Starting phenix.real_space_refine on Sun Sep 13 06:21:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pqp_20450/09_2026/6pqp_20450.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqp_20450/09_2026/6pqp_20450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2026/6pqp_20450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2026/6pqp_20450.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2026/6pqp_20450.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2026/6pqp_20450.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2026/6pqp_20450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqp_20450/09_2026/6pqp_20450.cif" } resolution = 3.06 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 152 5.16 5 C 13524 2.51 5 N 3216 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "H" 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 chiralities: 2 Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'6OU': 5, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 200 Unusual residues: {'6OU': 4, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'6OU': 5, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 282 Unusual residues: {'6OU': 6, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.01, per 1000 atoms: 0.24 Number of scatterers: 20492 At special positions: 0 Unit cell: (111.93, 111.93, 148.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 24 15.00 O 3576 8.00 N 3216 7.00 C 13524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 747 " " NAG F 1 " - " ASN D 747 " " NAG G 1 " - " ASN B 747 " " NAG H 1 " - " ASN C 747 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 843.0 milliseconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 8 sheets defined 73.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.513A pdb=" N TYR A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.525A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR A 670 " --> pdb=" O PRO A 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 671' Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.584A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.801A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 796 removed outlier: 3.586A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 827 through 846 removed outlier: 3.687A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN A 851 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER A 899 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 912 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1040 through 1072 Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.512A pdb=" N TYR D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.524A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 Processing helix chain 'D' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 removed outlier: 3.766A pdb=" N THR D 670 " --> pdb=" O PRO D 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 666 through 671' Processing helix chain 'D' and resid 672 through 677 Processing helix chain 'D' and resid 683 through 692 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 714 removed outlier: 3.584A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 739 removed outlier: 3.802A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 796 removed outlier: 3.586A pdb=" N THR D 772 " --> pdb=" O TYR D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 820 removed outlier: 3.760A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 819 " --> pdb=" O GLY D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 827 through 846 removed outlier: 3.687A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN D 851 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE D 877 " --> pdb=" O SER D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER D 899 " --> pdb=" O ASP D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 912 Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 922 through 928 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 Processing helix chain 'D' and resid 1016 through 1024 Processing helix chain 'D' and resid 1040 through 1072 Processing helix chain 'B' and resid 447 through 456 removed outlier: 3.513A pdb=" N TYR B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.524A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.612A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.853A pdb=" N ILE B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 671' Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 714 removed outlier: 3.583A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.802A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 796 removed outlier: 3.586A pdb=" N THR B 772 " --> pdb=" O TYR B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 827 through 846 removed outlier: 3.687A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN B 851 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER B 873 " --> pdb=" O THR B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE B 877 " --> pdb=" O SER B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER B 899 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 928 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.987A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 Processing helix chain 'B' and resid 1016 through 1024 Processing helix chain 'B' and resid 1040 through 1072 Processing helix chain 'C' and resid 447 through 456 removed outlier: 3.513A pdb=" N TYR C 456 " --> pdb=" O PHE C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.525A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR C 670 " --> pdb=" O PRO C 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 671 " --> pdb=" O LEU C 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 666 through 671' Processing helix chain 'C' and resid 672 through 677 Processing helix chain 'C' and resid 683 through 692 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 714 removed outlier: 3.583A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 739 removed outlier: 3.801A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 796 removed outlier: 3.587A pdb=" N THR C 772 " --> pdb=" O TYR C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 827 through 846 removed outlier: 3.686A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN C 851 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE C 877 " --> pdb=" O SER C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 3.613A pdb=" N SER C 899 " --> pdb=" O ASP C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 928 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 Processing helix chain 'C' and resid 1016 through 1024 Processing helix chain 'C' and resid 1040 through 1072 Processing sheet with id=AA1, first strand: chain 'A' and resid 656 through 659 Processing sheet with id=AA2, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 656 through 659 Processing sheet with id=AA4, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 656 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 656 through 659 Processing sheet with id=AA8, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3471 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: 3.51 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3064 1.30 - 1.43: 5374 1.43 - 1.56: 11947 1.56 - 1.68: 255 1.68 - 1.81: 276 Bond restraints: 20916 Sorted by residual: bond pdb=" O2 LBN C1208 " pdb=" P1 LBN C1208 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O2 LBN A1206 " pdb=" P1 LBN A1206 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O2 LBN D1205 " pdb=" P1 LBN D1205 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O2 LBN B1207 " pdb=" P1 LBN B1207 " ideal model delta sigma weight residual 1.650 1.796 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O22 6OU B1204 " pdb=" P23 6OU B1204 " ideal model delta sigma weight residual 1.643 1.738 -0.095 2.00e-02 2.50e+03 2.26e+01 ... (remaining 20911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 27152 3.07 - 6.14: 848 6.14 - 9.20: 120 9.20 - 12.27: 35 12.27 - 15.34: 13 Bond angle restraints: 28168 Sorted by residual: angle pdb=" N ILE C 611 " pdb=" CA ILE C 611 " pdb=" C ILE C 611 " ideal model delta sigma weight residual 108.23 119.24 -11.01 1.53e+00 4.27e-01 5.18e+01 angle pdb=" N ILE A 611 " pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 108.23 119.22 -10.99 1.53e+00 4.27e-01 5.16e+01 angle pdb=" N ILE B 611 " pdb=" CA ILE B 611 " pdb=" C ILE B 611 " ideal model delta sigma weight residual 108.23 119.20 -10.97 1.53e+00 4.27e-01 5.14e+01 angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 108.23 119.17 -10.94 1.53e+00 4.27e-01 5.11e+01 angle pdb=" O22 6OU D1204 " pdb=" P23 6OU D1204 " pdb=" O26 6OU D1204 " ideal model delta sigma weight residual 93.95 109.29 -15.34 3.00e+00 1.11e-01 2.61e+01 ... (remaining 28163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 12028 34.20 - 68.39: 328 68.39 - 102.59: 40 102.59 - 136.78: 0 136.78 - 170.98: 16 Dihedral angle restraints: 12412 sinusoidal: 5168 harmonic: 7244 Sorted by residual: dihedral pdb=" C1 LBN C1208 " pdb=" O1 LBN C1208 " pdb=" P1 LBN C1208 " pdb=" O3 LBN C1208 " ideal model delta sinusoidal sigma weight residual 275.40 104.42 170.98 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN D1205 " pdb=" O1 LBN D1205 " pdb=" P1 LBN D1205 " pdb=" O3 LBN D1205 " ideal model delta sinusoidal sigma weight residual 275.40 104.45 170.95 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN A1206 " pdb=" O1 LBN A1206 " pdb=" P1 LBN A1206 " pdb=" O3 LBN A1206 " ideal model delta sinusoidal sigma weight residual 275.40 104.46 170.94 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.215: 3220 1.215 - 2.431: 0 2.431 - 3.646: 0 3.646 - 4.861: 0 4.861 - 6.076: 4 Chirality restraints: 3224 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 747 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 3.68 -6.08 2.00e-01 2.50e+01 9.23e+02 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 747 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 3.68 -6.08 2.00e-01 2.50e+01 9.23e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 747 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 3.67 -6.07 2.00e-01 2.50e+01 9.23e+02 ... (remaining 3221 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.234 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG H 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.322 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.234 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG E 2 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.322 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.234 2.00e-02 2.50e+03 1.95e-01 4.73e+02 pdb=" C7 NAG F 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.322 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.014 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 347 2.69 - 3.24: 18481 3.24 - 3.79: 30503 3.79 - 4.35: 40445 4.35 - 4.90: 66550 Nonbonded interactions: 156326 Sorted by model distance: nonbonded pdb=" OD1 ASN D 747 " pdb=" N SER D 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN B 747 " pdb=" N SER B 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN A 747 " pdb=" N SER A 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN C 747 " pdb=" N SER C 748 " model vdw 2.132 3.120 nonbonded pdb=" O ILE B 810 " pdb=" OG1 THR B 814 " model vdw 2.284 3.040 ... (remaining 156321 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 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'B' and (resid 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'C' and (resid 446 through 1079 or resid 1204)) selection = (chain 'D' and (resid 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.290 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.014 0.451 20928 Z= 0.635 Angle : 1.388 35.721 28192 Z= 0.611 Chirality : 0.226 6.076 3224 Planarity : 0.011 0.195 3392 Dihedral : 16.307 170.977 7708 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.19 % Allowed : 4.80 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.14), residues: 2436 helix: -2.21 (0.09), residues: 1756 sheet: 1.02 (0.80), residues: 68 loop : -1.74 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 919 TYR 0.042 0.003 TYR C 785 PHE 0.035 0.004 PHE D 888 TRP 0.050 0.003 TRP B 515 HIS 0.011 0.003 HIS C 494 Details of bonding type rmsd/Z covalent geometry : bond 0.01199 / 0.55 (20916) covalent geometry : angle 1.29170 / 0.59 (28168) hydrogen bonds : bond 0.14840 / 10.35 ( 1173) hydrogen bonds : angle 6.08031 / 4.27 ( 3471) Misc. bond : bond 0.02139 / 1.07 ( 4) link_BETA1-4 : bond 0.00041 / 0.02 ( 4) link_BETA1-4 : angle 0.04874 / 0.04 ( 12) link_NAG-ASN : bond 0.45049 / 22.57 ( 4) link_NAG-ASN : angle 24.68929 / 17.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 614 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 720 MET cc_start: 0.7790 (mmm) cc_final: 0.7513 (mmm) REVERT: A 826 ILE cc_start: 0.8749 (mt) cc_final: 0.8521 (tt) REVERT: A 930 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 1042 MET cc_start: 0.7688 (ppp) cc_final: 0.7398 (ptt) REVERT: D 571 ASN cc_start: 0.8297 (m110) cc_final: 0.7993 (t0) REVERT: D 783 PHE cc_start: 0.8045 (m-80) cc_final: 0.7789 (m-10) REVERT: D 981 GLU cc_start: 0.8048 (tp30) cc_final: 0.7732 (mm-30) REVERT: D 986 LEU cc_start: 0.9266 (tt) cc_final: 0.8922 (tt) REVERT: D 1077 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 591 LYS cc_start: 0.9374 (mttt) cc_final: 0.9169 (mtmm) REVERT: B 643 LEU cc_start: 0.7727 (mp) cc_final: 0.7335 (mp) REVERT: B 1075 ILE cc_start: 0.7807 (mt) cc_final: 0.7078 (mm) REVERT: C 770 ILE cc_start: 0.9317 (mt) cc_final: 0.9084 (mm) REVERT: C 981 GLU cc_start: 0.7936 (tp30) cc_final: 0.7619 (tp30) REVERT: C 985 SER cc_start: 0.9199 (t) cc_final: 0.8779 (p) REVERT: C 1075 ILE cc_start: 0.8628 (mt) cc_final: 0.8006 (mm) outliers start: 4 outliers final: 3 residues processed: 614 average time/residue: 0.1542 time to fit residues: 145.5165 Evaluate side-chains 308 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 305 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain B residue 611 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS A 460 ASN A 476 ASN A 512 HIS A 519 HIS A 549 ASN A 570 HIS A 644 HIS A 700 HIS A 739 ASN A 805 ASN A 893 ASN A 983 HIS D 451 HIS D 460 ASN D 476 ASN D 512 HIS D 519 HIS D 549 ASN D 570 HIS D 577 ASN D 644 HIS D 700 HIS D 719 HIS D 805 ASN D 893 ASN D 907 GLN D 983 HIS D1047 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 460 ASN B 476 ASN B 512 HIS B 519 HIS B 549 ASN B 577 ASN B 644 HIS B 700 HIS B 719 HIS B 805 ASN B 983 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 460 ASN C 476 ASN C 512 HIS C 519 HIS ** C 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 644 HIS C 692 ASN C 700 HIS C 719 HIS C 805 ASN C 831 GLN C 893 ASN C 907 GLN C 970 HIS C 983 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095144 restraints weight = 33249.709| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.72 r_work: 0.3029 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20928 Z= 0.136 Angle : 0.697 15.777 28192 Z= 0.325 Chirality : 0.044 0.271 3224 Planarity : 0.005 0.064 3392 Dihedral : 19.120 156.191 3206 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.54 % Allowed : 11.66 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.78 (0.16), residues: 2436 helix: -0.31 (0.12), residues: 1760 sheet: 1.60 (0.79), residues: 68 loop : -0.96 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 996 TYR 0.014 0.001 TYR D 768 PHE 0.014 0.001 PHE D 823 TRP 0.015 0.001 TRP A 515 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (20916) covalent geometry : angle 0.66063 / 0.32 (28168) hydrogen bonds : bond 0.05040 / 3.50 ( 1173) hydrogen bonds : angle 4.37622 / 3.12 ( 3471) Misc. bond : bond 0.00089 / 0.04 ( 4) link_BETA1-4 : bond 0.01416 / 0.71 ( 4) link_BETA1-4 : angle 3.13873 / 2.15 ( 12) link_NAG-ASN : bond 0.00569 / 0.29 ( 4) link_NAG-ASN : angle 10.28311 / 7.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 351 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 483 MET cc_start: 0.8197 (mtt) cc_final: 0.7509 (mtp) REVERT: A 610 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8916 (mmtm) REVERT: A 625 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8778 (mm-30) REVERT: A 721 MET cc_start: 0.8603 (tpp) cc_final: 0.8391 (mmp) REVERT: A 783 PHE cc_start: 0.8108 (m-10) cc_final: 0.7873 (m-10) REVERT: A 852 ARG cc_start: 0.8591 (mpt180) cc_final: 0.8038 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8536 (tp30) cc_final: 0.8315 (mm-30) REVERT: A 1073 GLU cc_start: 0.7826 (tt0) cc_final: 0.7558 (tt0) REVERT: D 607 GLU cc_start: 0.8338 (mp0) cc_final: 0.8017 (mp0) REVERT: D 610 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8762 (mmtp) REVERT: D 657 GLU cc_start: 0.8411 (tt0) cc_final: 0.8163 (tm-30) REVERT: D 681 GLU cc_start: 0.8354 (pm20) cc_final: 0.8134 (pm20) REVERT: D 852 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7521 (mmm-85) REVERT: D 981 GLU cc_start: 0.8787 (tp30) cc_final: 0.8181 (tp30) REVERT: D 985 SER cc_start: 0.9441 (t) cc_final: 0.8673 (p) REVERT: B 488 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 591 LYS cc_start: 0.9467 (mttt) cc_final: 0.9242 (mtmm) REVERT: B 852 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7695 (mmm-85) REVERT: B 935 VAL cc_start: 0.9454 (t) cc_final: 0.9224 (p) REVERT: B 1073 GLU cc_start: 0.8090 (tt0) cc_final: 0.7530 (tt0) REVERT: B 1075 ILE cc_start: 0.8422 (mt) cc_final: 0.8116 (mp) REVERT: C 852 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7669 (mmm-85) REVERT: C 981 GLU cc_start: 0.8736 (tp30) cc_final: 0.8123 (tp30) REVERT: C 985 SER cc_start: 0.9340 (t) cc_final: 0.8666 (p) REVERT: C 998 VAL cc_start: 0.9118 (p) cc_final: 0.8739 (m) REVERT: C 1075 ILE cc_start: 0.8832 (mt) cc_final: 0.8482 (mp) outliers start: 53 outliers final: 20 residues processed: 388 average time/residue: 0.1257 time to fit residues: 79.2423 Evaluate side-chains 321 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 300 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 775 ILE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 933 HIS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 175 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 HIS A 590 ASN A 831 GLN A 907 GLN D 560 HIS D 590 ASN ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN B 590 ASN B 893 ASN C 537 ASN C 590 ASN ** C 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.084974 restraints weight = 32932.467| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.79 r_work: 0.2832 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20928 Z= 0.187 Angle : 0.664 11.421 28192 Z= 0.318 Chirality : 0.044 0.255 3224 Planarity : 0.004 0.069 3392 Dihedral : 17.148 143.117 3200 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.55 % Allowed : 12.33 % Favored : 84.12 % 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: 0.36 (0.17), residues: 2436 helix: 0.58 (0.12), residues: 1752 sheet: 1.71 (0.79), residues: 68 loop : -0.64 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 996 TYR 0.023 0.002 TYR C 768 PHE 0.016 0.002 PHE B 818 TRP 0.017 0.002 TRP A 515 HIS 0.008 0.001 HIS C 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (20916) covalent geometry : angle 0.64443 / 0.31 (28168) hydrogen bonds : bond 0.04813 / 3.30 ( 1173) hydrogen bonds : angle 4.00078 / 2.82 ( 3471) Misc. bond : bond 0.00126 / 0.06 ( 4) link_BETA1-4 : bond 0.00288 / 0.14 ( 4) link_BETA1-4 : angle 1.57531 / 1.03 ( 12) link_NAG-ASN : bond 0.01263 / 0.64 ( 4) link_NAG-ASN : angle 7.72493 / 5.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 315 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 464 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7601 (ttp80) REVERT: A 625 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8998 (mm-30) REVERT: A 721 MET cc_start: 0.8681 (tpp) cc_final: 0.8461 (mmp) REVERT: A 783 PHE cc_start: 0.8328 (m-10) cc_final: 0.8065 (m-10) REVERT: A 852 ARG cc_start: 0.8706 (mpt180) cc_final: 0.8242 (mmm-85) REVERT: A 891 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8981 (mp) REVERT: A 941 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9096 (tp) REVERT: A 1059 GLU cc_start: 0.8718 (tp30) cc_final: 0.8438 (mm-30) REVERT: A 1073 GLU cc_start: 0.8066 (tt0) cc_final: 0.7755 (tt0) REVERT: D 464 ARG cc_start: 0.8211 (mtt90) cc_final: 0.7903 (mtm110) REVERT: D 483 MET cc_start: 0.8845 (mtm) cc_final: 0.8621 (mtp) REVERT: D 610 LYS cc_start: 0.9158 (mmmm) cc_final: 0.8849 (mmtm) REVERT: D 681 GLU cc_start: 0.8547 (pm20) cc_final: 0.8267 (pm20) REVERT: D 981 GLU cc_start: 0.8869 (tp30) cc_final: 0.8466 (tp30) REVERT: D 985 SER cc_start: 0.9426 (t) cc_final: 0.8877 (p) REVERT: D 986 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9137 (tt) REVERT: B 591 LYS cc_start: 0.9441 (mttt) cc_final: 0.9198 (mtmm) REVERT: B 709 MET cc_start: 0.9261 (tmm) cc_final: 0.9053 (tmm) REVERT: B 785 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7469 (m-10) REVERT: B 852 ARG cc_start: 0.8144 (mmm-85) cc_final: 0.7833 (mmm-85) REVERT: B 987 GLU cc_start: 0.8805 (tt0) cc_final: 0.8596 (tt0) REVERT: B 998 VAL cc_start: 0.9192 (p) cc_final: 0.8962 (m) REVERT: B 1024 PHE cc_start: 0.9014 (m-80) cc_final: 0.8699 (m-80) REVERT: B 1059 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8569 (mm-30) REVERT: C 610 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8804 (mmtp) REVERT: C 709 MET cc_start: 0.9304 (tmm) cc_final: 0.9090 (tmm) REVERT: C 852 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7777 (mmm-85) REVERT: C 981 GLU cc_start: 0.8801 (tp30) cc_final: 0.8395 (tp30) REVERT: C 985 SER cc_start: 0.9408 (t) cc_final: 0.8910 (p) REVERT: C 998 VAL cc_start: 0.9265 (p) cc_final: 0.8860 (m) REVERT: C 1075 ILE cc_start: 0.8926 (mt) cc_final: 0.8656 (mm) outliers start: 74 outliers final: 27 residues processed: 366 average time/residue: 0.1372 time to fit residues: 80.4927 Evaluate side-chains 292 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 947 PHE Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain D residue 1002 SER Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 203 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 693 ASN A1047 GLN D1000 GLN B 907 GLN C 537 ASN ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.080693 restraints weight = 33292.067| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.72 r_work: 0.2777 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20928 Z= 0.225 Angle : 0.673 11.067 28192 Z= 0.317 Chirality : 0.045 0.210 3224 Planarity : 0.004 0.061 3392 Dihedral : 16.199 139.147 3200 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.83 % Allowed : 15.12 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2436 helix: 0.86 (0.12), residues: 1740 sheet: 1.56 (0.79), residues: 68 loop : -0.59 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 996 TYR 0.012 0.002 TYR A 842 PHE 0.011 0.002 PHE C 877 TRP 0.018 0.002 TRP A 515 HIS 0.009 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (20916) covalent geometry : angle 0.65533 / 0.31 (28168) hydrogen bonds : bond 0.04826 / 3.34 ( 1173) hydrogen bonds : angle 4.02575 / 2.84 ( 3471) Misc. bond : bond 0.00048 / 0.02 ( 4) link_BETA1-4 : bond 0.00475 / 0.24 ( 4) link_BETA1-4 : angle 1.63121 / 1.11 ( 12) link_NAG-ASN : bond 0.01058 / 0.53 ( 4) link_NAG-ASN : angle 7.37270 / 5.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 272 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 464 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7635 (ttp80) REVERT: A 681 GLU cc_start: 0.8120 (pm20) cc_final: 0.7832 (pm20) REVERT: A 721 MET cc_start: 0.8765 (tpp) cc_final: 0.8546 (mmp) REVERT: A 785 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8107 (m-10) REVERT: A 852 ARG cc_start: 0.8755 (mpt180) cc_final: 0.8271 (mmm-85) REVERT: A 941 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9109 (tp) REVERT: A 1059 GLU cc_start: 0.8762 (tp30) cc_final: 0.8465 (mm-30) REVERT: A 1073 GLU cc_start: 0.8293 (tt0) cc_final: 0.7943 (tt0) REVERT: D 483 MET cc_start: 0.8830 (mtm) cc_final: 0.8573 (mtp) REVERT: D 681 GLU cc_start: 0.8588 (pm20) cc_final: 0.8313 (pm20) REVERT: D 981 GLU cc_start: 0.8831 (tp30) cc_final: 0.8498 (tp30) REVERT: B 591 LYS cc_start: 0.9436 (mttt) cc_final: 0.9186 (mtmm) REVERT: B 781 SER cc_start: 0.8898 (m) cc_final: 0.8664 (p) REVERT: B 785 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: B 852 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7849 (mmm-85) REVERT: B 941 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9008 (tp) REVERT: B 987 GLU cc_start: 0.8837 (tt0) cc_final: 0.8455 (tt0) REVERT: B 1024 PHE cc_start: 0.9057 (m-80) cc_final: 0.8811 (m-80) REVERT: B 1059 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8556 (mm-30) REVERT: C 483 MET cc_start: 0.8972 (mtp) cc_final: 0.8678 (mtp) REVERT: C 504 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8381 (mtpp) REVERT: C 610 LYS cc_start: 0.9243 (mmtp) cc_final: 0.8856 (mmtp) REVERT: C 681 GLU cc_start: 0.8792 (pm20) cc_final: 0.8534 (pm20) REVERT: C 852 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.7778 (mmm-85) REVERT: C 981 GLU cc_start: 0.8831 (tp30) cc_final: 0.8362 (tp30) REVERT: C 985 SER cc_start: 0.9432 (t) cc_final: 0.8882 (p) outliers start: 59 outliers final: 33 residues processed: 314 average time/residue: 0.1364 time to fit residues: 69.1954 Evaluate side-chains 279 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1002 SER Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 181 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.083561 restraints weight = 32934.764| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.71 r_work: 0.2828 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20928 Z= 0.118 Angle : 0.578 9.812 28192 Z= 0.274 Chirality : 0.041 0.199 3224 Planarity : 0.004 0.058 3392 Dihedral : 15.412 142.413 3200 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.21 % Allowed : 15.74 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2436 helix: 1.22 (0.13), residues: 1740 sheet: 1.71 (0.79), residues: 68 loop : -0.40 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 996 TYR 0.009 0.001 TYR D 840 PHE 0.008 0.001 PHE B1022 TRP 0.009 0.001 TRP B 832 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (20916) covalent geometry : angle 0.56239 / 0.27 (28168) hydrogen bonds : bond 0.04005 / 2.77 ( 1173) hydrogen bonds : angle 3.78729 / 2.67 ( 3471) Misc. bond : bond 0.00029 / 0.01 ( 4) link_BETA1-4 : bond 0.00535 / 0.27 ( 4) link_BETA1-4 : angle 1.35610 / 0.94 ( 12) link_NAG-ASN : bond 0.01146 / 0.58 ( 4) link_NAG-ASN : angle 6.41121 / 4.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 464 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7635 (tmm160) REVERT: A 721 MET cc_start: 0.8700 (tpp) cc_final: 0.8481 (mmp) REVERT: A 785 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.8039 (m-10) REVERT: A 852 ARG cc_start: 0.8768 (mpt180) cc_final: 0.8230 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8763 (tp30) cc_final: 0.8519 (mm-30) REVERT: A 1073 GLU cc_start: 0.8216 (tt0) cc_final: 0.7906 (tt0) REVERT: D 530 MET cc_start: 0.8792 (mtm) cc_final: 0.8483 (mtt) REVERT: D 681 GLU cc_start: 0.8582 (pm20) cc_final: 0.8281 (pm20) REVERT: D 852 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7824 (mtm180) REVERT: D 981 GLU cc_start: 0.8833 (tp30) cc_final: 0.8508 (tp30) REVERT: B 591 LYS cc_start: 0.9432 (mttt) cc_final: 0.9195 (mtmm) REVERT: B 681 GLU cc_start: 0.8712 (pm20) cc_final: 0.8434 (pm20) REVERT: B 781 SER cc_start: 0.8864 (m) cc_final: 0.8635 (p) REVERT: B 852 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7878 (mmm-85) REVERT: B 941 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8970 (tp) REVERT: B 987 GLU cc_start: 0.8851 (tt0) cc_final: 0.8530 (tt0) REVERT: B 1024 PHE cc_start: 0.9019 (m-80) cc_final: 0.8776 (m-80) REVERT: B 1059 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8642 (mm-30) REVERT: C 610 LYS cc_start: 0.9242 (mmtp) cc_final: 0.8859 (mmtp) REVERT: C 681 GLU cc_start: 0.8787 (pm20) cc_final: 0.8519 (pm20) REVERT: C 808 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8545 (mm-30) REVERT: C 852 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7752 (mmm-85) REVERT: C 941 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9010 (tp) REVERT: C 981 GLU cc_start: 0.8786 (tp30) cc_final: 0.8369 (tp30) REVERT: C 985 SER cc_start: 0.9398 (t) cc_final: 0.8863 (p) outliers start: 46 outliers final: 24 residues processed: 290 average time/residue: 0.1372 time to fit residues: 64.1333 Evaluate side-chains 270 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 49 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 126 optimal weight: 0.1980 chunk 64 optimal weight: 0.1980 chunk 186 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.081234 restraints weight = 32987.806| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.70 r_work: 0.2791 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20928 Z= 0.163 Angle : 0.598 10.634 28192 Z= 0.282 Chirality : 0.042 0.212 3224 Planarity : 0.004 0.062 3392 Dihedral : 14.643 141.729 3200 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.59 % Allowed : 15.55 % Favored : 81.86 % 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: 1.37 (0.18), residues: 2436 helix: 1.38 (0.13), residues: 1740 sheet: 1.60 (0.79), residues: 68 loop : -0.36 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 996 TYR 0.022 0.001 TYR C 768 PHE 0.009 0.001 PHE C 818 TRP 0.011 0.001 TRP C 515 HIS 0.007 0.001 HIS C 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (20916) covalent geometry : angle 0.58412 / 0.28 (28168) hydrogen bonds : bond 0.04279 / 2.95 ( 1173) hydrogen bonds : angle 3.79413 / 2.67 ( 3471) Misc. bond : bond 0.00069 / 0.03 ( 4) link_BETA1-4 : bond 0.00390 / 0.20 ( 4) link_BETA1-4 : angle 1.26035 / 0.86 ( 12) link_NAG-ASN : bond 0.00960 / 0.48 ( 4) link_NAG-ASN : angle 6.02905 / 4.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.8723 (tpp) cc_final: 0.8496 (mmp) REVERT: A 785 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.8168 (m-10) REVERT: A 852 ARG cc_start: 0.8786 (mpt180) cc_final: 0.8235 (mmm-85) REVERT: A 981 GLU cc_start: 0.8734 (tp30) cc_final: 0.8484 (tp30) REVERT: A 1059 GLU cc_start: 0.8813 (tp30) cc_final: 0.8516 (mm-30) REVERT: D 681 GLU cc_start: 0.8609 (pm20) cc_final: 0.8333 (pm20) REVERT: D 852 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.7907 (mtm180) REVERT: D 981 GLU cc_start: 0.8792 (tp30) cc_final: 0.8470 (tp30) REVERT: B 591 LYS cc_start: 0.9429 (mttt) cc_final: 0.9204 (mtmm) REVERT: B 681 GLU cc_start: 0.8707 (pm20) cc_final: 0.8426 (pm20) REVERT: B 781 SER cc_start: 0.8908 (m) cc_final: 0.8655 (p) REVERT: B 785 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7766 (m-10) REVERT: B 852 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7892 (mmm-85) REVERT: B 941 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9043 (tp) REVERT: B 987 GLU cc_start: 0.8857 (tt0) cc_final: 0.8507 (tt0) REVERT: B 1059 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8631 (mm-30) REVERT: C 464 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7629 (ttp80) REVERT: C 681 GLU cc_start: 0.8787 (pm20) cc_final: 0.8510 (pm20) REVERT: C 842 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.8898 (m-80) REVERT: C 852 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7792 (mmm-85) REVERT: C 941 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9077 (tp) REVERT: C 981 GLU cc_start: 0.8833 (tp30) cc_final: 0.8455 (tp30) outliers start: 54 outliers final: 31 residues processed: 290 average time/residue: 0.1307 time to fit residues: 61.4543 Evaluate side-chains 272 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 191 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 71 optimal weight: 0.0050 chunk 211 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083576 restraints weight = 32888.974| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.71 r_work: 0.2850 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20928 Z= 0.107 Angle : 0.555 11.255 28192 Z= 0.263 Chirality : 0.040 0.195 3224 Planarity : 0.003 0.057 3392 Dihedral : 14.083 144.776 3200 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.87 % Allowed : 16.27 % Favored : 81.86 % 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: 1.63 (0.18), residues: 2436 helix: 1.51 (0.13), residues: 1756 sheet: 1.70 (0.78), residues: 68 loop : -0.11 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 996 TYR 0.015 0.001 TYR B 768 PHE 0.031 0.001 PHE C 823 TRP 0.009 0.001 TRP D 809 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (20916) covalent geometry : angle 0.54328 / 0.26 (28168) hydrogen bonds : bond 0.03731 / 2.57 ( 1173) hydrogen bonds : angle 3.67238 / 2.60 ( 3471) Misc. bond : bond 0.00038 / 0.02 ( 4) link_BETA1-4 : bond 0.00565 / 0.28 ( 4) link_BETA1-4 : angle 1.20593 / 0.83 ( 12) link_NAG-ASN : bond 0.01043 / 0.52 ( 4) link_NAG-ASN : angle 5.47115 / 3.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.8659 (tpp) cc_final: 0.8437 (mmp) REVERT: A 785 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.8136 (m-10) REVERT: A 852 ARG cc_start: 0.8766 (mpt180) cc_final: 0.8193 (mmm-85) REVERT: A 981 GLU cc_start: 0.8738 (tp30) cc_final: 0.8451 (tp30) REVERT: A 1059 GLU cc_start: 0.8815 (tp30) cc_final: 0.8526 (mm-30) REVERT: D 610 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8994 (mmtm) REVERT: D 681 GLU cc_start: 0.8617 (pm20) cc_final: 0.8313 (pm20) REVERT: D 852 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7947 (mtm180) REVERT: D 912 MET cc_start: 0.8927 (ttm) cc_final: 0.8690 (ttm) REVERT: D 981 GLU cc_start: 0.8820 (tp30) cc_final: 0.8494 (tp30) REVERT: B 591 LYS cc_start: 0.9438 (mttt) cc_final: 0.9217 (mtmm) REVERT: B 681 GLU cc_start: 0.8733 (pm20) cc_final: 0.8462 (pm20) REVERT: B 785 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: B 852 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7866 (mmm-85) REVERT: B 941 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9009 (tp) REVERT: B 987 GLU cc_start: 0.8755 (tt0) cc_final: 0.8438 (tt0) REVERT: B 1075 ILE cc_start: 0.8959 (mt) cc_final: 0.8744 (mp) REVERT: C 464 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7637 (ttp80) REVERT: C 681 GLU cc_start: 0.8773 (pm20) cc_final: 0.8497 (pm20) REVERT: C 842 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: C 852 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7804 (mmm-85) REVERT: C 941 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9074 (tp) REVERT: C 981 GLU cc_start: 0.8796 (tp30) cc_final: 0.8447 (tp30) outliers start: 39 outliers final: 26 residues processed: 276 average time/residue: 0.1411 time to fit residues: 62.4912 Evaluate side-chains 267 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 15 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 64 optimal weight: 0.1980 chunk 211 optimal weight: 0.9980 chunk 225 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** 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 = 0.3569 r_free = 0.3569 target = 0.118225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.084412 restraints weight = 32962.803| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.72 r_work: 0.2862 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20928 Z= 0.103 Angle : 0.547 10.473 28192 Z= 0.259 Chirality : 0.040 0.194 3224 Planarity : 0.003 0.057 3392 Dihedral : 13.473 148.128 3200 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.87 % Allowed : 16.55 % Favored : 81.57 % 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 (0.18), residues: 2436 helix: 1.61 (0.13), residues: 1756 sheet: 1.95 (0.78), residues: 68 loop : -0.09 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 464 TYR 0.013 0.001 TYR D 840 PHE 0.020 0.001 PHE C 823 TRP 0.009 0.001 TRP D 809 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (20916) covalent geometry : angle 0.53633 / 0.26 (28168) hydrogen bonds : bond 0.03578 / 2.47 ( 1173) hydrogen bonds : angle 3.59464 / 2.54 ( 3471) Misc. bond : bond 0.00038 / 0.02 ( 4) link_BETA1-4 : bond 0.00534 / 0.27 ( 4) link_BETA1-4 : angle 1.20395 / 0.82 ( 12) link_NAG-ASN : bond 0.00924 / 0.46 ( 4) link_NAG-ASN : angle 5.09415 / 3.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.8651 (tpp) cc_final: 0.8420 (mmp) REVERT: A 785 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8121 (m-10) REVERT: A 852 ARG cc_start: 0.8777 (mpt180) cc_final: 0.8212 (mmm-85) REVERT: A 981 GLU cc_start: 0.8741 (tp30) cc_final: 0.8430 (tp30) REVERT: A 1059 GLU cc_start: 0.8824 (tp30) cc_final: 0.8532 (mm-30) REVERT: D 610 LYS cc_start: 0.9268 (mmmm) cc_final: 0.9012 (mmtm) REVERT: D 852 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8002 (mtm180) REVERT: D 981 GLU cc_start: 0.8817 (tp30) cc_final: 0.8491 (tp30) REVERT: B 591 LYS cc_start: 0.9436 (mttt) cc_final: 0.9219 (mtmm) REVERT: B 785 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7653 (m-10) REVERT: B 852 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7884 (mmm-85) REVERT: B 981 GLU cc_start: 0.8630 (tp30) cc_final: 0.8409 (tm-30) REVERT: B 987 GLU cc_start: 0.8737 (tt0) cc_final: 0.8435 (tt0) REVERT: C 464 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7666 (ttp80) REVERT: C 681 GLU cc_start: 0.8757 (pm20) cc_final: 0.8472 (pm20) REVERT: C 852 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7815 (mmm-85) REVERT: C 981 GLU cc_start: 0.8794 (tp30) cc_final: 0.8445 (tp30) outliers start: 39 outliers final: 23 residues processed: 282 average time/residue: 0.1365 time to fit residues: 62.4320 Evaluate side-chains 265 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 39 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.084857 restraints weight = 32900.556| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.71 r_work: 0.2862 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20928 Z= 0.107 Angle : 0.550 9.261 28192 Z= 0.260 Chirality : 0.040 0.195 3224 Planarity : 0.003 0.056 3392 Dihedral : 13.016 149.713 3200 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.82 % Allowed : 16.94 % Favored : 81.24 % 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: 1.82 (0.18), residues: 2436 helix: 1.65 (0.13), residues: 1756 sheet: 1.98 (0.78), residues: 68 loop : -0.05 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 996 TYR 0.016 0.001 TYR D 842 PHE 0.017 0.001 PHE C 823 TRP 0.008 0.001 TRP D 809 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (20916) covalent geometry : angle 0.54020 / 0.26 (28168) hydrogen bonds : bond 0.03557 / 2.45 ( 1173) hydrogen bonds : angle 3.56538 / 2.52 ( 3471) Misc. bond : bond 0.00040 / 0.02 ( 4) link_BETA1-4 : bond 0.00483 / 0.24 ( 4) link_BETA1-4 : angle 1.16863 / 0.79 ( 12) link_NAG-ASN : bond 0.00872 / 0.44 ( 4) link_NAG-ASN : angle 4.88434 / 3.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 546 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8470 (pp20) REVERT: A 721 MET cc_start: 0.8657 (tpp) cc_final: 0.8423 (mmp) REVERT: A 785 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: A 852 ARG cc_start: 0.8748 (mpt180) cc_final: 0.8209 (mmm-85) REVERT: A 981 GLU cc_start: 0.8750 (tp30) cc_final: 0.8412 (tp30) REVERT: A 1059 GLU cc_start: 0.8838 (tp30) cc_final: 0.8550 (mm-30) REVERT: D 530 MET cc_start: 0.8757 (mtp) cc_final: 0.8449 (mtp) REVERT: D 610 LYS cc_start: 0.9276 (mmmm) cc_final: 0.9038 (mmtm) REVERT: D 852 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7983 (mtm180) REVERT: D 941 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9060 (tp) REVERT: D 981 GLU cc_start: 0.8791 (tp30) cc_final: 0.8484 (tp30) REVERT: B 591 LYS cc_start: 0.9449 (mttt) cc_final: 0.9239 (mtmm) REVERT: B 681 GLU cc_start: 0.8739 (pm20) cc_final: 0.8528 (pm20) REVERT: B 785 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7647 (m-10) REVERT: B 852 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7887 (mmm-85) REVERT: B 981 GLU cc_start: 0.8647 (tp30) cc_final: 0.8416 (tm-30) REVERT: B 987 GLU cc_start: 0.8714 (tt0) cc_final: 0.8414 (tt0) REVERT: B 996 ARG cc_start: 0.9056 (ttm-80) cc_final: 0.8647 (mtp85) REVERT: B 1059 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8556 (mm-30) REVERT: C 464 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7747 (ttp80) REVERT: C 842 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: C 852 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7813 (mmm-85) REVERT: C 981 GLU cc_start: 0.8775 (tp30) cc_final: 0.8448 (tp30) outliers start: 38 outliers final: 24 residues processed: 273 average time/residue: 0.1394 time to fit residues: 61.8707 Evaluate side-chains 269 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 151 optimal weight: 0.0000 chunk 48 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN ** C1061 GLN ** 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 = 0.3573 r_free = 0.3573 target = 0.118526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.084637 restraints weight = 33136.450| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.74 r_work: 0.2866 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20928 Z= 0.107 Angle : 0.552 9.578 28192 Z= 0.261 Chirality : 0.040 0.203 3224 Planarity : 0.003 0.056 3392 Dihedral : 12.681 150.905 3200 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.58 % Allowed : 17.03 % Favored : 81.38 % 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: 1.90 (0.18), residues: 2436 helix: 1.69 (0.13), residues: 1756 sheet: 4.27 (0.81), residues: 48 loop : -0.09 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 464 TYR 0.013 0.001 TYR D 842 PHE 0.017 0.001 PHE D1022 TRP 0.010 0.001 TRP D 809 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (20916) covalent geometry : angle 0.54279 / 0.26 (28168) hydrogen bonds : bond 0.03506 / 2.41 ( 1173) hydrogen bonds : angle 3.54183 / 2.50 ( 3471) Misc. bond : bond 0.00038 / 0.02 ( 4) link_BETA1-4 : bond 0.00456 / 0.23 ( 4) link_BETA1-4 : angle 1.15471 / 0.79 ( 12) link_NAG-ASN : bond 0.00889 / 0.45 ( 4) link_NAG-ASN : angle 4.77853 / 3.25 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 546 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8469 (pp20) REVERT: A 721 MET cc_start: 0.8648 (tpp) cc_final: 0.8417 (mmp) REVERT: A 785 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.8190 (m-10) REVERT: A 852 ARG cc_start: 0.8753 (mpt180) cc_final: 0.8244 (mmm-85) REVERT: A 981 GLU cc_start: 0.8755 (tp30) cc_final: 0.8423 (tp30) REVERT: A 1059 GLU cc_start: 0.8833 (tp30) cc_final: 0.8545 (mm-30) REVERT: D 464 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7652 (ttp80) REVERT: D 530 MET cc_start: 0.8751 (mtp) cc_final: 0.8398 (mtp) REVERT: D 852 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.7996 (mtm180) REVERT: D 941 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9061 (tp) REVERT: D 981 GLU cc_start: 0.8803 (tp30) cc_final: 0.8502 (tp30) REVERT: B 591 LYS cc_start: 0.9451 (mttt) cc_final: 0.9239 (mtmm) REVERT: B 681 GLU cc_start: 0.8746 (pm20) cc_final: 0.8538 (pm20) REVERT: B 785 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: B 852 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7778 (mmm-85) REVERT: B 912 MET cc_start: 0.9123 (ttp) cc_final: 0.8847 (ttm) REVERT: B 981 GLU cc_start: 0.8665 (tp30) cc_final: 0.8419 (tm-30) REVERT: B 987 GLU cc_start: 0.8719 (tt0) cc_final: 0.8438 (tt0) REVERT: B 996 ARG cc_start: 0.9084 (ttm-80) cc_final: 0.8652 (mtp85) REVERT: B 1059 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8515 (mm-30) REVERT: C 464 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7765 (ttp80) REVERT: C 842 TYR cc_start: 0.9275 (OUTLIER) cc_final: 0.8666 (m-80) REVERT: C 852 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.7817 (mmm-85) REVERT: C 981 GLU cc_start: 0.8797 (tp30) cc_final: 0.8473 (tp30) outliers start: 33 outliers final: 24 residues processed: 274 average time/residue: 0.1375 time to fit residues: 61.1848 Evaluate side-chains 270 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 174 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 199 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 182 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084967 restraints weight = 33166.311| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.74 r_work: 0.2870 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20928 Z= 0.106 Angle : 0.555 9.402 28192 Z= 0.264 Chirality : 0.040 0.192 3224 Planarity : 0.003 0.055 3392 Dihedral : 12.411 151.627 3200 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.63 % Allowed : 16.99 % Favored : 81.38 % 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: 1.97 (0.18), residues: 2436 helix: 1.79 (0.13), residues: 1732 sheet: 4.18 (0.81), residues: 48 loop : -0.14 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 996 TYR 0.019 0.001 TYR B 768 PHE 0.015 0.001 PHE C 823 TRP 0.010 0.001 TRP D 809 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (20916) covalent geometry : angle 0.54644 / 0.26 (28168) hydrogen bonds : bond 0.03472 / 2.39 ( 1173) hydrogen bonds : angle 3.52334 / 2.49 ( 3471) Misc. bond : bond 0.00035 / 0.02 ( 4) link_BETA1-4 : bond 0.00448 / 0.23 ( 4) link_BETA1-4 : angle 1.18222 / 0.80 ( 12) link_NAG-ASN : bond 0.00855 / 0.43 ( 4) link_NAG-ASN : angle 4.56670 / 3.12 ( 12) =============================================================================== Job complete usr+sys time: 4332.35 seconds wall clock time: 75 minutes 15.82 seconds (4515.82 seconds total)