Starting phenix.real_space_refine on Mon Oct 26 14:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pqo_20449/10_2026/6pqo_20449.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqo_20449/10_2026/6pqo_20449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pqo_20449/10_2026/6pqo_20449.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pqo_20449/10_2026/6pqo_20449.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pqo_20449/10_2026/6pqo_20449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqo_20449/10_2026/6pqo_20449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqo_20449/10_2026/6pqo_20449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqo_20449/10_2026/6pqo_20449.map" } resolution = 2.88 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= 0.008 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 144 5.16 5 C 13360 2.51 5 N 3208 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 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20312 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 278 Unusual residues: {'6OU': 5, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'6OU': 3, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 237 Unusual residues: {'6OU': 4, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 237 Unusual residues: {'6OU': 4, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: F, G, H Time building chain proxies: 5.33, per 1000 atoms: 0.26 Number of scatterers: 20312 At special positions: 0 Unit cell: (113.4, 113.4, 149.04, 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 144 16.00 P 24 15.00 O 3576 8.00 N 3208 7.00 C 13360 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 D 747 " " NAG F 1 " - " ASN A 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: 1.60 Conformation dependent library (CDL) restraints added in 915.8 milliseconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 71.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'D' and resid 446 through 455 Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.674A 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: 3.551A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.522A pdb=" N HIS D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) 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: 3.952A pdb=" N ILE D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.591A pdb=" N MET D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 670 Processing helix chain 'D' and resid 683 through 691 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 714 removed outlier: 3.645A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 739 removed outlier: 3.797A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 796 removed outlier: 3.698A pdb=" N THR D 772 " --> pdb=" O TYR D 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 796 " --> pdb=" O ILE D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 820 removed outlier: 3.927A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.706A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 853 removed outlier: 3.719A pdb=" N GLN D 851 " --> pdb=" O LEU D 848 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 852 " --> pdb=" O TYR D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 892 removed outlier: 3.663A pdb=" N ILE D 860 " --> pdb=" O CYS D 856 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.540A 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 927 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'D' and resid 970 through 987 removed outlier: 3.782A 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 'A' and resid 447 through 455 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.675A 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: 3.551A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.522A pdb=" N HIS A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) 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: 3.953A pdb=" N ILE A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.592A pdb=" N MET A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.644A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 removed outlier: 3.796A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 796 removed outlier: 3.697A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 796 " --> pdb=" O ILE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.927A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.707A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.719A pdb=" N GLN A 851 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 852 " --> pdb=" O TYR A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 892 removed outlier: 3.663A pdb=" N ILE A 860 " --> pdb=" O CYS A 856 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.540A 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 927 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 969 Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.782A 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 'B' and resid 447 through 455 Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.675A 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: 3.551A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.521A pdb=" N HIS B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.614A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.953A pdb=" N ILE B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.590A pdb=" N MET B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 670 Processing helix chain 'B' and resid 683 through 691 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 714 removed outlier: 3.644A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 removed outlier: 3.797A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 796 removed outlier: 3.698A pdb=" N THR B 772 " --> pdb=" O TYR B 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 796 " --> pdb=" O ILE B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.927A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.706A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.720A pdb=" N GLN B 851 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 852 " --> pdb=" O TYR B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 892 removed outlier: 3.663A pdb=" N ILE B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.540A 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 927 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 969 Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.782A 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 455 Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.675A 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: 3.551A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 removed outlier: 3.522A pdb=" N HIS C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) 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: 3.952A pdb=" N ILE C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 629 Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.590A pdb=" N MET C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 670 Processing helix chain 'C' and resid 683 through 691 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 714 removed outlier: 3.646A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 739 removed outlier: 3.797A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 796 removed outlier: 3.698A pdb=" N THR C 772 " --> pdb=" O TYR C 768 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 796 " --> pdb=" O ILE C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 820 removed outlier: 3.927A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.706A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.719A pdb=" N GLN C 851 " --> pdb=" O LEU C 848 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 852 " --> pdb=" O TYR C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 892 removed outlier: 3.663A pdb=" N ILE C 860 " --> pdb=" O CYS C 856 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 3.539A 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 927 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 969 Processing helix chain 'C' and resid 970 through 987 removed outlier: 3.782A 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 'D' and resid 642 through 644 Processing sheet with id=AA2, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.001A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AA4, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 642 through 644 Processing sheet with id=AA6, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 642 through 644 Processing sheet with id=AA8, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 1165 hydrogen bonds defined for protein. 3411 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: 3.24 Time building geometry restraints manager: 2.16 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: 3060 1.30 - 1.43: 5286 1.43 - 1.56: 11863 1.56 - 1.69: 235 1.69 - 1.81: 276 Bond restraints: 20720 Sorted by residual: bond pdb=" O2 LBN B1205 " pdb=" P1 LBN B1205 " ideal model delta sigma weight residual 1.650 1.770 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" O2 LBN A1205 " pdb=" P1 LBN A1205 " ideal model delta sigma weight residual 1.650 1.770 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" O2 LBN D1304 " pdb=" P1 LBN D1304 " ideal model delta sigma weight residual 1.650 1.770 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" O2 LBN C1206 " pdb=" P1 LBN C1206 " ideal model delta sigma weight residual 1.650 1.770 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" O2 LBN A1206 " pdb=" P1 LBN A1206 " ideal model delta sigma weight residual 1.650 1.767 -0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 20715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 26984 3.19 - 6.37: 796 6.37 - 9.56: 112 9.56 - 12.75: 36 12.75 - 15.94: 16 Bond angle restraints: 27944 Sorted by residual: angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 107.73 123.67 -15.94 1.56e+00 4.11e-01 1.04e+02 angle pdb=" N ILE B 611 " pdb=" CA ILE B 611 " pdb=" C ILE B 611 " ideal model delta sigma weight residual 107.73 123.67 -15.94 1.56e+00 4.11e-01 1.04e+02 angle pdb=" N ILE A 611 " pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 107.73 123.66 -15.93 1.56e+00 4.11e-01 1.04e+02 angle pdb=" N ILE C 611 " pdb=" CA ILE C 611 " pdb=" C ILE C 611 " ideal model delta sigma weight residual 107.73 123.66 -15.93 1.56e+00 4.11e-01 1.04e+02 angle pdb=" C ILE B 611 " pdb=" CA ILE B 611 " pdb=" CB ILE B 611 " ideal model delta sigma weight residual 111.25 103.78 7.47 1.27e+00 6.20e-01 3.46e+01 ... (remaining 27939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 11992 35.43 - 70.86: 276 70.86 - 106.29: 16 106.29 - 141.72: 8 141.72 - 177.15: 8 Dihedral angle restraints: 12300 sinusoidal: 5080 harmonic: 7220 Sorted by residual: 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 98.25 177.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN C1207 " pdb=" O1 LBN C1207 " pdb=" P1 LBN C1207 " pdb=" O3 LBN C1207 " ideal model delta sinusoidal sigma weight residual 275.40 98.27 177.13 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN D1305 " pdb=" O1 LBN D1305 " pdb=" P1 LBN D1305 " pdb=" O3 LBN D1305 " ideal model delta sinusoidal sigma weight residual 275.40 98.28 177.12 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 3180 0.182 - 0.364: 8 0.364 - 0.546: 8 0.546 - 0.728: 12 0.728 - 0.910: 4 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.23e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.16e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.15e+01 ... (remaining 3209 not shown) Planarity restraints: 3368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 JT0 C1205 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 C1205 " -0.641 2.00e-02 2.50e+03 pdb=" C09 JT0 C1205 " 0.471 2.00e-02 2.50e+03 pdb=" C22 JT0 C1205 " -1.000 2.00e-02 2.50e+03 pdb=" N03 JT0 C1205 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 C1205 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 JT0 D1303 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 D1303 " -0.641 2.00e-02 2.50e+03 pdb=" C09 JT0 D1303 " 0.472 2.00e-02 2.50e+03 pdb=" C22 JT0 D1303 " -1.000 2.00e-02 2.50e+03 pdb=" N03 JT0 D1303 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 D1303 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 JT0 B1204 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 B1204 " -0.642 2.00e-02 2.50e+03 pdb=" C09 JT0 B1204 " 0.472 2.00e-02 2.50e+03 pdb=" C22 JT0 B1204 " -0.999 2.00e-02 2.50e+03 pdb=" N03 JT0 B1204 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 B1204 " 0.939 2.00e-02 2.50e+03 ... (remaining 3365 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3044 2.76 - 3.29: 18154 3.29 - 3.83: 31360 3.83 - 4.36: 36391 4.36 - 4.90: 62978 Nonbonded interactions: 151927 Sorted by model distance: nonbonded pdb=" OD1 ASN B 747 " pdb=" N SER B 748 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASN D 747 " pdb=" N SER D 748 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASN A 747 " pdb=" N SER A 748 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASN C 747 " pdb=" N SER C 748 " model vdw 2.223 3.120 nonbonded pdb=" O ILE A 810 " pdb=" OG1 THR A 814 " model vdw 2.301 3.040 ... (remaining 151922 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 1208 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 1208)) selection = (chain 'C' and (resid 446 through 1079 or (resid 1208 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 'D' and (resid 446 through 1079 or (resid 1308 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: 1.430 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: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 18.860 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.012 0.339 20732 Z= 0.583 Angle : 1.300 15.937 27968 Z= 0.578 Chirality : 0.079 0.910 3212 Planarity : 0.026 0.651 3364 Dihedral : 15.405 177.148 7604 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.58 % Allowed : 4.09 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.14), residues: 2416 helix: -2.04 (0.10), residues: 1732 sheet: 0.83 (0.76), residues: 68 loop : -1.27 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 919 TYR 0.034 0.003 TYR B 785 PHE 0.027 0.003 PHE C 783 TRP 0.044 0.003 TRP C 515 HIS 0.011 0.002 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.01134 / 0.53 (20720) covalent geometry : angle 1.28845 / 0.57 (27944) hydrogen bonds : bond 0.15245 / 10.37 ( 1165) hydrogen bonds : angle 5.35433 / 3.80 ( 3411) Misc. bond : bond 0.00116 / 0.06 ( 4) link_BETA1-4 : bond 0.00095 / 0.05 ( 4) link_BETA1-4 : angle 0.22966 / 0.16 ( 12) link_NAG-ASN : bond 0.33856 / 16.96 ( 4) link_NAG-ASN : angle 8.64155 / 5.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 602 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 483 MET cc_start: 0.7988 (mtt) cc_final: 0.7436 (mtm) REVERT: D 558 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7080 (mm-30) REVERT: D 591 LYS cc_start: 0.8962 (mttt) cc_final: 0.8639 (mtmm) REVERT: D 669 PHE cc_start: 0.7510 (m-80) cc_final: 0.7210 (m-80) REVERT: D 717 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6367 (ttt90) REVERT: D 721 MET cc_start: 0.7408 (ttm) cc_final: 0.6878 (mmp) REVERT: D 768 TYR cc_start: 0.7736 (t80) cc_final: 0.7454 (t80) REVERT: D 864 GLU cc_start: 0.7202 (tt0) cc_final: 0.6812 (tt0) REVERT: D 920 GLU cc_start: 0.8022 (tt0) cc_final: 0.7650 (mp0) REVERT: D 924 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7370 (mt-10) REVERT: D 928 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7721 (mtm-85) REVERT: D 963 ASP cc_start: 0.7393 (m-30) cc_final: 0.7112 (m-30) REVERT: D 969 LYS cc_start: 0.7667 (tttt) cc_final: 0.7318 (ttpp) REVERT: D 981 GLU cc_start: 0.7512 (tp30) cc_final: 0.7173 (tp30) REVERT: D 1049 TYR cc_start: 0.8094 (m-10) cc_final: 0.7862 (m-10) REVERT: A 483 MET cc_start: 0.8211 (mtt) cc_final: 0.7670 (mtm) REVERT: A 523 MET cc_start: 0.8180 (tpt) cc_final: 0.7924 (tpt) REVERT: A 558 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 562 LYS cc_start: 0.7755 (mttt) cc_final: 0.7533 (mptp) REVERT: A 579 GLN cc_start: 0.8400 (mt0) cc_final: 0.8195 (mm-40) REVERT: A 591 LYS cc_start: 0.8986 (mttt) cc_final: 0.8701 (mtmm) REVERT: A 657 GLU cc_start: 0.7138 (tt0) cc_final: 0.6866 (tm-30) REVERT: A 669 PHE cc_start: 0.7609 (m-80) cc_final: 0.7290 (m-80) REVERT: A 705 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 717 ARG cc_start: 0.6691 (ttt180) cc_final: 0.6120 (ttt90) REVERT: A 720 MET cc_start: 0.6859 (mmm) cc_final: 0.6626 (mmm) REVERT: A 721 MET cc_start: 0.7208 (ttm) cc_final: 0.6760 (mmp) REVERT: A 768 TYR cc_start: 0.7747 (t80) cc_final: 0.7424 (t80) REVERT: A 825 GLU cc_start: 0.8246 (tt0) cc_final: 0.7991 (tm-30) REVERT: A 852 ARG cc_start: 0.7669 (mtt90) cc_final: 0.7456 (mmt90) REVERT: A 864 GLU cc_start: 0.7065 (tt0) cc_final: 0.6701 (tt0) REVERT: A 920 GLU cc_start: 0.8278 (tt0) cc_final: 0.7464 (mp0) REVERT: A 924 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 928 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7853 (mtm-85) REVERT: A 981 GLU cc_start: 0.7438 (tp30) cc_final: 0.7113 (tp30) REVERT: A 1042 MET cc_start: 0.7190 (ppp) cc_final: 0.6736 (mmp) REVERT: A 1049 TYR cc_start: 0.8057 (m-10) cc_final: 0.7843 (m-10) REVERT: A 1050 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7319 (ttm110) REVERT: B 483 MET cc_start: 0.8033 (mtt) cc_final: 0.7497 (mtm) REVERT: B 523 MET cc_start: 0.7845 (tpt) cc_final: 0.7581 (tpt) REVERT: B 558 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 562 LYS cc_start: 0.7720 (mttt) cc_final: 0.7512 (mptp) REVERT: B 591 LYS cc_start: 0.8970 (mttt) cc_final: 0.8683 (mtmm) REVERT: B 603 LYS cc_start: 0.8817 (mttt) cc_final: 0.8592 (mtpt) REVERT: B 657 GLU cc_start: 0.7116 (tt0) cc_final: 0.6841 (tm-30) REVERT: B 669 PHE cc_start: 0.7651 (m-80) cc_final: 0.7225 (m-80) REVERT: B 689 MET cc_start: 0.7853 (mtm) cc_final: 0.7648 (mtp) REVERT: B 705 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6940 (mm-30) REVERT: B 717 ARG cc_start: 0.6742 (ttt180) cc_final: 0.6213 (ttt90) REVERT: B 720 MET cc_start: 0.6809 (mmm) cc_final: 0.6550 (mmm) REVERT: B 721 MET cc_start: 0.7262 (ttm) cc_final: 0.6729 (mmp) REVERT: B 768 TYR cc_start: 0.7864 (t80) cc_final: 0.7540 (t80) REVERT: B 825 GLU cc_start: 0.8299 (tt0) cc_final: 0.8050 (tm-30) REVERT: B 864 GLU cc_start: 0.7171 (tt0) cc_final: 0.6791 (tt0) REVERT: B 920 GLU cc_start: 0.8171 (tt0) cc_final: 0.7661 (mp0) REVERT: B 924 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 963 ASP cc_start: 0.7550 (m-30) cc_final: 0.7283 (m-30) REVERT: B 969 LYS cc_start: 0.7734 (tttt) cc_final: 0.7385 (ttpp) REVERT: B 981 GLU cc_start: 0.7420 (tp30) cc_final: 0.7096 (tp30) REVERT: B 1049 TYR cc_start: 0.8148 (m-10) cc_final: 0.7869 (m-10) REVERT: B 1050 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.7234 (ttm110) REVERT: C 562 LYS cc_start: 0.8349 (mttt) cc_final: 0.8093 (mptp) REVERT: C 571 ASN cc_start: 0.8525 (m110) cc_final: 0.8290 (m-40) REVERT: C 591 LYS cc_start: 0.8983 (mttt) cc_final: 0.8739 (mttm) REVERT: C 594 GLU cc_start: 0.7774 (tp30) cc_final: 0.7313 (tp30) REVERT: C 630 LEU cc_start: 0.8077 (mt) cc_final: 0.7823 (mt) REVERT: C 635 LYS cc_start: 0.7137 (tttt) cc_final: 0.6776 (tptm) REVERT: C 699 ASN cc_start: 0.8293 (m-40) cc_final: 0.8009 (m-40) REVERT: C 704 LYS cc_start: 0.7073 (mttt) cc_final: 0.6801 (mtpp) REVERT: C 719 HIS cc_start: 0.6772 (t-90) cc_final: 0.6550 (t70) REVERT: C 720 MET cc_start: 0.7096 (mmm) cc_final: 0.6677 (mmm) REVERT: C 768 TYR cc_start: 0.8179 (t80) cc_final: 0.7900 (t80) REVERT: C 825 GLU cc_start: 0.7973 (tt0) cc_final: 0.7601 (tm-30) REVERT: C 852 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7240 (mmt90) REVERT: C 864 GLU cc_start: 0.7215 (tt0) cc_final: 0.7000 (tt0) REVERT: C 900 SER cc_start: 0.8421 (m) cc_final: 0.8082 (t) REVERT: C 969 LYS cc_start: 0.7641 (tttt) cc_final: 0.7264 (ttpp) REVERT: C 1050 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6905 (ttp-110) REVERT: C 1073 GLU cc_start: 0.7748 (tt0) cc_final: 0.7546 (tt0) outliers start: 12 outliers final: 3 residues processed: 610 average time/residue: 0.5916 time to fit residues: 406.4849 Evaluate side-chains 312 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 309 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 451 HIS D 512 HIS D 519 HIS D 549 ASN D 644 HIS D 700 HIS D 719 HIS D 805 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 460 ASN A 512 HIS A 519 HIS A 549 ASN A 644 HIS A 700 HIS A 719 HIS A 805 ASN A 851 GLN A 970 HIS B 451 HIS B 512 HIS B 519 HIS B 549 ASN B 644 HIS B 700 HIS B 719 HIS B 805 ASN B 851 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 460 ASN C 512 HIS C 519 HIS C 570 HIS C 577 ASN C 644 HIS C 700 HIS C 719 HIS C 739 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103482 restraints weight = 25273.016| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.27 r_work: 0.3018 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20732 Z= 0.143 Angle : 0.668 14.249 27968 Z= 0.317 Chirality : 0.041 0.193 3212 Planarity : 0.005 0.066 3364 Dihedral : 17.582 157.370 3138 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.55 % Allowed : 12.60 % Favored : 83.85 % 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: -0.43 (0.16), residues: 2416 helix: -0.12 (0.12), residues: 1720 sheet: 1.35 (0.73), residues: 68 loop : -0.51 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 601 TYR 0.015 0.001 TYR A 785 PHE 0.011 0.001 PHE C 823 TRP 0.013 0.001 TRP C 515 HIS 0.006 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (20720) covalent geometry : angle 0.64282 / 0.31 (27944) hydrogen bonds : bond 0.06081 / 4.19 ( 1165) hydrogen bonds : angle 3.93178 / 2.80 ( 3411) Misc. bond : bond 0.00395 / 0.20 ( 4) link_BETA1-4 : bond 0.01676 / 0.84 ( 4) link_BETA1-4 : angle 1.77189 / 1.25 ( 12) link_NAG-ASN : bond 0.01568 / 0.79 ( 4) link_NAG-ASN : angle 8.55992 / 5.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 326 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: D 483 MET cc_start: 0.8565 (mtt) cc_final: 0.8254 (mtm) REVERT: D 547 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7850 (t0) REVERT: D 669 PHE cc_start: 0.7862 (m-80) cc_final: 0.7449 (m-80) REVERT: D 717 ARG cc_start: 0.7674 (ttt180) cc_final: 0.7212 (ttt90) REVERT: D 721 MET cc_start: 0.8283 (ttm) cc_final: 0.7897 (mmp) REVERT: D 768 TYR cc_start: 0.7840 (t80) cc_final: 0.7583 (t80) REVERT: D 966 GLU cc_start: 0.8278 (tt0) cc_final: 0.7990 (mm-30) REVERT: D 981 GLU cc_start: 0.8084 (tp30) cc_final: 0.7851 (tp30) REVERT: A 669 PHE cc_start: 0.8062 (m-80) cc_final: 0.7678 (m-80) REVERT: A 696 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: A 717 ARG cc_start: 0.7648 (ttt180) cc_final: 0.7218 (ttt90) REVERT: A 720 MET cc_start: 0.7863 (mmm) cc_final: 0.7614 (mmm) REVERT: A 721 MET cc_start: 0.8186 (ttm) cc_final: 0.7702 (mmp) REVERT: A 768 TYR cc_start: 0.7961 (t80) cc_final: 0.7760 (t80) REVERT: A 808 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8041 (mp0) REVERT: A 864 GLU cc_start: 0.8323 (tt0) cc_final: 0.8081 (tt0) REVERT: A 920 GLU cc_start: 0.8889 (tt0) cc_final: 0.8502 (mp0) REVERT: A 981 GLU cc_start: 0.8080 (tp30) cc_final: 0.7850 (tp30) REVERT: A 1050 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7984 (ttm110) REVERT: A 1067 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8556 (tp) REVERT: B 547 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7865 (t0) REVERT: B 669 PHE cc_start: 0.8085 (m-80) cc_final: 0.7628 (m-80) REVERT: B 717 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7273 (ttt90) REVERT: B 720 MET cc_start: 0.7803 (mmm) cc_final: 0.7553 (mmm) REVERT: B 721 MET cc_start: 0.8182 (ttm) cc_final: 0.7670 (mmp) REVERT: B 768 TYR cc_start: 0.8032 (t80) cc_final: 0.7807 (t80) REVERT: B 864 GLU cc_start: 0.8378 (tt0) cc_final: 0.8156 (tt0) REVERT: B 966 GLU cc_start: 0.8253 (tt0) cc_final: 0.7976 (mm-30) REVERT: B 969 LYS cc_start: 0.8069 (tttt) cc_final: 0.7699 (ttpp) REVERT: B 981 GLU cc_start: 0.8100 (tp30) cc_final: 0.7866 (tp30) REVERT: B 1049 TYR cc_start: 0.8394 (m-10) cc_final: 0.8192 (m-10) REVERT: B 1050 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7727 (ttm110) REVERT: B 1067 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8628 (tp) REVERT: C 530 MET cc_start: 0.8468 (ttp) cc_final: 0.8211 (mtp) REVERT: C 544 LEU cc_start: 0.8841 (mt) cc_final: 0.8376 (mm) REVERT: C 594 GLU cc_start: 0.8240 (tp30) cc_final: 0.7829 (tp30) REVERT: C 635 LYS cc_start: 0.7876 (tttt) cc_final: 0.7599 (tptm) REVERT: C 704 LYS cc_start: 0.8009 (mttt) cc_final: 0.7734 (mtpp) REVERT: C 719 HIS cc_start: 0.7685 (t70) cc_final: 0.7381 (t70) REVERT: C 720 MET cc_start: 0.7898 (mmm) cc_final: 0.7540 (mmm) REVERT: C 768 TYR cc_start: 0.8252 (t80) cc_final: 0.8040 (t80) REVERT: C 920 GLU cc_start: 0.8675 (tt0) cc_final: 0.8473 (mp0) REVERT: C 974 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8105 (tmtt) REVERT: C 981 GLU cc_start: 0.8010 (tp30) cc_final: 0.7581 (tm-30) outliers start: 73 outliers final: 24 residues processed: 384 average time/residue: 0.5981 time to fit residues: 259.5132 Evaluate side-chains 285 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 974 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [216, 95, 161, 115, 143, 152, 164, 60, 231, 159, 7] chunk 216 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 152 optimal weight: 0.0770 chunk 164 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 691 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN A 983 HIS B 855 ASN B 907 GLN B 983 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 577 ASN C 805 ASN C 907 GLN C 970 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096174 restraints weight = 25163.195| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.18 r_work: 0.2903 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20732 Z= 0.167 Angle : 0.617 8.228 27968 Z= 0.303 Chirality : 0.043 0.377 3212 Planarity : 0.005 0.065 3364 Dihedral : 15.494 154.268 3132 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.01 % Allowed : 14.01 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2416 helix: 0.83 (0.12), residues: 1708 sheet: 1.68 (0.73), residues: 68 loop : -0.47 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 601 TYR 0.019 0.002 TYR A 785 PHE 0.014 0.002 PHE D 660 TRP 0.023 0.002 TRP C 515 HIS 0.007 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (20720) covalent geometry : angle 0.60878 / 0.30 (27944) hydrogen bonds : bond 0.06349 / 4.39 ( 1165) hydrogen bonds : angle 3.69213 / 2.63 ( 3411) Misc. bond : bond 0.00025 / 0.01 ( 4) link_BETA1-4 : bond 0.01028 / 0.53 ( 4) link_BETA1-4 : angle 1.25181 / 0.87 ( 12) link_NAG-ASN : bond 0.00920 / 0.45 ( 4) link_NAG-ASN : angle 4.79067 / 3.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 288 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: D 483 MET cc_start: 0.8575 (mtt) cc_final: 0.8349 (mtp) REVERT: D 544 LEU cc_start: 0.8960 (mt) cc_final: 0.8738 (mm) REVERT: D 547 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7978 (t0) REVERT: D 669 PHE cc_start: 0.8064 (m-80) cc_final: 0.7559 (m-80) REVERT: D 717 ARG cc_start: 0.7928 (ttt180) cc_final: 0.7534 (ttt90) REVERT: D 721 MET cc_start: 0.8440 (ttm) cc_final: 0.7882 (mmp) REVERT: D 768 TYR cc_start: 0.7997 (t80) cc_final: 0.7741 (t80) REVERT: D 941 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8388 (tp) REVERT: D 966 GLU cc_start: 0.8378 (tt0) cc_final: 0.8072 (mm-30) REVERT: D 981 GLU cc_start: 0.8312 (tp30) cc_final: 0.8011 (tp30) REVERT: A 544 LEU cc_start: 0.9005 (mt) cc_final: 0.8764 (mm) REVERT: A 669 PHE cc_start: 0.8016 (m-80) cc_final: 0.7578 (m-80) REVERT: A 717 ARG cc_start: 0.7843 (ttt180) cc_final: 0.7399 (ttt90) REVERT: A 721 MET cc_start: 0.8391 (ttm) cc_final: 0.7878 (mmp) REVERT: A 768 TYR cc_start: 0.8082 (t80) cc_final: 0.7878 (t80) REVERT: A 808 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8263 (mp0) REVERT: A 920 GLU cc_start: 0.9039 (tt0) cc_final: 0.8622 (mp0) REVERT: A 941 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 981 GLU cc_start: 0.8307 (tp30) cc_final: 0.8042 (tp30) REVERT: A 1063 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: A 1067 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8662 (tp) REVERT: B 544 LEU cc_start: 0.9013 (mt) cc_final: 0.8729 (mm) REVERT: B 547 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7954 (t0) REVERT: B 669 PHE cc_start: 0.8009 (m-80) cc_final: 0.7552 (m-80) REVERT: B 717 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7465 (ttt90) REVERT: B 721 MET cc_start: 0.8417 (ttm) cc_final: 0.7822 (mmp) REVERT: B 768 TYR cc_start: 0.8193 (t80) cc_final: 0.7967 (t80) REVERT: B 941 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8401 (tp) REVERT: B 966 GLU cc_start: 0.8366 (tt0) cc_final: 0.8130 (mm-30) REVERT: B 981 GLU cc_start: 0.8305 (tp30) cc_final: 0.8031 (tp30) REVERT: B 1067 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8714 (tp) REVERT: C 500 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7835 (tp) REVERT: C 530 MET cc_start: 0.8685 (ttp) cc_final: 0.8485 (mtp) REVERT: C 544 LEU cc_start: 0.8842 (mt) cc_final: 0.8501 (mm) REVERT: C 597 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8406 (mp) REVERT: C 604 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.5977 (mtm-85) REVERT: C 704 LYS cc_start: 0.8141 (mttt) cc_final: 0.7900 (mttp) REVERT: C 768 TYR cc_start: 0.8413 (t80) cc_final: 0.8201 (t80) REVERT: C 920 GLU cc_start: 0.8883 (tt0) cc_final: 0.8526 (mp0) REVERT: C 1063 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: C 1067 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8710 (tp) outliers start: 103 outliers final: 36 residues processed: 368 average time/residue: 0.5511 time to fit residues: 232.0022 Evaluate side-chains 295 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [144, 26, 37, 218, 234, 49, 38, 95, 147, 138, 197] chunk 144 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 460 ASN D 691 GLN D 907 GLN D 983 HIS B 460 ASN B 691 GLN B 970 HIS C 983 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096628 restraints weight = 25197.727| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.19 r_work: 0.2904 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20732 Z= 0.134 Angle : 0.543 7.681 27968 Z= 0.272 Chirality : 0.040 0.154 3212 Planarity : 0.004 0.062 3364 Dihedral : 14.756 154.627 3132 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.57 % Allowed : 14.98 % Favored : 80.45 % 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: 1.21 (0.17), residues: 2416 helix: 1.21 (0.13), residues: 1720 sheet: 2.88 (0.85), residues: 48 loop : -0.29 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 601 TYR 0.012 0.001 TYR A 785 PHE 0.010 0.001 PHE C 583 TRP 0.014 0.001 TRP D 515 HIS 0.006 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (20720) covalent geometry : angle 0.53620 / 0.27 (27944) hydrogen bonds : bond 0.05602 / 3.86 ( 1165) hydrogen bonds : angle 3.57933 / 2.55 ( 3411) Misc. bond : bond 0.00015 / 0.01 ( 4) link_BETA1-4 : bond 0.00849 / 0.42 ( 4) link_BETA1-4 : angle 1.27663 / 0.90 ( 12) link_NAG-ASN : bond 0.00658 / 0.33 ( 4) link_NAG-ASN : angle 3.86962 / 2.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 268 time to evaluate : 0.740 Fit side-chains REVERT: D 483 MET cc_start: 0.8563 (mtt) cc_final: 0.8350 (mmm) REVERT: D 544 LEU cc_start: 0.8981 (mt) cc_final: 0.8738 (mm) REVERT: D 547 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7984 (t0) REVERT: D 669 PHE cc_start: 0.7987 (m-80) cc_final: 0.7458 (m-80) REVERT: D 717 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7556 (ttt90) REVERT: D 721 MET cc_start: 0.8409 (ttm) cc_final: 0.7836 (mmp) REVERT: D 768 TYR cc_start: 0.7949 (t80) cc_final: 0.7720 (t80) REVERT: D 941 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8327 (tp) REVERT: D 966 GLU cc_start: 0.8336 (tt0) cc_final: 0.8037 (mm-30) REVERT: D 981 GLU cc_start: 0.8322 (tp30) cc_final: 0.8054 (tp30) REVERT: A 544 LEU cc_start: 0.9006 (mt) cc_final: 0.8768 (mm) REVERT: A 578 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.6811 (mppt) REVERT: A 669 PHE cc_start: 0.7972 (m-80) cc_final: 0.7460 (m-80) REVERT: A 717 ARG cc_start: 0.7807 (ttt180) cc_final: 0.7357 (ttt90) REVERT: A 721 MET cc_start: 0.8377 (ttm) cc_final: 0.7868 (mmp) REVERT: A 723 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8100 (tp) REVERT: A 768 TYR cc_start: 0.8089 (t80) cc_final: 0.7873 (t80) REVERT: A 920 GLU cc_start: 0.9010 (tt0) cc_final: 0.8575 (mp0) REVERT: A 941 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 981 GLU cc_start: 0.8310 (tp30) cc_final: 0.8037 (tp30) REVERT: A 1063 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: A 1067 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8617 (tp) REVERT: B 544 LEU cc_start: 0.8998 (mt) cc_final: 0.8696 (mm) REVERT: B 547 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7949 (t0) REVERT: B 669 PHE cc_start: 0.7936 (m-80) cc_final: 0.7438 (m-80) REVERT: B 717 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7520 (ttt90) REVERT: B 721 MET cc_start: 0.8357 (ttm) cc_final: 0.7756 (mmp) REVERT: B 768 TYR cc_start: 0.8103 (t80) cc_final: 0.7891 (t80) REVERT: B 855 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8229 (p0) REVERT: B 941 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8378 (tp) REVERT: B 966 GLU cc_start: 0.8331 (tt0) cc_final: 0.8095 (mm-30) REVERT: B 981 GLU cc_start: 0.8289 (tp30) cc_final: 0.8035 (tp30) REVERT: B 1067 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8706 (tp) REVERT: C 544 LEU cc_start: 0.8852 (mt) cc_final: 0.8505 (mm) REVERT: C 604 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.6044 (mtm-85) REVERT: C 606 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: C 704 LYS cc_start: 0.7990 (mttt) cc_final: 0.7743 (mttp) REVERT: C 768 TYR cc_start: 0.8380 (t80) cc_final: 0.8122 (t80) REVERT: C 808 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8246 (mp0) REVERT: C 920 GLU cc_start: 0.8833 (tt0) cc_final: 0.8486 (mp0) REVERT: C 941 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8251 (tp) REVERT: C 969 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7722 (ttpp) REVERT: C 981 GLU cc_start: 0.8453 (tp30) cc_final: 0.7946 (tm-30) REVERT: C 1063 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: C 1067 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8619 (tp) outliers start: 94 outliers final: 37 residues processed: 335 average time/residue: 0.5464 time to fit residues: 209.0218 Evaluate side-chains 300 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [20, 25, 67, 166, 87, 135, 148, 111, 155, 142, 143] chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 166 optimal weight: 0.0030 chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 691 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 549 ASN C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095579 restraints weight = 24851.026| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.42 r_work: 0.2876 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20732 Z= 0.116 Angle : 0.509 7.395 27968 Z= 0.257 Chirality : 0.039 0.154 3212 Planarity : 0.004 0.062 3364 Dihedral : 14.073 154.187 3132 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.23 % Allowed : 15.61 % Favored : 80.16 % 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: 1.57 (0.18), residues: 2416 helix: 1.48 (0.13), residues: 1720 sheet: 2.93 (0.85), residues: 48 loop : -0.15 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 601 TYR 0.009 0.001 TYR B 785 PHE 0.008 0.001 PHE C 746 TRP 0.010 0.001 TRP D 832 HIS 0.004 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (20720) covalent geometry : angle 0.50454 / 0.26 (27944) hydrogen bonds : bond 0.05117 / 3.52 ( 1165) hydrogen bonds : angle 3.46700 / 2.47 ( 3411) Misc. bond : bond 0.00020 / 0.01 ( 4) link_BETA1-4 : bond 0.00788 / 0.40 ( 4) link_BETA1-4 : angle 1.21058 / 0.84 ( 12) link_NAG-ASN : bond 0.00533 / 0.27 ( 4) link_NAG-ASN : angle 3.18195 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 267 time to evaluate : 0.808 Fit side-chains REVERT: D 544 LEU cc_start: 0.8956 (mt) cc_final: 0.8690 (mm) REVERT: D 547 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7890 (t0) REVERT: D 669 PHE cc_start: 0.8017 (m-80) cc_final: 0.7458 (m-80) REVERT: D 717 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7249 (ttt90) REVERT: D 721 MET cc_start: 0.8145 (ttm) cc_final: 0.7573 (mmp) REVERT: D 768 TYR cc_start: 0.7775 (t80) cc_final: 0.7552 (t80) REVERT: D 864 GLU cc_start: 0.8212 (tt0) cc_final: 0.7934 (tt0) REVERT: D 941 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8237 (tp) REVERT: D 966 GLU cc_start: 0.8192 (tt0) cc_final: 0.7934 (mm-30) REVERT: D 981 GLU cc_start: 0.8096 (tp30) cc_final: 0.7828 (tp30) REVERT: A 544 LEU cc_start: 0.8952 (mt) cc_final: 0.8687 (mm) REVERT: A 669 PHE cc_start: 0.7968 (m-80) cc_final: 0.7466 (m-80) REVERT: A 717 ARG cc_start: 0.7665 (ttt180) cc_final: 0.7225 (ttt90) REVERT: A 721 MET cc_start: 0.8111 (ttm) cc_final: 0.7603 (mmp) REVERT: A 723 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7887 (tp) REVERT: A 768 TYR cc_start: 0.7953 (t80) cc_final: 0.7716 (t80) REVERT: A 920 GLU cc_start: 0.8741 (tt0) cc_final: 0.8433 (mp0) REVERT: A 941 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 981 GLU cc_start: 0.8094 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1063 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 1067 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8507 (tp) REVERT: B 463 GLN cc_start: 0.8007 (mt0) cc_final: 0.7773 (mt0) REVERT: B 544 LEU cc_start: 0.8966 (mt) cc_final: 0.8674 (mm) REVERT: B 669 PHE cc_start: 0.7971 (m-80) cc_final: 0.7434 (m-80) REVERT: B 717 ARG cc_start: 0.7652 (ttt180) cc_final: 0.7224 (ttt90) REVERT: B 721 MET cc_start: 0.8106 (ttm) cc_final: 0.7506 (mmp) REVERT: B 768 TYR cc_start: 0.7965 (t80) cc_final: 0.7742 (t80) REVERT: B 881 LEU cc_start: 0.8641 (tp) cc_final: 0.8255 (tp) REVERT: B 941 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8198 (tp) REVERT: B 966 GLU cc_start: 0.8168 (tt0) cc_final: 0.7926 (mm-30) REVERT: B 981 GLU cc_start: 0.8065 (tp30) cc_final: 0.7814 (tp30) REVERT: B 1067 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8544 (tp) REVERT: C 544 LEU cc_start: 0.8861 (mt) cc_final: 0.8498 (mm) REVERT: C 604 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.6043 (mtm-85) REVERT: C 606 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: C 768 TYR cc_start: 0.8233 (t80) cc_final: 0.7980 (t80) REVERT: C 808 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7974 (mp0) REVERT: C 920 GLU cc_start: 0.8662 (tt0) cc_final: 0.8424 (mp0) REVERT: C 941 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8181 (tp) REVERT: C 981 GLU cc_start: 0.8293 (tp30) cc_final: 0.7983 (tp30) REVERT: C 1063 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: C 1067 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8437 (tp) outliers start: 87 outliers final: 45 residues processed: 325 average time/residue: 0.5500 time to fit residues: 204.0186 Evaluate side-chains 309 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [39, 70, 161, 101, 230, 145, 93, 120, 86, 150, 139] chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 150 optimal weight: 0.0870 chunk 139 optimal weight: 0.9980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 719 HIS D 855 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.096672 restraints weight = 24673.771| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.44 r_work: 0.2888 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20732 Z= 0.111 Angle : 0.502 7.204 27968 Z= 0.254 Chirality : 0.039 0.162 3212 Planarity : 0.004 0.061 3364 Dihedral : 13.359 153.851 3132 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.89 % Allowed : 16.49 % Favored : 79.62 % 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: 2416 helix: 1.65 (0.13), residues: 1724 sheet: 3.02 (0.83), residues: 48 loop : 0.00 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C1050 TYR 0.013 0.001 TYR A 785 PHE 0.008 0.001 PHE C 612 TRP 0.010 0.001 TRP A 515 HIS 0.005 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (20720) covalent geometry : angle 0.49892 / 0.25 (27944) hydrogen bonds : bond 0.04781 / 3.30 ( 1165) hydrogen bonds : angle 3.38384 / 2.41 ( 3411) Misc. bond : bond 0.00028 / 0.01 ( 4) link_BETA1-4 : bond 0.00655 / 0.33 ( 4) link_BETA1-4 : angle 1.08572 / 0.75 ( 12) link_NAG-ASN : bond 0.00497 / 0.25 ( 4) link_NAG-ASN : angle 2.67225 / 1.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 279 time to evaluate : 0.887 Fit side-chains REVERT: D 544 LEU cc_start: 0.8914 (mt) cc_final: 0.8630 (mm) REVERT: D 547 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7783 (t0) REVERT: D 669 PHE cc_start: 0.7852 (m-80) cc_final: 0.7219 (m-80) REVERT: D 717 ARG cc_start: 0.7581 (ttt180) cc_final: 0.7087 (ttt90) REVERT: D 721 MET cc_start: 0.8066 (ttm) cc_final: 0.7466 (mmp) REVERT: D 768 TYR cc_start: 0.7739 (t80) cc_final: 0.7493 (t80) REVERT: D 966 GLU cc_start: 0.8084 (tt0) cc_final: 0.7824 (mm-30) REVERT: D 981 GLU cc_start: 0.8007 (tp30) cc_final: 0.7734 (tp30) REVERT: A 483 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8381 (mtm) REVERT: A 544 LEU cc_start: 0.8933 (mt) cc_final: 0.8660 (mm) REVERT: A 578 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.6805 (mppt) REVERT: A 669 PHE cc_start: 0.7808 (m-80) cc_final: 0.7216 (m-80) REVERT: A 717 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7119 (ttt90) REVERT: A 721 MET cc_start: 0.8006 (ttm) cc_final: 0.7494 (mmp) REVERT: A 723 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7805 (tp) REVERT: A 808 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 881 LEU cc_start: 0.8631 (tp) cc_final: 0.7904 (mp) REVERT: A 920 GLU cc_start: 0.8633 (tt0) cc_final: 0.8283 (mp0) REVERT: A 981 GLU cc_start: 0.8010 (tp30) cc_final: 0.7742 (tp30) REVERT: A 999 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8002 (t0) REVERT: A 1063 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: A 1067 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8359 (tp) REVERT: B 463 GLN cc_start: 0.8008 (mt0) cc_final: 0.7777 (mt0) REVERT: B 483 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: B 544 LEU cc_start: 0.8944 (mt) cc_final: 0.8639 (mm) REVERT: B 634 MET cc_start: 0.8310 (tpt) cc_final: 0.7999 (tpt) REVERT: B 669 PHE cc_start: 0.7916 (m-80) cc_final: 0.7357 (m-80) REVERT: B 717 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7069 (ttt90) REVERT: B 721 MET cc_start: 0.8008 (ttm) cc_final: 0.7419 (mmp) REVERT: B 768 TYR cc_start: 0.7904 (t80) cc_final: 0.7697 (t80) REVERT: B 966 GLU cc_start: 0.8071 (tt0) cc_final: 0.7860 (mm-30) REVERT: B 981 GLU cc_start: 0.7996 (tp30) cc_final: 0.7732 (tp30) REVERT: B 1067 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8324 (tp) REVERT: C 483 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8331 (mtp) REVERT: C 544 LEU cc_start: 0.8837 (mt) cc_final: 0.8447 (mm) REVERT: C 604 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.5969 (mtm-85) REVERT: C 606 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: C 634 MET cc_start: 0.8352 (tpt) cc_final: 0.8149 (tpt) REVERT: C 768 TYR cc_start: 0.8160 (t80) cc_final: 0.7899 (t80) REVERT: C 808 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7905 (mp0) REVERT: C 881 LEU cc_start: 0.8553 (tp) cc_final: 0.8275 (tp) REVERT: C 920 GLU cc_start: 0.8630 (tt0) cc_final: 0.8360 (mp0) REVERT: C 941 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8107 (tp) REVERT: C 981 GLU cc_start: 0.8191 (tp30) cc_final: 0.7902 (tp30) REVERT: C 1063 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: C 1067 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8332 (tp) outliers start: 80 outliers final: 31 residues processed: 332 average time/residue: 0.5513 time to fit residues: 209.1134 Evaluate side-chains 301 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [210, 46, 174, 16, 205, 225, 178, 166, 212, 12, 32] chunk 210 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 166 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096950 restraints weight = 24944.622| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.46 r_work: 0.2862 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20732 Z= 0.116 Angle : 0.511 7.536 27968 Z= 0.257 Chirality : 0.039 0.157 3212 Planarity : 0.004 0.059 3364 Dihedral : 12.993 151.688 3132 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.79 % Allowed : 17.07 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2416 helix: 1.73 (0.13), residues: 1724 sheet: 3.15 (0.83), residues: 48 loop : 0.07 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1050 TYR 0.009 0.001 TYR A 785 PHE 0.009 0.001 PHE D 583 TRP 0.010 0.001 TRP B 515 HIS 0.004 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20720) covalent geometry : angle 0.50769 / 0.26 (27944) hydrogen bonds : bond 0.04904 / 3.38 ( 1165) hydrogen bonds : angle 3.38687 / 2.41 ( 3411) Misc. bond : bond 0.00019 / 0.01 ( 4) link_BETA1-4 : bond 0.00594 / 0.29 ( 4) link_BETA1-4 : angle 0.97512 / 0.67 ( 12) link_NAG-ASN : bond 0.00432 / 0.22 ( 4) link_NAG-ASN : angle 2.55029 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 265 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: D 463 GLN cc_start: 0.8023 (mt0) cc_final: 0.7811 (mt0) REVERT: D 544 LEU cc_start: 0.8993 (mt) cc_final: 0.8732 (mm) REVERT: D 669 PHE cc_start: 0.7892 (m-80) cc_final: 0.7280 (m-80) REVERT: D 681 GLU cc_start: 0.8264 (pt0) cc_final: 0.7746 (pt0) REVERT: D 717 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7406 (ttt90) REVERT: D 721 MET cc_start: 0.8269 (ttm) cc_final: 0.7692 (mmp) REVERT: D 768 TYR cc_start: 0.7801 (t80) cc_final: 0.7571 (t80) REVERT: D 920 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: D 981 GLU cc_start: 0.8129 (tp30) cc_final: 0.7903 (tp30) REVERT: A 463 GLN cc_start: 0.7989 (mt0) cc_final: 0.7783 (mt0) REVERT: A 483 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8483 (mtp) REVERT: A 544 LEU cc_start: 0.9004 (mt) cc_final: 0.8757 (mm) REVERT: A 578 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7058 (mppt) REVERT: A 669 PHE cc_start: 0.7926 (m-80) cc_final: 0.7360 (m-80) REVERT: A 681 GLU cc_start: 0.8292 (pt0) cc_final: 0.7811 (pt0) REVERT: A 717 ARG cc_start: 0.7809 (ttt180) cc_final: 0.7415 (ttt90) REVERT: A 721 MET cc_start: 0.8237 (ttm) cc_final: 0.7740 (mmp) REVERT: A 723 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 920 GLU cc_start: 0.8753 (tt0) cc_final: 0.8541 (mp0) REVERT: A 981 GLU cc_start: 0.8186 (tp30) cc_final: 0.7949 (tp30) REVERT: A 1063 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: A 1067 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8630 (tp) REVERT: B 463 GLN cc_start: 0.8044 (mt0) cc_final: 0.7820 (mt0) REVERT: B 483 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8457 (mtm) REVERT: B 544 LEU cc_start: 0.9020 (mt) cc_final: 0.8738 (mm) REVERT: B 634 MET cc_start: 0.8574 (tpt) cc_final: 0.8278 (tpt) REVERT: B 669 PHE cc_start: 0.7912 (m-80) cc_final: 0.7321 (m-80) REVERT: B 717 ARG cc_start: 0.7781 (ttt180) cc_final: 0.7414 (ttt90) REVERT: B 721 MET cc_start: 0.8221 (ttm) cc_final: 0.7664 (mmp) REVERT: B 920 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: B 981 GLU cc_start: 0.8135 (tp30) cc_final: 0.7927 (tp30) REVERT: B 1067 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8613 (tp) REVERT: C 483 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8461 (mtp) REVERT: C 544 LEU cc_start: 0.8933 (mt) cc_final: 0.8560 (mm) REVERT: C 604 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6118 (mtm-85) REVERT: C 606 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: C 768 TYR cc_start: 0.8203 (t80) cc_final: 0.7937 (t80) REVERT: C 808 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8052 (mp0) REVERT: C 864 GLU cc_start: 0.8353 (tt0) cc_final: 0.8142 (tt0) REVERT: C 941 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8394 (tp) REVERT: C 966 GLU cc_start: 0.8411 (tp30) cc_final: 0.8200 (mm-30) REVERT: C 981 GLU cc_start: 0.8416 (tp30) cc_final: 0.8201 (tp30) REVERT: C 1063 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: C 1067 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8619 (tp) outliers start: 78 outliers final: 39 residues processed: 313 average time/residue: 0.5721 time to fit residues: 203.3693 Evaluate side-chains 308 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [93, 107, 205, 15, 49, 243, 119, 135, 111, 214, 168] chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 719 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097951 restraints weight = 24839.351| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.16 r_work: 0.2901 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20732 Z= 0.118 Angle : 0.515 7.232 27968 Z= 0.260 Chirality : 0.039 0.174 3212 Planarity : 0.004 0.060 3364 Dihedral : 12.615 149.679 3132 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.40 % Allowed : 17.56 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.18), residues: 2416 helix: 1.78 (0.13), residues: 1720 sheet: 3.18 (0.83), residues: 48 loop : 0.05 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 717 TYR 0.009 0.001 TYR A 785 PHE 0.009 0.001 PHE C 583 TRP 0.011 0.001 TRP D 515 HIS 0.004 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (20720) covalent geometry : angle 0.51262 / 0.26 (27944) hydrogen bonds : bond 0.04936 / 3.39 ( 1165) hydrogen bonds : angle 3.39390 / 2.41 ( 3411) Misc. bond : bond 0.00022 / 0.01 ( 4) link_BETA1-4 : bond 0.00609 / 0.31 ( 4) link_BETA1-4 : angle 0.92202 / 0.63 ( 12) link_NAG-ASN : bond 0.00400 / 0.20 ( 4) link_NAG-ASN : angle 2.40000 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: D 544 LEU cc_start: 0.9102 (mt) cc_final: 0.8878 (mm) REVERT: D 669 PHE cc_start: 0.7930 (m-80) cc_final: 0.7312 (m-80) REVERT: D 681 GLU cc_start: 0.8220 (pt0) cc_final: 0.7761 (pt0) REVERT: D 717 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7790 (ttt90) REVERT: D 721 MET cc_start: 0.8520 (ttm) cc_final: 0.7985 (mmp) REVERT: D 768 TYR cc_start: 0.7956 (t80) cc_final: 0.7742 (t80) REVERT: D 864 GLU cc_start: 0.8670 (tt0) cc_final: 0.8459 (tt0) REVERT: D 920 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: D 999 ASP cc_start: 0.8411 (t0) cc_final: 0.8121 (t0) REVERT: A 483 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8594 (mtp) REVERT: A 544 LEU cc_start: 0.9062 (mt) cc_final: 0.8845 (mm) REVERT: A 578 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7165 (mppt) REVERT: A 669 PHE cc_start: 0.7969 (m-80) cc_final: 0.7353 (m-80) REVERT: A 681 GLU cc_start: 0.8262 (pt0) cc_final: 0.7826 (pt0) REVERT: A 717 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7782 (ttt90) REVERT: A 721 MET cc_start: 0.8555 (ttm) cc_final: 0.8094 (mmp) REVERT: A 723 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8378 (tp) REVERT: A 999 ASP cc_start: 0.8502 (t70) cc_final: 0.8023 (t0) REVERT: A 1063 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: A 1067 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8876 (tp) REVERT: B 463 GLN cc_start: 0.8280 (mt0) cc_final: 0.8064 (mt0) REVERT: B 483 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: B 544 LEU cc_start: 0.9091 (mt) cc_final: 0.8843 (mm) REVERT: B 634 MET cc_start: 0.8838 (tpt) cc_final: 0.8608 (tpt) REVERT: B 669 PHE cc_start: 0.7951 (m-80) cc_final: 0.7351 (m-80) REVERT: B 717 ARG cc_start: 0.8132 (ttt180) cc_final: 0.7793 (ttt90) REVERT: B 721 MET cc_start: 0.8485 (ttm) cc_final: 0.7972 (mmp) REVERT: B 920 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: B 999 ASP cc_start: 0.8065 (t0) cc_final: 0.7855 (OUTLIER) REVERT: B 1067 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8886 (tp) REVERT: C 597 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8716 (mt) REVERT: C 604 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6237 (mtm-85) REVERT: C 606 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8199 (m-30) REVERT: C 808 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8359 (mp0) REVERT: C 941 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8664 (tp) REVERT: C 981 GLU cc_start: 0.8645 (tp30) cc_final: 0.8443 (tp30) REVERT: C 1063 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: C 1067 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8872 (tp) outliers start: 70 outliers final: 42 residues processed: 307 average time/residue: 0.5817 time to fit residues: 202.8448 Evaluate side-chains 307 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [8, 229, 206, 159, 101, 31, 151, 197, 61, 213, 126] chunk 8 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 151 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 213 optimal weight: 0.0980 chunk 126 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 463 GLN D 719 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 719 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 719 HIS ** 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 = 0.3675 r_free = 0.3675 target = 0.142459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100285 restraints weight = 24934.311| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.17 r_work: 0.2965 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20732 Z= 0.102 Angle : 0.502 8.110 27968 Z= 0.255 Chirality : 0.038 0.139 3212 Planarity : 0.004 0.059 3364 Dihedral : 12.288 149.214 3132 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.58 % Allowed : 18.87 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.18), residues: 2416 helix: 1.91 (0.13), residues: 1716 sheet: 3.27 (0.82), residues: 48 loop : 0.13 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 717 TYR 0.008 0.001 TYR D1049 PHE 0.008 0.001 PHE C 823 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (20720) covalent geometry : angle 0.50025 / 0.25 (27944) hydrogen bonds : bond 0.04312 / 2.96 ( 1165) hydrogen bonds : angle 3.32619 / 2.36 ( 3411) Misc. bond : bond 0.00026 / 0.01 ( 4) link_BETA1-4 : bond 0.00671 / 0.34 ( 4) link_BETA1-4 : angle 0.88958 / 0.61 ( 12) link_NAG-ASN : bond 0.00453 / 0.23 ( 4) link_NAG-ASN : angle 2.08903 / 1.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: D 544 LEU cc_start: 0.9103 (mt) cc_final: 0.8886 (mm) REVERT: D 681 GLU cc_start: 0.8181 (pt0) cc_final: 0.7747 (pt0) REVERT: D 717 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7770 (ttt90) REVERT: D 721 MET cc_start: 0.8522 (ttm) cc_final: 0.7985 (mmp) REVERT: D 966 GLU cc_start: 0.8651 (tp30) cc_final: 0.8433 (mm-30) REVERT: D 981 GLU cc_start: 0.8676 (tp30) cc_final: 0.8416 (tm-30) REVERT: D 999 ASP cc_start: 0.8398 (t0) cc_final: 0.8112 (t0) REVERT: A 544 LEU cc_start: 0.9066 (mt) cc_final: 0.8857 (mm) REVERT: A 669 PHE cc_start: 0.8012 (m-80) cc_final: 0.7382 (m-80) REVERT: A 681 GLU cc_start: 0.8213 (pt0) cc_final: 0.7799 (pt0) REVERT: A 717 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7799 (ttt90) REVERT: A 721 MET cc_start: 0.8560 (ttm) cc_final: 0.8115 (mmp) REVERT: A 723 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8396 (tp) REVERT: A 981 GLU cc_start: 0.8790 (tp30) cc_final: 0.8509 (tm-30) REVERT: A 1063 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: B 463 GLN cc_start: 0.8301 (mt0) cc_final: 0.8089 (mt0) REVERT: B 544 LEU cc_start: 0.9073 (mt) cc_final: 0.8842 (mm) REVERT: B 634 MET cc_start: 0.8866 (tpt) cc_final: 0.8604 (tpt) REVERT: B 669 PHE cc_start: 0.7975 (m-80) cc_final: 0.7357 (m-80) REVERT: B 717 ARG cc_start: 0.8108 (ttt180) cc_final: 0.7814 (ttt90) REVERT: B 721 MET cc_start: 0.8450 (ttm) cc_final: 0.7980 (mmp) REVERT: B 966 GLU cc_start: 0.8645 (tp30) cc_final: 0.8439 (mm-30) REVERT: B 981 GLU cc_start: 0.8720 (tp30) cc_final: 0.8453 (tm-30) REVERT: B 999 ASP cc_start: 0.7936 (t0) cc_final: 0.7696 (OUTLIER) REVERT: C 483 MET cc_start: 0.8848 (mtp) cc_final: 0.8585 (mmm) REVERT: C 544 LEU cc_start: 0.9021 (mt) cc_final: 0.8763 (mm) REVERT: C 597 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8748 (mt) REVERT: C 604 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.6247 (mtm-85) REVERT: C 606 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: C 808 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8364 (mp0) REVERT: C 881 LEU cc_start: 0.8911 (tp) cc_final: 0.8698 (tp) REVERT: C 941 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8654 (tp) REVERT: C 999 ASP cc_start: 0.8388 (t0) cc_final: 0.8183 (t0) REVERT: C 1063 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: C 1067 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8834 (tp) outliers start: 53 outliers final: 30 residues processed: 303 average time/residue: 0.5589 time to fit residues: 193.5853 Evaluate side-chains 292 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [213, 139, 112, 13, 39, 168, 7, 179, 122, 221, 164] chunk 213 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 570 HIS D 719 HIS A 570 HIS A 719 HIS B 570 HIS B 719 HIS C 577 ASN C 719 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.093854 restraints weight = 25017.523| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.17 r_work: 0.2859 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20732 Z= 0.191 Angle : 0.596 8.236 27968 Z= 0.300 Chirality : 0.042 0.153 3212 Planarity : 0.004 0.057 3364 Dihedral : 12.293 144.433 3132 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.53 % Allowed : 19.50 % Favored : 77.97 % 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: 1.88 (0.18), residues: 2416 helix: 1.67 (0.13), residues: 1720 sheet: 3.22 (0.81), residues: 48 loop : 0.08 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 717 TYR 0.011 0.002 TYR B 812 PHE 0.015 0.002 PHE B 818 TRP 0.022 0.002 TRP D 515 HIS 0.009 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.19 (20720) covalent geometry : angle 0.59318 / 0.30 (27944) hydrogen bonds : bond 0.06257 / 4.31 ( 1165) hydrogen bonds : angle 3.55259 / 2.53 ( 3411) Misc. bond : bond 0.00011 / 0.01 ( 4) link_BETA1-4 : bond 0.00499 / 0.25 ( 4) link_BETA1-4 : angle 0.84653 / 0.58 ( 12) link_NAG-ASN : bond 0.00188 / 0.09 ( 4) link_NAG-ASN : angle 2.78306 / 1.87 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: D 544 LEU cc_start: 0.9148 (mt) cc_final: 0.8899 (mm) REVERT: D 669 PHE cc_start: 0.7945 (m-80) cc_final: 0.7376 (m-80) REVERT: D 681 GLU cc_start: 0.8186 (pt0) cc_final: 0.7742 (pt0) REVERT: D 717 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7875 (ttt90) REVERT: D 721 MET cc_start: 0.8546 (ttm) cc_final: 0.7984 (mmp) REVERT: D 864 GLU cc_start: 0.8749 (tt0) cc_final: 0.8526 (tt0) REVERT: D 966 GLU cc_start: 0.8683 (tp30) cc_final: 0.8440 (mm-30) REVERT: D 981 GLU cc_start: 0.8716 (tp30) cc_final: 0.8433 (tm-30) REVERT: D 999 ASP cc_start: 0.8479 (t0) cc_final: 0.8181 (t0) REVERT: A 544 LEU cc_start: 0.9091 (mt) cc_final: 0.8860 (mm) REVERT: A 669 PHE cc_start: 0.7998 (m-80) cc_final: 0.7365 (m-80) REVERT: A 681 GLU cc_start: 0.8232 (pt0) cc_final: 0.7815 (pt0) REVERT: A 717 ARG cc_start: 0.8217 (ttt180) cc_final: 0.7862 (ttt90) REVERT: A 721 MET cc_start: 0.8612 (ttm) cc_final: 0.8083 (mmp) REVERT: A 723 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8444 (tp) REVERT: A 808 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: A 871 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 981 GLU cc_start: 0.8775 (tp30) cc_final: 0.8498 (tm-30) REVERT: A 999 ASP cc_start: 0.8520 (t70) cc_final: 0.8059 (t0) REVERT: A 1063 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: B 544 LEU cc_start: 0.9129 (mt) cc_final: 0.8873 (mm) REVERT: B 634 MET cc_start: 0.8946 (tpt) cc_final: 0.8705 (tpt) REVERT: B 669 PHE cc_start: 0.7967 (m-80) cc_final: 0.7359 (m-80) REVERT: B 717 ARG cc_start: 0.8207 (ttt180) cc_final: 0.7885 (ttt90) REVERT: B 721 MET cc_start: 0.8537 (ttm) cc_final: 0.7986 (mmp) REVERT: B 920 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: B 966 GLU cc_start: 0.8667 (tp30) cc_final: 0.8460 (mm-30) REVERT: B 981 GLU cc_start: 0.8688 (tp30) cc_final: 0.8390 (tm-30) REVERT: B 999 ASP cc_start: 0.8028 (t0) cc_final: 0.7772 (OUTLIER) REVERT: B 1067 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9008 (tp) REVERT: C 483 MET cc_start: 0.8824 (mtp) cc_final: 0.8523 (mmm) REVERT: C 597 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8760 (mt) REVERT: C 604 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6332 (mtm-85) REVERT: C 808 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8381 (mp0) REVERT: C 941 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8714 (tp) REVERT: C 966 GLU cc_start: 0.8656 (tp30) cc_final: 0.8451 (mm-30) REVERT: C 981 GLU cc_start: 0.8771 (tp30) cc_final: 0.8467 (tm-30) REVERT: C 1063 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: C 1067 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8983 (tp) outliers start: 52 outliers final: 29 residues processed: 288 average time/residue: 0.6093 time to fit residues: 198.5834 Evaluate side-chains 290 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain C residue 1067 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: [147, 100, 230, 186, 7, 67, 204, 130, 91, 209, 183] chunk 147 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 204 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 183 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 719 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS A 719 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN B 570 HIS B 719 HIS B 739 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099303 restraints weight = 25000.180| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.17 r_work: 0.2951 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20732 Z= 0.107 Angle : 0.507 8.913 27968 Z= 0.259 Chirality : 0.038 0.145 3212 Planarity : 0.004 0.056 3364 Dihedral : 11.712 144.805 3132 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.09 % Allowed : 19.80 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.18), residues: 2416 helix: 1.89 (0.13), residues: 1716 sheet: 3.39 (0.82), residues: 48 loop : 0.15 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 717 TYR 0.007 0.001 TYR D 706 PHE 0.008 0.001 PHE C 612 TRP 0.011 0.001 TRP D 809 HIS 0.005 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (20720) covalent geometry : angle 0.50571 / 0.26 (27944) hydrogen bonds : bond 0.04461 / 3.07 ( 1165) hydrogen bonds : angle 3.38463 / 2.40 ( 3411) Misc. bond : bond 0.00021 / 0.01 ( 4) link_BETA1-4 : bond 0.00617 / 0.31 ( 4) link_BETA1-4 : angle 0.77275 / 0.53 ( 12) link_NAG-ASN : bond 0.00458 / 0.23 ( 4) link_NAG-ASN : angle 2.00583 / 1.39 ( 12) =============================================================================== Job complete usr+sys time: 6968.23 seconds wall clock time: 119 minutes 6.15 seconds (7146.15 seconds total)