link_NAG-ASN : angle 2.59474 / 1.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.504 Fit side-chains REVERT: A 270 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8055 (t80) REVERT: A 635 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8731 (mt) REVERT: B 635 ILE cc_start: 0.8977 (mt) cc_final: 0.8609 (mt) REVERT: B 641 PRO cc_start: 0.8124 (Cg_exo) cc_final: 0.7904 (Cg_endo) outliers start: 26 outliers final: 21 residues processed: 164 average time/residue: 0.1117 time to fit residues: 27.5057 Evaluate side-chains 176 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 58 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN B 90 ASN B 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102247 restraints weight = 19637.741| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.20 r_work: 0.2929 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13439 Z= 0.159 Angle : 0.575 8.812 18266 Z= 0.297 Chirality : 0.046 0.260 2052 Planarity : 0.004 0.048 2291 Dihedral : 7.981 73.047 1995 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.00 % Allowed : 9.44 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.21), residues: 1606 helix: 0.71 (0.20), residues: 703 sheet: -1.07 (0.38), residues: 194 loop : -1.64 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.022 0.002 TYR A 573 PHE 0.011 0.001 PHE B 311 TRP 0.013 0.002 TRP B 299 HIS 0.004 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (13411) covalent geometry : angle 0.56449 / 0.30 (18199) SS BOND : bond 0.00327 / 0.22 ( 17) SS BOND : angle 0.95271 / 0.68 ( 34) hydrogen bonds : bond 0.04972 / 3.29 ( 497) hydrogen bonds : angle 4.03364 / 2.76 ( 1449) link_BETA1-4 : bond 0.00185 / 0.10 ( 1) link_BETA1-4 : angle 1.70687 / 0.90 ( 3) link_NAG-ASN : bond 0.00395 / 0.27 ( 10) link_NAG-ASN : angle 2.56233 / 1.81 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.430 Fit side-chains REVERT: A 270 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8080 (t80) REVERT: A 635 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8724 (mt) REVERT: B 635 ILE cc_start: 0.8965 (mt) cc_final: 0.8585 (mt) REVERT: B 641 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7873 (Cg_endo) outliers start: 28 outliers final: 24 residues processed: 166 average time/residue: 0.1102 time to fit residues: 27.5595 Evaluate side-chains 177 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 114 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 59 optimal weight: 0.0010 chunk 11 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN B 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102121 restraints weight = 19804.600| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.20 r_work: 0.2928 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13439 Z= 0.159 Angle : 0.576 8.817 18266 Z= 0.298 Chirality : 0.046 0.268 2052 Planarity : 0.004 0.048 2291 Dihedral : 7.972 74.281 1995 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.22 % Allowed : 9.37 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1606 helix: 0.74 (0.20), residues: 703 sheet: -1.07 (0.38), residues: 194 loop : -1.64 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.019 0.002 TYR A 573 PHE 0.012 0.001 PHE B 311 TRP 0.013 0.002 TRP B 299 HIS 0.004 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (13411) covalent geometry : angle 0.56616 / 0.30 (18199) SS BOND : bond 0.00335 / 0.22 ( 17) SS BOND : angle 0.93203 / 0.66 ( 34) hydrogen bonds : bond 0.04985 / 3.29 ( 497) hydrogen bonds : angle 4.03728 / 2.76 ( 1449) link_BETA1-4 : bond 0.00171 / 0.09 ( 1) link_BETA1-4 : angle 1.72205 / 0.90 ( 3) link_NAG-ASN : bond 0.00440 / 0.32 ( 10) link_NAG-ASN : angle 2.54139 / 1.79 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 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 : 0.507 Fit side-chains REVERT: A 270 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8087 (t80) REVERT: A 635 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8715 (mt) REVERT: B 635 ILE cc_start: 0.8956 (mt) cc_final: 0.8577 (mt) REVERT: B 641 PRO cc_start: 0.8180 (Cg_exo) cc_final: 0.7962 (Cg_endo) outliers start: 31 outliers final: 26 residues processed: 169 average time/residue: 0.1093 time to fit residues: 28.0184 Evaluate side-chains 180 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097991 restraints weight = 19900.300| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.33 r_work: 0.2869 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13439 Z= 0.211 Angle : 0.638 9.278 18266 Z= 0.328 Chirality : 0.048 0.272 2052 Planarity : 0.005 0.050 2291 Dihedral : 8.089 73.744 1995 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.00 % Allowed : 9.59 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.20), residues: 1606 helix: 0.65 (0.20), residues: 702 sheet: -1.01 (0.39), residues: 191 loop : -1.74 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.024 0.002 TYR A 411 PHE 0.013 0.002 PHE B 226 TRP 0.011 0.002 TRP B 208 HIS 0.004 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.21 (13411) covalent geometry : angle 0.62648 / 0.33 (18199) SS BOND : bond 0.00438 / 0.29 ( 17) SS BOND : angle 1.11889 / 0.80 ( 34) hydrogen bonds : bond 0.05829 / 3.85 ( 497) hydrogen bonds : angle 4.16664 / 2.85 ( 1449) link_BETA1-4 : bond 0.00053 / 0.03 ( 1) link_BETA1-4 : angle 2.00888 / 1.06 ( 3) link_NAG-ASN : bond 0.00390 / 0.26 ( 10) link_NAG-ASN : angle 2.76012 / 1.98 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.491 Fit side-chains REVERT: A 270 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8178 (t80) REVERT: A 635 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8719 (mt) REVERT: B 635 ILE cc_start: 0.8960 (mt) cc_final: 0.8577 (mt) REVERT: B 641 PRO cc_start: 0.8096 (Cg_exo) cc_final: 0.7846 (Cg_endo) outliers start: 28 outliers final: 26 residues processed: 170 average time/residue: 0.1165 time to fit residues: 29.3857 Evaluate side-chains 180 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102358 restraints weight = 19669.843| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.18 r_work: 0.2935 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13439 Z= 0.150 Angle : 0.576 9.664 18266 Z= 0.297 Chirality : 0.046 0.280 2052 Planarity : 0.004 0.048 2291 Dihedral : 7.925 75.844 1995 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.00 % Allowed : 9.80 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1606 helix: 0.81 (0.20), residues: 702 sheet: -1.11 (0.38), residues: 194 loop : -1.65 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.027 0.002 TYR A 573 PHE 0.012 0.001 PHE B 311 TRP 0.014 0.002 TRP B 299 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (13411) covalent geometry : angle 0.56359 / 0.29 (18199) SS BOND : bond 0.00347 / 0.23 ( 17) SS BOND : angle 1.22570 / 0.89 ( 34) hydrogen bonds : bond 0.04870 / 3.22 ( 497) hydrogen bonds : angle 4.04356 / 2.76 ( 1449) link_BETA1-4 : bond 0.00203 / 0.11 ( 1) link_BETA1-4 : angle 1.73796 / 0.92 ( 3) link_NAG-ASN : bond 0.00383 / 0.25 ( 10) link_NAG-ASN : angle 2.68078 / 1.92 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.07 seconds wall clock time: 54 minutes 15.68 seconds (3255.68 seconds total)