Starting phenix.real_space_refine on Fri Jul 3 08:22:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m3e_23652/07_2026/7m3e_23652_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3e_23652/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m3e_23652/07_2026/7m3e_23652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3e_23652/07_2026/7m3e_23652.map" model { file = "/net/cci-nas-00/data/ceres_data/7m3e_23652/07_2026/7m3e_23652_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3e_23652/07_2026/7m3e_23652_neut.cif" } 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-dev-6108/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, 105 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 4, 'PO4': 1, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 906 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain breaks: 3 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, 119 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 5, 'PO4': 1, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B 907 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.40, per 1000 atoms: 0.18 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: 0.76 Conformation dependent library (CDL) restraints added in 387.4 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: 0.35 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: 2.24 Time building geometry restraints manager: 1.03 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.850 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.200 ------------------------------------------------------------------------------- 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 : 0.300 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: 0.1065 time to fit residues: 28.5190 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 : 0.454 ------------------------------------------------------------------------------- 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 = 0.123192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103121 restraints weight = 19573.084| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.24 r_work: 0.2973 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1033 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= 0.162 Angle : 0.620 9.815 18266 Z= 0.322 Chirality : 0.046 0.298 2052 Planarity : 0.006 0.085 2291 Dihedral : 9.088 78.609 1995 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.79 % Allowed : 5.22 % 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: -1.77 (0.19), residues: 1606 helix: -0.61 (0.19), residues: 693 sheet: -1.01 (0.37), residues: 196 loop : -1.71 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.00385 / 0.16 (13411) covalent geometry : angle 0.60722 / 0.32 (18199) SS BOND : bond 0.00330 / 0.23 ( 17) SS BOND : angle 1.07619 / 0.77 ( 34) hydrogen bonds : bond 0.05695 / 3.77 ( 497) hydrogen bonds : angle 4.57897 / 3.12 ( 1449) link_BETA1-4 : bond 0.00319 / 0.17 ( 1) link_BETA1-4 : angle 1.65143 / 0.86 ( 3) link_NAG-ASN : bond 0.00449 / 0.30 ( 10) link_NAG-ASN : angle 2.90058 / 2.05 ( 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 179 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.403 Fit side-chains REVERT: A 253 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7968 (mp10) REVERT: B 205 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7689 (mmm160) REVERT: B 602 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7413 (mm-30) outliers start: 11 outliers final: 8 residues processed: 174 average time/residue: 0.1055 time to fit residues: 26.8836 Evaluate side-chains 172 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 0.0370 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.121600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101679 restraints weight = 19862.986| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.26 r_work: 0.2903 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13439 Z= 0.199 Angle : 0.640 9.803 18266 Z= 0.330 Chirality : 0.048 0.286 2052 Planarity : 0.005 0.071 2291 Dihedral : 8.638 73.771 1995 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.86 % Allowed : 7.73 % Favored : 91.42 % 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: -1.51 (0.20), residues: 1606 helix: -0.16 (0.19), residues: 701 sheet: -1.04 (0.37), residues: 194 loop : -1.82 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.021 0.002 TYR A 411 PHE 0.026 0.002 PHE B 330 TRP 0.016 0.002 TRP B 299 HIS 0.005 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (13411) covalent geometry : angle 0.62850 / 0.33 (18199) SS BOND : bond 0.00404 / 0.27 ( 17) SS BOND : angle 1.12200 / 0.80 ( 34) hydrogen bonds : bond 0.05899 / 3.90 ( 497) hydrogen bonds : angle 4.39366 / 3.00 ( 1449) link_BETA1-4 : bond 0.00177 / 0.09 ( 1) link_BETA1-4 : angle 1.97166 / 1.04 ( 3) link_NAG-ASN : bond 0.00418 / 0.28 ( 10) link_NAG-ASN : angle 2.86646 / 2.04 ( 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 174 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.505 Fit side-chains REVERT: A 573 TYR cc_start: 0.7060 (p90) cc_final: 0.6752 (p90) REVERT: A 578 ASP cc_start: 0.7845 (t0) cc_final: 0.7425 (t70) REVERT: A 625 PHE cc_start: 0.8105 (m-80) cc_final: 0.7856 (m-80) REVERT: B 575 ASP cc_start: 0.7845 (p0) cc_final: 0.7504 (p0) REVERT: B 635 ILE cc_start: 0.9003 (mt) cc_final: 0.8657 (mt) outliers start: 12 outliers final: 12 residues processed: 168 average time/residue: 0.1064 time to fit residues: 26.2044 Evaluate side-chains 170 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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: 0.0470 chunk 141 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN B 207 ASN B 724 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104077 restraints weight = 19727.189| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.36 r_work: 0.2946 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13439 Z= 0.107 Angle : 0.529 9.598 18266 Z= 0.275 Chirality : 0.044 0.268 2052 Planarity : 0.004 0.054 2291 Dihedral : 8.089 76.233 1995 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.50 % Allowed : 9.23 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.10 (0.20), residues: 1606 helix: 0.36 (0.20), residues: 693 sheet: -1.19 (0.35), residues: 210 loop : -1.66 (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 0.010 0.001 PHE B 539 TRP 0.015 0.001 TRP B 299 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (13411) covalent geometry : angle 0.51780 / 0.27 (18199) SS BOND : bond 0.00212 / 0.15 ( 17) SS BOND : angle 0.75174 / 0.53 ( 34) hydrogen bonds : bond 0.04055 / 2.69 ( 497) hydrogen bonds : angle 4.04342 / 2.75 ( 1449) link_BETA1-4 : bond 0.00469 / 0.25 ( 1) link_BETA1-4 : angle 1.31920 / 0.67 ( 3) link_NAG-ASN : bond 0.00380 / 0.25 ( 10) link_NAG-ASN : angle 2.58343 / 1.83 ( 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 170 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.403 Fit side-chains REVERT: A 573 TYR cc_start: 0.6891 (p90) cc_final: 0.6656 (p90) REVERT: A 625 PHE cc_start: 0.8037 (m-80) cc_final: 0.7796 (m-80) REVERT: B 635 ILE cc_start: 0.8919 (mt) cc_final: 0.8588 (mt) REVERT: B 641 PRO cc_start: 0.8176 (Cg_exo) cc_final: 0.7793 (Cg_endo) REVERT: B 729 PHE cc_start: 0.7940 (t80) cc_final: 0.7651 (t80) outliers start: 7 outliers final: 3 residues processed: 166 average time/residue: 0.1009 time to fit residues: 24.9471 Evaluate side-chains 163 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 566 VAL 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: 1.9990 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.119279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098584 restraints weight = 19742.382| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.21 r_work: 0.2898 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13439 Z= 0.217 Angle : 0.636 10.292 18266 Z= 0.326 Chirality : 0.049 0.315 2052 Planarity : 0.005 0.061 2291 Dihedral : 8.321 71.163 1995 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.22 % Allowed : 9.08 % 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: -1.12 (0.20), residues: 1606 helix: 0.34 (0.20), residues: 696 sheet: -1.00 (0.38), residues: 192 loop : -1.75 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.023 0.002 TYR A 411 PHE 0.017 0.002 PHE B 330 TRP 0.017 0.002 TRP B 206 HIS 0.005 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 (13411) covalent geometry : angle 0.62417 / 0.32 (18199) SS BOND : bond 0.00418 / 0.28 ( 17) SS BOND : angle 1.10226 / 0.78 ( 34) hydrogen bonds : bond 0.05838 / 3.86 ( 497) hydrogen bonds : angle 4.22621 / 2.89 ( 1449) link_BETA1-4 : bond 0.00061 / 0.03 ( 1) link_BETA1-4 : angle 2.02811 / 1.08 ( 3) link_NAG-ASN : bond 0.00399 / 0.27 ( 10) link_NAG-ASN : angle 2.79511 / 1.99 ( 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 173 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.498 Fit side-chains REVERT: A 270 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8101 (t80) REVERT: A 578 ASP cc_start: 0.7866 (t0) cc_final: 0.7446 (t70) REVERT: B 575 ASP cc_start: 0.7801 (p0) cc_final: 0.7527 (p0) REVERT: B 635 ILE cc_start: 0.8995 (mt) cc_final: 0.8632 (mt) REVERT: B 641 PRO cc_start: 0.8177 (Cg_exo) cc_final: 0.7877 (Cg_endo) outliers start: 17 outliers final: 13 residues processed: 164 average time/residue: 0.1095 time to fit residues: 26.4808 Evaluate side-chains 168 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 208 TRP Chi-restraints excluded: chain B residue 343 VAL 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 828 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 120 optimal weight: 0.0070 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102668 restraints weight = 19650.732| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.32 r_work: 0.2921 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1698 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= 0.122 Angle : 0.543 9.688 18266 Z= 0.281 Chirality : 0.045 0.277 2052 Planarity : 0.004 0.048 2291 Dihedral : 7.972 72.105 1995 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.00 % Allowed : 9.87 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1606 helix: 0.64 (0.20), residues: 696 sheet: -1.16 (0.36), residues: 208 loop : -1.66 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.014 0.001 TYR A 573 PHE 0.010 0.001 PHE B 311 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 0.00281 / 0.12 (13411) covalent geometry : angle 0.53180 / 0.28 (18199) SS BOND : bond 0.00259 / 0.18 ( 17) SS BOND : angle 0.81882 / 0.57 ( 34) hydrogen bonds : bond 0.04372 / 2.89 ( 497) hydrogen bonds : angle 4.00177 / 2.73 ( 1449) link_BETA1-4 : bond 0.00281 / 0.15 ( 1) link_BETA1-4 : angle 1.50076 / 0.78 ( 3) link_NAG-ASN : bond 0.00390 / 0.26 ( 10) link_NAG-ASN : angle 2.59490 / 1.84 ( 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 171 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.338 Fit side-chains REVERT: A 270 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8019 (t80) REVERT: B 635 ILE cc_start: 0.8967 (mt) cc_final: 0.8608 (mt) REVERT: B 641 PRO cc_start: 0.8153 (Cg_exo) cc_final: 0.7902 (Cg_endo) outliers start: 14 outliers final: 12 residues processed: 164 average time/residue: 0.0979 time to fit residues: 23.9638 Evaluate side-chains 168 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 272 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 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: 0.6980 chunk 36 optimal weight: 0.7980 chunk 119 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 141 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 50 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.123250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103156 restraints weight = 19710.736| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.31 r_work: 0.2905 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1762 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= 0.119 Angle : 0.538 9.689 18266 Z= 0.278 Chirality : 0.044 0.281 2052 Planarity : 0.004 0.047 2291 Dihedral : 7.846 73.548 1995 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.50 % Allowed : 9.44 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1606 helix: 0.86 (0.20), residues: 693 sheet: -1.03 (0.38), residues: 193 loop : -1.56 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.019 0.001 TYR A 573 PHE 0.009 0.001 PHE B 311 TRP 0.013 0.001 TRP B 299 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13411) covalent geometry : angle 0.52732 / 0.28 (18199) SS BOND : bond 0.00244 / 0.16 ( 17) SS BOND : angle 0.82530 / 0.58 ( 34) hydrogen bonds : bond 0.04309 / 2.85 ( 497) hydrogen bonds : angle 3.92739 / 2.68 ( 1449) link_BETA1-4 : bond 0.00296 / 0.16 ( 1) link_BETA1-4 : angle 1.46011 / 0.76 ( 3) link_NAG-ASN : bond 0.00379 / 0.25 ( 10) link_NAG-ASN : angle 2.51436 / 1.79 ( 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: 21 poor density : 158 time to evaluate : 0.492 Fit side-chains REVERT: A 270 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8024 (t80) REVERT: B 635 ILE cc_start: 0.8985 (mt) cc_final: 0.8638 (mt) REVERT: B 641 PRO cc_start: 0.8233 (Cg_exo) cc_final: 0.8012 (Cg_endo) REVERT: B 729 PHE cc_start: 0.8099 (t80) cc_final: 0.7883 (t80) outliers start: 21 outliers final: 18 residues processed: 168 average time/residue: 0.0990 time to fit residues: 24.8518 Evaluate side-chains 175 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 689 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 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 473 MET 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: 0.0570 chunk 109 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.124380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.103968 restraints weight = 19557.536| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.31 r_work: 0.2948 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13439 Z= 0.104 Angle : 0.517 9.697 18266 Z= 0.268 Chirality : 0.044 0.269 2052 Planarity : 0.004 0.046 2291 Dihedral : 7.658 74.837 1995 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.50 % Allowed : 10.37 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1606 helix: 1.08 (0.20), residues: 690 sheet: -1.10 (0.36), residues: 207 loop : -1.46 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.014 0.001 TYR A 573 PHE 0.010 0.001 PHE B 539 TRP 0.013 0.001 TRP B 299 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (13411) covalent geometry : angle 0.50646 / 0.27 (18199) SS BOND : bond 0.00203 / 0.14 ( 17) SS BOND : angle 0.70556 / 0.49 ( 34) hydrogen bonds : bond 0.03818 / 2.53 ( 497) hydrogen bonds : angle 3.81484 / 2.60 ( 1449) link_BETA1-4 : bond 0.00297 / 0.16 ( 1) link_BETA1-4 : angle 1.28285 / 0.67 ( 3) link_NAG-ASN : bond 0.00395 / 0.27 ( 10) link_NAG-ASN : angle 2.47170 / 1.77 ( 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: 21 poor density : 159 time to evaluate : 0.441 Fit side-chains REVERT: A 270 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8003 (t80) REVERT: A 906 TRP cc_start: 0.8385 (m100) cc_final: 0.8111 (m100) outliers start: 21 outliers final: 15 residues processed: 171 average time/residue: 0.0952 time to fit residues: 24.6747 Evaluate side-chains 172 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 523 ILE Chi-restraints excluded: chain A residue 603 ILE 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 357 ASN Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL 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: 0.7980 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 148 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.122759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102663 restraints weight = 19723.731| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.25 r_work: 0.2920 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13439 Z= 0.139 Angle : 0.557 9.771 18266 Z= 0.287 Chirality : 0.045 0.292 2052 Planarity : 0.004 0.046 2291 Dihedral : 7.732 74.220 1995 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.65 % Allowed : 10.37 % Favored : 87.98 % 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: -0.45 (0.21), residues: 1606 helix: 1.08 (0.20), residues: 695 sheet: -1.03 (0.38), residues: 194 loop : -1.48 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.018 0.002 TYR A 573 PHE 0.011 0.001 PHE B 311 TRP 0.010 0.001 TRP B 299 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13411) covalent geometry : angle 0.54681 / 0.29 (18199) SS BOND : bond 0.00273 / 0.18 ( 17) SS BOND : angle 0.86473 / 0.61 ( 34) hydrogen bonds : bond 0.04570 / 3.02 ( 497) hydrogen bonds : angle 3.91389 / 2.67 ( 1449) link_BETA1-4 : bond 0.00150 / 0.08 ( 1) link_BETA1-4 : angle 1.59528 / 0.83 ( 3) link_NAG-ASN : bond 0.00375 / 0.25 ( 10) link_NAG-ASN : angle 2.50285 / 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 178 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.455 Fit side-chains REVERT: A 270 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8024 (t80) REVERT: A 585 CYS cc_start: 0.7021 (t) cc_final: 0.6811 (t) REVERT: B 635 ILE cc_start: 0.8922 (mt) cc_final: 0.8545 (mt) outliers start: 23 outliers final: 19 residues processed: 170 average time/residue: 0.0997 time to fit residues: 25.4408 Evaluate side-chains 174 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 523 ILE 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 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 445 THR Chi-restraints excluded: chain B residue 455 VAL 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 754 GLN 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: 1.9990 chunk 112 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.119194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098568 restraints weight = 19801.698| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.23 r_work: 0.2895 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13439 Z= 0.202 Angle : 0.628 10.040 18266 Z= 0.323 Chirality : 0.048 0.287 2052 Planarity : 0.005 0.049 2291 Dihedral : 7.993 73.555 1995 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.50 % Allowed : 10.66 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1606 helix: 0.82 (0.20), residues: 703 sheet: -1.08 (0.38), residues: 194 loop : -1.62 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.024 0.002 TYR A 411 PHE 0.013 0.002 PHE B 330 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 0.00500 / 0.20 (13411) covalent geometry : angle 0.61675 / 0.32 (18199) SS BOND : bond 0.00393 / 0.25 ( 17) SS BOND : angle 1.07333 / 0.76 ( 34) hydrogen bonds : bond 0.05663 / 3.74 ( 497) hydrogen bonds : angle 4.10010 / 2.80 ( 1449) link_BETA1-4 : bond 0.00040 / 0.02 ( 1) link_BETA1-4 : angle 2.02711 / 1.07 ( 3) link_NAG-ASN : bond 0.00384 / 0.26 ( 10) link_NAG-ASN : angle 2.77001 / 2.00 ( 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 174 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.580 Fit side-chains REVERT: A 270 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8141 (t80) REVERT: A 585 CYS cc_start: 0.7111 (t) cc_final: 0.6823 (t) REVERT: A 635 ILE cc_start: 0.9001 (mt) cc_final: 0.8624 (mt) REVERT: B 635 ILE cc_start: 0.8967 (mt) cc_final: 0.8582 (mt) outliers start: 21 outliers final: 20 residues processed: 166 average time/residue: 0.1137 time to fit residues: 27.9762 Evaluate side-chains 173 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 523 ILE Chi-restraints excluded: chain A residue 603 ILE 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 523 ILE Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 754 GLN 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: 1.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102252 restraints weight = 19611.333| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.19 r_work: 0.2942 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13439 Z= 0.146 Angle : 0.569 9.663 18266 Z= 0.294 Chirality : 0.046 0.280 2052 Planarity : 0.004 0.047 2291 Dihedral : 7.812 75.899 1995 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.57 % Allowed : 10.80 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1606 helix: 0.99 (0.20), residues: 701 sheet: -1.12 (0.38), residues: 194 loop : -1.55 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.024 0.002 TYR A 573 PHE 0.012 0.001 PHE B 311 TRP 0.012 0.001 TRP A 299 HIS 0.003 0.001 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13411) covalent geometry : angle 0.55858 / 0.29 (18199) SS BOND : bond 0.00303 / 0.20 ( 17) SS BOND : angle 0.98321 / 0.70 ( 34) hydrogen bonds : bond 0.04754 / 3.14 ( 497) hydrogen bonds : angle 3.98852 / 2.72 ( 1449) link_BETA1-4 : bond 0.00192 / 0.10 ( 1) link_BETA1-4 : angle 1.69099 / 0.89 ( 3) link_NAG-ASN : bond 0.00384 / 0.26 ( 10) link_NAG-ASN : angle 2.58686 / 1.85 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.44 seconds wall clock time: 52 minutes 20.26 seconds (3140.26 seconds total)