Starting phenix.real_space_refine on Thu Mar 5 10:13:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqp_20450/03_2026/6pqp_20450.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqp_20450/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6pqp_20450/03_2026/6pqp_20450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqp_20450/03_2026/6pqp_20450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqp_20450/03_2026/6pqp_20450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqp_20450/03_2026/6pqp_20450.map" } 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-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 70 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: 62 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: 70 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: 78 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.13, per 1000 atoms: 0.25 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: 1.82 Conformation dependent library (CDL) restraints added in 977.9 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: 0.82 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: 3.40 Time building geometry restraints manager: 2.39 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: 12192 34.20 - 68.39: 420 68.39 - 102.59: 136 102.59 - 136.78: 32 136.78 - 170.98: 32 Dihedral angle restraints: 12812 sinusoidal: 5568 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 12809 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: 1.060 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.400 Find NCS groups from input model: 0.540 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 21.817 170.977 8108 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 covalent geometry : bond 0.01199 (20916) covalent geometry : angle 1.29170 (28168) hydrogen bonds : bond 0.14840 ( 1173) hydrogen bonds : angle 6.08031 ( 3471) Misc. bond : bond 0.02139 ( 4) link_BETA1-4 : bond 0.00041 ( 4) link_BETA1-4 : angle 0.04874 ( 12) link_NAG-ASN : bond 0.45049 ( 4) link_NAG-ASN : angle 24.68929 ( 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 : 0.784 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: 0.1527 time to fit residues: 143.3473 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 : 0.688 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS ** D 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 HIS D 719 HIS D 805 ASN D 893 ASN D 983 HIS ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 590 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 590 ASN C 644 HIS ** C 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN C 700 HIS C 719 HIS C 805 ASN C 893 ASN C 907 GLN C 970 HIS C 983 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094227 restraints weight = 33140.005| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.74 r_work: 0.3012 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20928 Z= 0.140 Angle : 0.716 15.821 28192 Z= 0.328 Chirality : 0.045 0.226 3224 Planarity : 0.005 0.065 3392 Dihedral : 23.127 156.553 3606 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.50 % Allowed : 11.66 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2436 helix: -0.26 (0.12), residues: 1760 sheet: 1.64 (0.79), residues: 68 loop : -0.95 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 996 TYR 0.015 0.001 TYR D 768 PHE 0.013 0.001 PHE D 823 TRP 0.014 0.002 TRP A 515 HIS 0.004 0.001 HIS A 970 Details of bonding type rmsd covalent geometry : bond 0.00301 (20916) covalent geometry : angle 0.67187 (28168) hydrogen bonds : bond 0.04792 ( 1173) hydrogen bonds : angle 4.31802 ( 3471) Misc. bond : bond 0.00071 ( 4) link_BETA1-4 : bond 0.01113 ( 4) link_BETA1-4 : angle 6.18452 ( 12) link_NAG-ASN : bond 0.00446 ( 4) link_NAG-ASN : angle 10.33096 ( 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 412 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 610 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8938 (mmtm) REVERT: A 625 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8791 (mm-30) REVERT: A 721 MET cc_start: 0.8607 (tpp) cc_final: 0.8398 (mmp) REVERT: A 783 PHE cc_start: 0.8056 (m-10) cc_final: 0.7779 (m-10) REVERT: A 852 ARG cc_start: 0.8595 (mpt180) cc_final: 0.8059 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8564 (tp30) cc_final: 0.8334 (mm-30) REVERT: D 607 GLU cc_start: 0.8358 (mp0) cc_final: 0.8060 (mp0) REVERT: D 610 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8797 (mmtp) REVERT: D 657 GLU cc_start: 0.8415 (tt0) cc_final: 0.8142 (tm-30) REVERT: D 681 GLU cc_start: 0.8367 (pm20) cc_final: 0.8138 (pm20) REVERT: D 852 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7542 (mmm-85) REVERT: D 981 GLU cc_start: 0.8796 (tp30) cc_final: 0.8200 (tp30) REVERT: D 985 SER cc_start: 0.9418 (t) cc_final: 0.8665 (p) REVERT: B 488 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8299 (mt) REVERT: B 591 LYS cc_start: 0.9463 (mttt) cc_final: 0.9240 (mtmm) REVERT: B 852 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7713 (mmm-85) REVERT: B 935 VAL cc_start: 0.9452 (t) cc_final: 0.9215 (p) REVERT: B 985 SER cc_start: 0.9338 (t) cc_final: 0.9032 (p) REVERT: B 1073 GLU cc_start: 0.8077 (tt0) cc_final: 0.7516 (tt0) REVERT: B 1075 ILE cc_start: 0.8442 (mt) cc_final: 0.8146 (mp) REVERT: C 852 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7691 (mmm-85) REVERT: C 981 GLU cc_start: 0.8747 (tp30) cc_final: 0.8126 (tp30) REVERT: C 985 SER cc_start: 0.9304 (t) cc_final: 0.8619 (p) REVERT: C 998 VAL cc_start: 0.9116 (p) cc_final: 0.8771 (m) REVERT: C 1075 ILE cc_start: 0.8871 (mt) cc_final: 0.8473 (mp) outliers start: 52 outliers final: 17 residues processed: 395 average time/residue: 0.1348 time to fit residues: 86.6934 Evaluate side-chains 315 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 824 VAL 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 887 SER 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: 2.9990 chunk 12 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 179 optimal weight: 6.9990 chunk 241 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 ASN C 537 ASN C 687 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088501 restraints weight = 32967.719| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.74 r_work: 0.2926 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20928 Z= 0.138 Angle : 0.636 12.254 28192 Z= 0.296 Chirality : 0.042 0.212 3224 Planarity : 0.004 0.066 3392 Dihedral : 21.239 149.665 3600 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.78 % Allowed : 13.15 % Favored : 84.07 % 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: 0.41 (0.17), residues: 2436 helix: 0.58 (0.12), residues: 1768 sheet: 4.17 (0.85), residues: 48 loop : -0.67 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 996 TYR 0.022 0.001 TYR C 768 PHE 0.017 0.001 PHE D 823 TRP 0.013 0.001 TRP A 515 HIS 0.006 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00320 (20916) covalent geometry : angle 0.61084 (28168) hydrogen bonds : bond 0.04362 ( 1173) hydrogen bonds : angle 3.88619 ( 3471) Misc. bond : bond 0.00098 ( 4) link_BETA1-4 : bond 0.00622 ( 4) link_BETA1-4 : angle 3.03825 ( 12) link_NAG-ASN : bond 0.01601 ( 4) link_NAG-ASN : angle 8.14547 ( 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 388 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 330 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 625 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8853 (mm-30) REVERT: A 681 GLU cc_start: 0.8169 (pm20) cc_final: 0.7923 (pm20) REVERT: A 721 MET cc_start: 0.8611 (tpp) cc_final: 0.8410 (mmp) REVERT: A 783 PHE cc_start: 0.8213 (m-10) cc_final: 0.7944 (m-10) REVERT: A 852 ARG cc_start: 0.8683 (mpt180) cc_final: 0.8178 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8660 (tp30) cc_final: 0.8406 (mm-30) REVERT: D 464 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7863 (mtm110) REVERT: D 504 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8620 (mmmm) REVERT: D 643 LEU cc_start: 0.8251 (mp) cc_final: 0.7948 (mt) REVERT: D 852 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7659 (mmm-85) REVERT: D 981 GLU cc_start: 0.8835 (tp30) cc_final: 0.8415 (tp30) REVERT: D 985 SER cc_start: 0.9395 (t) cc_final: 0.8853 (p) REVERT: D 987 GLU cc_start: 0.8779 (tt0) cc_final: 0.8566 (tt0) REVERT: B 483 MET cc_start: 0.8667 (mtt) cc_final: 0.8063 (mtp) REVERT: B 488 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8514 (mm) REVERT: B 591 LYS cc_start: 0.9439 (mttt) cc_final: 0.9211 (mtmm) REVERT: B 709 MET cc_start: 0.9274 (tmm) cc_final: 0.9011 (tmm) REVERT: B 852 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: B 912 MET cc_start: 0.9126 (ttp) cc_final: 0.8874 (ttm) REVERT: B 946 ILE cc_start: 0.9386 (mm) cc_final: 0.9178 (mt) REVERT: B 998 VAL cc_start: 0.9118 (p) cc_final: 0.8709 (m) REVERT: B 1059 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8505 (mm-30) REVERT: B 1075 ILE cc_start: 0.8947 (mt) cc_final: 0.8578 (mt) REVERT: C 610 LYS cc_start: 0.9126 (mmtp) cc_final: 0.8821 (mmtp) REVERT: C 852 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7780 (mmm-85) REVERT: C 981 GLU cc_start: 0.8802 (tp30) cc_final: 0.8398 (tp30) REVERT: C 985 SER cc_start: 0.9376 (t) cc_final: 0.8820 (p) REVERT: C 998 VAL cc_start: 0.9175 (p) cc_final: 0.8819 (m) REVERT: C 1075 ILE cc_start: 0.8936 (mt) cc_final: 0.8574 (mm) outliers start: 58 outliers final: 23 residues processed: 373 average time/residue: 0.1358 time to fit residues: 81.2209 Evaluate side-chains 306 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU 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 947 PHE Chi-restraints excluded: chain B residue 488 LEU 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 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 203 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 187 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN A 831 GLN A 907 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 HIS ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1000 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN C 739 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084653 restraints weight = 33241.854| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.71 r_work: 0.2843 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20928 Z= 0.159 Angle : 0.636 11.398 28192 Z= 0.299 Chirality : 0.043 0.181 3224 Planarity : 0.004 0.060 3392 Dihedral : 19.689 152.988 3600 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.83 % Allowed : 14.40 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2436 helix: 1.06 (0.13), residues: 1748 sheet: 1.93 (0.78), residues: 68 loop : -0.45 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 996 TYR 0.012 0.001 TYR B 714 PHE 0.012 0.001 PHE B1022 TRP 0.017 0.001 TRP A 515 HIS 0.007 0.001 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00377 (20916) covalent geometry : angle 0.61207 (28168) hydrogen bonds : bond 0.04299 ( 1173) hydrogen bonds : angle 3.84775 ( 3471) Misc. bond : bond 0.00008 ( 4) link_BETA1-4 : bond 0.00768 ( 4) link_BETA1-4 : angle 4.28338 ( 12) link_NAG-ASN : bond 0.01134 ( 4) link_NAG-ASN : angle 7.18081 ( 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 348 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 289 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 464 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7580 (tmm160) REVERT: A 530 MET cc_start: 0.8930 (mtm) cc_final: 0.8716 (mtm) REVERT: A 625 GLU cc_start: 0.9207 (mm-30) cc_final: 0.9000 (mm-30) REVERT: A 681 GLU cc_start: 0.8242 (pm20) cc_final: 0.8036 (pm20) REVERT: A 721 MET cc_start: 0.8671 (tpp) cc_final: 0.8446 (mmp) REVERT: A 783 PHE cc_start: 0.8386 (m-10) cc_final: 0.8113 (m-10) REVERT: A 785 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7910 (m-10) REVERT: A 852 ARG cc_start: 0.8720 (mpt180) cc_final: 0.8204 (mmm-85) REVERT: A 911 MET cc_start: 0.8948 (mtp) cc_final: 0.8573 (mtm) REVERT: A 1059 GLU cc_start: 0.8733 (tp30) cc_final: 0.8429 (mm-30) REVERT: D 464 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7869 (mtm110) REVERT: D 530 MET cc_start: 0.8727 (mtm) cc_final: 0.8469 (mtt) REVERT: D 610 LYS cc_start: 0.9261 (mmmm) cc_final: 0.8965 (mmtm) REVERT: D 681 GLU cc_start: 0.8477 (pm20) cc_final: 0.8221 (pm20) REVERT: D 852 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7749 (mmm-85) REVERT: D 981 GLU cc_start: 0.8846 (tp30) cc_final: 0.8401 (tp30) REVERT: D 985 SER cc_start: 0.9429 (t) cc_final: 0.8893 (p) REVERT: D 987 GLU cc_start: 0.8790 (tt0) cc_final: 0.8546 (tt0) REVERT: B 591 LYS cc_start: 0.9439 (mttt) cc_final: 0.9223 (mtmm) REVERT: B 781 SER cc_start: 0.8820 (m) cc_final: 0.8578 (p) REVERT: B 785 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7555 (m-10) REVERT: B 852 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7832 (mmm-85) REVERT: B 912 MET cc_start: 0.9190 (ttp) cc_final: 0.8954 (ttm) REVERT: B 941 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8918 (tp) REVERT: B 987 GLU cc_start: 0.8856 (tt0) cc_final: 0.8433 (tt0) REVERT: B 1059 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8564 (mm-30) REVERT: C 610 LYS cc_start: 0.9235 (mmtp) cc_final: 0.8883 (mmtp) REVERT: C 709 MET cc_start: 0.9310 (tmm) cc_final: 0.9104 (tmm) REVERT: C 852 ARG cc_start: 0.8144 (mmm-85) cc_final: 0.7786 (mmm-85) REVERT: C 941 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8953 (tp) REVERT: C 981 GLU cc_start: 0.8799 (tp30) cc_final: 0.8374 (tp30) REVERT: C 985 SER cc_start: 0.9413 (t) cc_final: 0.8928 (p) outliers start: 59 outliers final: 30 residues processed: 325 average time/residue: 0.1453 time to fit residues: 75.7964 Evaluate side-chains 289 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 986 LEU 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 935 VAL Chi-restraints excluded: chain D residue 941 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 877 PHE 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 484 THR 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 900 SER Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 982 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: 0.9990 chunk 135 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1000 GLN B 907 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 = 0.3576 r_free = 0.3576 target = 0.118574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.084794 restraints weight = 32986.124| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.70 r_work: 0.2861 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20928 Z= 0.130 Angle : 0.590 10.026 28192 Z= 0.277 Chirality : 0.041 0.189 3224 Planarity : 0.004 0.059 3392 Dihedral : 18.914 157.308 3600 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.40 % Allowed : 15.45 % Favored : 82.15 % 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: 1.32 (0.18), residues: 2436 helix: 1.28 (0.13), residues: 1752 sheet: 1.93 (0.78), residues: 68 loop : -0.26 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 996 TYR 0.022 0.001 TYR C 768 PHE 0.008 0.001 PHE C 746 TRP 0.009 0.001 TRP B 832 HIS 0.005 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00303 (20916) covalent geometry : angle 0.57101 (28168) hydrogen bonds : bond 0.03999 ( 1173) hydrogen bonds : angle 3.73661 ( 3471) Misc. bond : bond 0.00052 ( 4) link_BETA1-4 : bond 0.00651 ( 4) link_BETA1-4 : angle 3.52848 ( 12) link_NAG-ASN : bond 0.01082 ( 4) link_NAG-ASN : angle 6.35532 ( 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 322 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 464 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7593 (tmm160) REVERT: A 681 GLU cc_start: 0.8253 (pm20) cc_final: 0.8043 (pm20) REVERT: A 721 MET cc_start: 0.8682 (tpp) cc_final: 0.8454 (mmp) REVERT: A 785 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7968 (m-10) REVERT: A 852 ARG cc_start: 0.8737 (mpt180) cc_final: 0.8266 (mmm-85) REVERT: A 911 MET cc_start: 0.8983 (mtp) cc_final: 0.8705 (mtm) REVERT: A 1059 GLU cc_start: 0.8739 (tp30) cc_final: 0.8495 (mm-30) REVERT: D 464 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7866 (mtm110) REVERT: D 852 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7780 (mmm-85) REVERT: D 981 GLU cc_start: 0.8821 (tp30) cc_final: 0.8390 (tp30) REVERT: D 985 SER cc_start: 0.9427 (t) cc_final: 0.8853 (p) REVERT: D 987 GLU cc_start: 0.8794 (tt0) cc_final: 0.8564 (tt0) REVERT: B 591 LYS cc_start: 0.9440 (mttt) cc_final: 0.9226 (mtmm) REVERT: B 681 GLU cc_start: 0.8638 (pm20) cc_final: 0.8377 (pm20) REVERT: B 785 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: B 852 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7836 (mmm-85) REVERT: B 912 MET cc_start: 0.9174 (ttp) cc_final: 0.8906 (ttm) REVERT: B 940 GLN cc_start: 0.8972 (tp40) cc_final: 0.8714 (tp40) REVERT: B 941 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 987 GLU cc_start: 0.8868 (tt0) cc_final: 0.8474 (tt0) REVERT: B 1059 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8627 (mm-30) REVERT: C 610 LYS cc_start: 0.9255 (mmtp) cc_final: 0.8872 (mmtp) REVERT: C 852 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.7711 (mmm-85) REVERT: C 941 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9009 (tp) REVERT: C 981 GLU cc_start: 0.8820 (tp30) cc_final: 0.8410 (tp30) REVERT: C 985 SER cc_start: 0.9423 (t) cc_final: 0.8919 (p) outliers start: 50 outliers final: 30 residues processed: 307 average time/residue: 0.1391 time to fit residues: 68.8331 Evaluate side-chains 284 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 935 VAL Chi-restraints excluded: chain A residue 986 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 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 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE 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 B residue 1045 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 887 SER Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 982 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 49 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080890 restraints weight = 32939.709| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.68 r_work: 0.2785 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20928 Z= 0.191 Angle : 0.622 10.017 28192 Z= 0.293 Chirality : 0.043 0.160 3224 Planarity : 0.004 0.060 3392 Dihedral : 18.422 160.363 3600 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.98 % Allowed : 15.64 % 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: 1.33 (0.18), residues: 2436 helix: 1.34 (0.13), residues: 1740 sheet: 1.75 (0.78), residues: 68 loop : -0.36 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 996 TYR 0.014 0.001 TYR D 842 PHE 0.021 0.002 PHE C 818 TRP 0.015 0.002 TRP D 515 HIS 0.008 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00466 (20916) covalent geometry : angle 0.60566 (28168) hydrogen bonds : bond 0.04490 ( 1173) hydrogen bonds : angle 3.82828 ( 3471) Misc. bond : bond 0.00089 ( 4) link_BETA1-4 : bond 0.00705 ( 4) link_BETA1-4 : angle 3.61276 ( 12) link_NAG-ASN : bond 0.00883 ( 4) link_NAG-ASN : angle 5.81070 ( 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 314 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 530 MET cc_start: 0.8972 (mtm) cc_final: 0.8763 (mtm) REVERT: A 721 MET cc_start: 0.8741 (tpp) cc_final: 0.8504 (mmp) REVERT: A 785 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8251 (m-10) REVERT: A 852 ARG cc_start: 0.8737 (mpt180) cc_final: 0.8272 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8834 (tp30) cc_final: 0.8540 (mm-30) REVERT: D 464 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7885 (mtm110) REVERT: D 852 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7746 (mmm-85) REVERT: D 981 GLU cc_start: 0.8819 (tp30) cc_final: 0.8470 (tp30) REVERT: D 987 GLU cc_start: 0.8859 (tt0) cc_final: 0.8602 (tt0) REVERT: B 591 LYS cc_start: 0.9438 (mttt) cc_final: 0.9217 (mtmm) REVERT: B 785 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: B 852 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.7817 (mmm-85) REVERT: B 912 MET cc_start: 0.9225 (ttp) cc_final: 0.8972 (ttm) REVERT: B 941 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9049 (tp) REVERT: B 987 GLU cc_start: 0.8794 (tt0) cc_final: 0.8409 (tt0) REVERT: B 996 ARG cc_start: 0.9047 (ttm-80) cc_final: 0.8781 (ttm-80) REVERT: B 1059 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8621 (mm-30) REVERT: C 464 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7640 (ttp80) REVERT: C 504 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8479 (mtpp) REVERT: C 610 LYS cc_start: 0.9304 (mmtp) cc_final: 0.8936 (mmtp) REVERT: C 681 GLU cc_start: 0.8787 (pm20) cc_final: 0.8524 (pm20) REVERT: C 852 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7733 (mmm-85) REVERT: C 941 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9097 (tp) REVERT: C 981 GLU cc_start: 0.8833 (tp30) cc_final: 0.8245 (tp30) REVERT: C 985 SER cc_start: 0.9478 (t) cc_final: 0.8723 (p) outliers start: 62 outliers final: 39 residues processed: 297 average time/residue: 0.1353 time to fit residues: 65.0354 Evaluate side-chains 280 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 806 VAL 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 986 LEU Chi-restraints excluded: chain D residue 474 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 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 1002 SER 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 816 ILE 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 B residue 1002 SER Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 474 LEU 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 752 ILE Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 982 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: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 739 ASN ** 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 = 0.3540 r_free = 0.3540 target = 0.116125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.082047 restraints weight = 32983.772| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.69 r_work: 0.2812 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20928 Z= 0.152 Angle : 0.588 9.119 28192 Z= 0.277 Chirality : 0.041 0.157 3224 Planarity : 0.004 0.058 3392 Dihedral : 17.964 164.270 3600 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.54 % Allowed : 15.74 % Favored : 81.72 % 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: 1.49 (0.18), residues: 2436 helix: 1.46 (0.13), residues: 1740 sheet: 1.80 (0.78), residues: 68 loop : -0.30 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 996 TYR 0.015 0.001 TYR B 768 PHE 0.008 0.001 PHE D 583 TRP 0.011 0.001 TRP C 515 HIS 0.006 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00363 (20916) covalent geometry : angle 0.57351 (28168) hydrogen bonds : bond 0.04200 ( 1173) hydrogen bonds : angle 3.74820 ( 3471) Misc. bond : bond 0.00069 ( 4) link_BETA1-4 : bond 0.00771 ( 4) link_BETA1-4 : angle 3.31078 ( 12) link_NAG-ASN : bond 0.00843 ( 4) link_NAG-ASN : angle 5.32046 ( 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 295 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 530 MET cc_start: 0.8985 (mtm) cc_final: 0.8741 (mtm) REVERT: A 721 MET cc_start: 0.8722 (tpp) cc_final: 0.8490 (mmp) REVERT: A 785 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8190 (m-10) REVERT: A 852 ARG cc_start: 0.8739 (mpt180) cc_final: 0.8252 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8852 (tp30) cc_final: 0.8573 (mm-30) REVERT: D 464 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7837 (mtm110) REVERT: D 852 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7777 (mmm-85) REVERT: D 981 GLU cc_start: 0.8825 (tp30) cc_final: 0.8487 (tp30) REVERT: D 987 GLU cc_start: 0.8860 (tt0) cc_final: 0.8551 (tt0) REVERT: B 591 LYS cc_start: 0.9454 (mttt) cc_final: 0.9235 (mtmm) REVERT: B 785 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8093 (m-10) REVERT: B 852 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7831 (mmm-85) REVERT: B 912 MET cc_start: 0.9164 (ttp) cc_final: 0.8899 (ttm) REVERT: B 941 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9041 (tp) REVERT: B 981 GLU cc_start: 0.8675 (tp30) cc_final: 0.8442 (tm-30) REVERT: B 987 GLU cc_start: 0.8772 (tt0) cc_final: 0.8386 (tt0) REVERT: B 1059 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8612 (mm-30) REVERT: C 610 LYS cc_start: 0.9310 (mmtp) cc_final: 0.9034 (mmtm) REVERT: C 852 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7752 (mmm-85) REVERT: C 941 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9081 (tp) REVERT: C 981 GLU cc_start: 0.8822 (tp30) cc_final: 0.8471 (tp30) outliers start: 53 outliers final: 37 residues processed: 281 average time/residue: 0.1333 time to fit residues: 60.9849 Evaluate side-chains 278 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 935 VAL 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 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 935 VAL 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 488 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE 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 B residue 1002 SER Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 982 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: 0.4980 chunk 141 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 64 optimal weight: 0.0370 chunk 211 optimal weight: 0.2980 chunk 225 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 979 GLN ** 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** B 979 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS C 619 ASN C 979 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.085324 restraints weight = 32931.240| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.71 r_work: 0.2872 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20928 Z= 0.102 Angle : 0.558 11.549 28192 Z= 0.262 Chirality : 0.039 0.164 3224 Planarity : 0.004 0.058 3392 Dihedral : 17.339 170.437 3600 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.02 % Allowed : 16.07 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.18), residues: 2436 helix: 1.56 (0.13), residues: 1756 sheet: 1.88 (0.78), residues: 68 loop : -0.08 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 996 TYR 0.011 0.001 TYR D 768 PHE 0.026 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 covalent geometry : bond 0.00220 (20916) covalent geometry : angle 0.54619 (28168) hydrogen bonds : bond 0.03593 ( 1173) hydrogen bonds : angle 3.60237 ( 3471) Misc. bond : bond 0.00037 ( 4) link_BETA1-4 : bond 0.00828 ( 4) link_BETA1-4 : angle 3.00865 ( 12) link_NAG-ASN : bond 0.00865 ( 4) link_NAG-ASN : angle 4.64991 ( 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 300 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8504 (pp20) REVERT: A 721 MET cc_start: 0.8657 (tpp) cc_final: 0.8425 (mmp) REVERT: A 785 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.8063 (m-10) REVERT: A 852 ARG cc_start: 0.8685 (mpt180) cc_final: 0.8215 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8819 (tp30) cc_final: 0.8531 (mm-30) REVERT: D 852 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7789 (mmm-85) REVERT: D 941 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9081 (tp) REVERT: D 981 GLU cc_start: 0.8813 (tp30) cc_final: 0.8452 (tp30) REVERT: D 985 SER cc_start: 0.9434 (t) cc_final: 0.8940 (p) REVERT: B 591 LYS cc_start: 0.9459 (mttt) cc_final: 0.9252 (mtmm) REVERT: B 785 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.8159 (m-10) REVERT: B 852 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7845 (mmm-85) REVERT: B 912 MET cc_start: 0.9131 (ttp) cc_final: 0.8854 (ttm) REVERT: B 941 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8967 (tp) REVERT: B 981 GLU cc_start: 0.8639 (tp30) cc_final: 0.8403 (tm-30) REVERT: B 987 GLU cc_start: 0.8742 (tt0) cc_final: 0.8383 (tt0) REVERT: C 464 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7617 (ttp80) REVERT: C 610 LYS cc_start: 0.9304 (mmtp) cc_final: 0.9034 (mmtm) REVERT: C 852 ARG cc_start: 0.8113 (mmm-85) cc_final: 0.7770 (mmm-85) REVERT: C 981 GLU cc_start: 0.8808 (tp30) cc_final: 0.8475 (tp30) REVERT: C 1000 GLN cc_start: 0.8574 (mt0) cc_final: 0.8356 (mp10) outliers start: 42 outliers final: 26 residues processed: 287 average time/residue: 0.1370 time to fit residues: 63.1338 Evaluate side-chains 272 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET 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 1002 SER 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 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 935 VAL 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: 3.9990 chunk 184 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** 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 = 0.3530 r_free = 0.3530 target = 0.115505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.081257 restraints weight = 32887.427| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.68 r_work: 0.2811 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20928 Z= 0.162 Angle : 0.594 11.644 28192 Z= 0.280 Chirality : 0.041 0.170 3224 Planarity : 0.004 0.057 3392 Dihedral : 17.201 177.511 3600 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.78 % Allowed : 16.17 % 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: 1.67 (0.18), residues: 2436 helix: 1.58 (0.13), residues: 1744 sheet: 1.83 (0.78), residues: 68 loop : -0.21 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 996 TYR 0.011 0.001 TYR B 842 PHE 0.022 0.001 PHE C 823 TRP 0.012 0.001 TRP B 515 HIS 0.007 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00390 (20916) covalent geometry : angle 0.58392 (28168) hydrogen bonds : bond 0.04158 ( 1173) hydrogen bonds : angle 3.68543 ( 3471) Misc. bond : bond 0.00072 ( 4) link_BETA1-4 : bond 0.00656 ( 4) link_BETA1-4 : angle 2.77757 ( 12) link_NAG-ASN : bond 0.00690 ( 4) link_NAG-ASN : angle 4.56468 ( 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 276 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.8667 (tpp) cc_final: 0.8431 (mmp) REVERT: A 785 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8178 (m-10) REVERT: A 852 ARG cc_start: 0.8726 (mpt180) cc_final: 0.8280 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8869 (tp30) cc_final: 0.8581 (mm-30) REVERT: D 852 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7800 (mmm-85) REVERT: D 981 GLU cc_start: 0.8822 (tp30) cc_final: 0.8490 (tp30) REVERT: D 987 GLU cc_start: 0.8852 (tt0) cc_final: 0.8579 (tt0) REVERT: B 591 LYS cc_start: 0.9465 (mttt) cc_final: 0.9253 (mtmm) REVERT: B 785 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: B 852 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7836 (mmm-85) REVERT: B 912 MET cc_start: 0.9160 (ttp) cc_final: 0.8894 (ttm) REVERT: B 941 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8970 (tp) REVERT: B 987 GLU cc_start: 0.8771 (tt0) cc_final: 0.8339 (tt0) REVERT: C 464 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7658 (ttp80) REVERT: C 610 LYS cc_start: 0.9322 (mmtp) cc_final: 0.8950 (mmtp) REVERT: C 852 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7737 (mmm-85) REVERT: C 981 GLU cc_start: 0.8772 (tp30) cc_final: 0.8439 (tp30) outliers start: 37 outliers final: 29 residues processed: 264 average time/residue: 0.1262 time to fit residues: 54.5334 Evaluate side-chains 265 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 900 SER Chi-restraints excluded: chain A residue 935 VAL 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 510 SER Chi-restraints excluded: chain D residue 709 MET 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 1002 SER 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 816 ILE 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 B residue 1045 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 900 SER Chi-restraints excluded: chain C residue 935 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 151 optimal weight: 0.0270 chunk 48 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 218 optimal weight: 0.0670 chunk 139 optimal weight: 0.0970 chunk 68 optimal weight: 6.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3581 r_free = 0.3581 target = 0.119063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.085239 restraints weight = 33021.629| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.72 r_work: 0.2861 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20928 Z= 0.103 Angle : 0.549 9.507 28192 Z= 0.259 Chirality : 0.039 0.163 3224 Planarity : 0.004 0.057 3392 Dihedral : 16.749 178.224 3600 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.78 % Allowed : 16.07 % Favored : 82.15 % 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: 1.83 (0.18), residues: 2436 helix: 1.73 (0.13), residues: 1732 sheet: 1.93 (0.77), residues: 68 loop : -0.20 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 996 TYR 0.011 0.001 TYR D 842 PHE 0.018 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 covalent geometry : bond 0.00224 (20916) covalent geometry : angle 0.54025 (28168) hydrogen bonds : bond 0.03526 ( 1173) hydrogen bonds : angle 3.57607 ( 3471) Misc. bond : bond 0.00034 ( 4) link_BETA1-4 : bond 0.00730 ( 4) link_BETA1-4 : angle 2.46450 ( 12) link_NAG-ASN : bond 0.00756 ( 4) link_NAG-ASN : angle 4.17163 ( 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 295 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.8645 (tpp) cc_final: 0.8419 (mmp) REVERT: A 785 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.8032 (m-10) REVERT: A 852 ARG cc_start: 0.8662 (mpt180) cc_final: 0.8225 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8859 (tp30) cc_final: 0.8570 (mm-30) REVERT: D 852 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7789 (mmm-85) REVERT: D 941 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9051 (tp) REVERT: D 981 GLU cc_start: 0.8813 (tp30) cc_final: 0.8444 (tp30) REVERT: D 985 SER cc_start: 0.9437 (t) cc_final: 0.8896 (p) REVERT: B 591 LYS cc_start: 0.9457 (mttt) cc_final: 0.9253 (mtmm) REVERT: B 785 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8247 (m-10) REVERT: B 852 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7841 (mmm-85) REVERT: B 912 MET cc_start: 0.9132 (ttp) cc_final: 0.8864 (ttm) REVERT: B 941 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8903 (tp) REVERT: B 981 GLU cc_start: 0.8637 (tp30) cc_final: 0.8423 (tm-30) REVERT: B 987 GLU cc_start: 0.8771 (tt0) cc_final: 0.8378 (tt0) REVERT: B 1059 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8540 (mm-30) REVERT: C 464 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7666 (ttp80) REVERT: C 610 LYS cc_start: 0.9324 (mmtp) cc_final: 0.8927 (mmtp) REVERT: C 852 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7749 (mmm-85) REVERT: C 912 MET cc_start: 0.9216 (ttp) cc_final: 0.8774 (ttm) REVERT: C 981 GLU cc_start: 0.8791 (tp30) cc_final: 0.8449 (tp30) outliers start: 37 outliers final: 28 residues processed: 283 average time/residue: 0.1291 time to fit residues: 59.3528 Evaluate side-chains 277 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 900 SER Chi-restraints excluded: chain A residue 935 VAL 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 510 SER Chi-restraints excluded: chain D residue 709 MET 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 1002 SER 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 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 877 PHE 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 900 SER Chi-restraints excluded: chain C residue 935 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 174 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** 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 = 0.3576 r_free = 0.3576 target = 0.118692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084712 restraints weight = 33140.571| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.72 r_work: 0.2861 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20928 Z= 0.110 Angle : 0.555 9.611 28192 Z= 0.263 Chirality : 0.039 0.156 3224 Planarity : 0.003 0.056 3392 Dihedral : 16.447 173.367 3600 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.87 % Allowed : 15.79 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.18), residues: 2436 helix: 1.74 (0.13), residues: 1732 sheet: 1.93 (0.77), residues: 68 loop : -0.18 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 996 TYR 0.016 0.001 TYR D 842 PHE 0.020 0.001 PHE D 823 TRP 0.008 0.001 TRP A 832 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00251 (20916) covalent geometry : angle 0.54740 (28168) hydrogen bonds : bond 0.03588 ( 1173) hydrogen bonds : angle 3.55400 ( 3471) Misc. bond : bond 0.00038 ( 4) link_BETA1-4 : bond 0.00687 ( 4) link_BETA1-4 : angle 2.26926 ( 12) link_NAG-ASN : bond 0.00677 ( 4) link_NAG-ASN : angle 3.95764 ( 12) =============================================================================== Job complete usr+sys time: 4626.51 seconds wall clock time: 80 minutes 7.15 seconds (4807.15 seconds total)