Starting phenix.real_space_refine on Sat Jul 4 11:05:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7or0_13036/07_2026/7or0_13036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7or0_13036/07_2026/7or0_13036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7or0_13036/07_2026/7or0_13036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7or0_13036/07_2026/7or0_13036.map" model { file = "/net/cci-nas-00/data/ceres_data/7or0_13036/07_2026/7or0_13036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7or0_13036/07_2026/7or0_13036.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7or0_13036/07_2026/7or0_13036.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7or0_13036/07_2026/7or0_13036.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 32 5.49 5 S 144 5.16 5 C 12900 2.51 5 N 3168 2.21 5 O 3620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19869 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 174 Unusual residues: {' CA': 2, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 4.32, per 1000 atoms: 0.22 Number of scatterers: 19869 At special positions: 0 Unit cell: (113.36, 114.45, 148.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 144 16.00 P 32 15.00 O 3620 8.00 N 3168 7.00 C 12900 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=0, 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 A1205 " - " ASN A 753 " " NAG B1205 " - " ASN B 753 " " NAG C1205 " - " ASN C 753 " " NAG D1206 " - " ASN D 753 " " NAG E 1 " - " ASN A 747 " " NAG F 1 " - " ASN B 747 " " NAG G 1 " - " ASN C 747 " " NAG H 1 " - " ASN D 747 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 712.6 milliseconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4568 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 8 sheets defined 71.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 534 Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.559A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.687A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 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 738 removed outlier: 6.231A pdb=" N PHE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 4.291A 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 792 Processing helix chain 'A' and resid 802 through 819 removed outlier: 4.012A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 823 Processing helix chain 'A' and resid 827 through 851 removed outlier: 3.919A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 872 removed outlier: 3.615A pdb=" N VAL A 861 " --> pdb=" O GLY A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 removed outlier: 3.681A pdb=" N ILE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 900 through 911 Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 970 removed outlier: 4.024A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 988 removed outlier: 3.605A pdb=" N GLN A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1039 through 1072 Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 534 Processing helix chain 'B' and resid 550 through 559 removed outlier: 3.559A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 582 through 590 Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 604 through 611 Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.687A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 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 738 removed outlier: 6.231A pdb=" N PHE B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 722 " --> pdb=" O ALA B 718 " (cutoff:3.500A) removed outlier: 4.291A 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 792 Processing helix chain 'B' and resid 802 through 819 removed outlier: 4.012A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 817 " --> pdb=" O THR B 813 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 823 Processing helix chain 'B' and resid 827 through 851 removed outlier: 3.920A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 872 removed outlier: 3.617A pdb=" N VAL B 861 " --> pdb=" O GLY B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 892 removed outlier: 3.680A pdb=" N ILE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 Processing helix chain 'B' and resid 900 through 911 Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 928 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 970 removed outlier: 4.024A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 988 removed outlier: 3.604A pdb=" N GLN B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 Processing helix chain 'B' and resid 1039 through 1072 Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 494 through 503 Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 526 through 534 Processing helix chain 'C' and resid 550 through 559 removed outlier: 3.559A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 582 through 590 Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 604 through 611 Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.687A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 669 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 738 removed outlier: 6.231A pdb=" N PHE C 716 " --> pdb=" O LEU C 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 722 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 4.290A 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 792 Processing helix chain 'C' and resid 802 through 819 removed outlier: 4.012A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 817 " --> pdb=" O THR C 813 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 823 Processing helix chain 'C' and resid 827 through 851 removed outlier: 3.920A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 872 removed outlier: 3.615A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 892 removed outlier: 3.680A pdb=" N ILE C 890 " --> pdb=" O LEU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 Processing helix chain 'C' and resid 900 through 911 Processing helix chain 'C' and resid 912 through 914 No H-bonds generated for 'chain 'C' and resid 912 through 914' Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 928 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 970 removed outlier: 4.024A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 988 removed outlier: 3.604A pdb=" N GLN C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 Processing helix chain 'C' and resid 1039 through 1072 Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 494 through 503 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 534 Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.560A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 582 through 590 Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 604 through 611 Processing helix chain 'D' and resid 621 through 630 Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.687A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 669 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 738 removed outlier: 6.230A pdb=" N PHE D 716 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.291A 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 792 Processing helix chain 'D' and resid 802 through 819 removed outlier: 4.012A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 817 " --> pdb=" O THR D 813 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 819 " --> pdb=" O GLY D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 823 Processing helix chain 'D' and resid 827 through 851 removed outlier: 3.919A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 872 removed outlier: 3.615A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 892 removed outlier: 3.680A pdb=" N ILE D 890 " --> pdb=" O LEU D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 900 through 911 Processing helix chain 'D' and resid 912 through 914 No H-bonds generated for 'chain 'D' and resid 912 through 914' Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 922 through 928 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 970 removed outlier: 4.023A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 988 removed outlier: 3.604A pdb=" N GLN D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 Processing helix chain 'D' and resid 1039 through 1072 Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AA2, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.229A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 642 through 644 Processing sheet with id=AA4, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.229A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 642 through 644 Processing sheet with id=AA6, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.228A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 642 through 644 Processing sheet with id=AA8, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.228A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3339 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: 3.59 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3044 1.29 - 1.42: 5038 1.42 - 1.55: 11882 1.55 - 1.68: 40 1.68 - 1.81: 232 Bond restraints: 20236 Sorted by residual: bond pdb=" C2 0IG B1201 " pdb=" N1 0IG B1201 " ideal model delta sigma weight residual 1.317 1.466 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C2 0IG C1201 " pdb=" N1 0IG C1201 " ideal model delta sigma weight residual 1.317 1.465 -0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C2 0IG A1201 " pdb=" N1 0IG A1201 " ideal model delta sigma weight residual 1.317 1.465 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C2 0IG D1202 " pdb=" N1 0IG D1202 " ideal model delta sigma weight residual 1.317 1.465 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" N6 0IG C1201 " pdb=" N7 0IG C1201 " ideal model delta sigma weight residual 1.161 1.293 -0.132 2.00e-02 2.50e+03 4.33e+01 ... (remaining 20231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 27205 3.62 - 7.25: 179 7.25 - 10.87: 16 10.87 - 14.49: 8 14.49 - 18.12: 4 Bond angle restraints: 27412 Sorted by residual: angle pdb=" C1 0IG B1201 " pdb=" N 0IG B1201 " pdb=" C2 0IG B1201 " ideal model delta sigma weight residual 127.53 109.41 18.12 3.00e+00 1.11e-01 3.65e+01 angle pdb=" C1 0IG A1201 " pdb=" N 0IG A1201 " pdb=" C2 0IG A1201 " ideal model delta sigma weight residual 127.53 109.42 18.11 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C1 0IG C1201 " pdb=" N 0IG C1201 " pdb=" C2 0IG C1201 " ideal model delta sigma weight residual 127.53 109.45 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C1 0IG D1202 " pdb=" N 0IG D1202 " pdb=" C2 0IG D1202 " ideal model delta sigma weight residual 127.53 109.49 18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" C14 0IG A1201 " pdb=" N6 0IG A1201 " pdb=" N7 0IG A1201 " ideal model delta sigma weight residual 130.27 117.66 12.61 3.00e+00 1.11e-01 1.77e+01 ... (remaining 27407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11052 18.00 - 36.00: 668 36.00 - 53.99: 156 53.99 - 71.99: 36 71.99 - 89.99: 16 Dihedral angle restraints: 11928 sinusoidal: 4900 harmonic: 7028 Sorted by residual: dihedral pdb=" CA SER A 602 " pdb=" C SER A 602 " pdb=" N LYS A 603 " pdb=" CA LYS A 603 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA SER C 602 " pdb=" C SER C 602 " pdb=" N LYS C 603 " pdb=" CA LYS C 603 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA SER B 602 " pdb=" C SER B 602 " pdb=" N LYS B 603 " pdb=" CA LYS B 603 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 11925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 3164 1.007 - 2.013: 0 2.013 - 3.019: 0 3.019 - 4.026: 0 4.026 - 5.032: 16 Chirality restraints: 3180 Sorted by residual: chirality pdb=" C5 IHP D1201 " pdb=" C4 IHP D1201 " pdb=" C6 IHP D1201 " pdb=" O15 IHP D1201 " both_signs ideal model delta sigma weight residual False -2.42 2.62 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C5 IHP A1206 " pdb=" C4 IHP A1206 " pdb=" C6 IHP A1206 " pdb=" O15 IHP A1206 " both_signs ideal model delta sigma weight residual False -2.42 2.61 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C5 IHP B1206 " pdb=" C4 IHP B1206 " pdb=" C6 IHP B1206 " pdb=" O15 IHP B1206 " both_signs ideal model delta sigma weight residual False -2.42 2.61 -5.03 2.00e-01 2.50e+01 6.32e+02 ... (remaining 3177 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 0IG A1201 " 0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG A1201 " 0.075 2.00e-02 2.50e+03 pdb=" C12 0IG A1201 " 0.229 2.00e-02 2.50e+03 pdb=" C13 0IG A1201 " 0.082 2.00e-02 2.50e+03 pdb=" C14 0IG A1201 " -0.219 2.00e-02 2.50e+03 pdb=" C15 0IG A1201 " -0.373 2.00e-02 2.50e+03 pdb=" C16 0IG A1201 " -0.227 2.00e-02 2.50e+03 pdb=" N6 0IG A1201 " -0.371 2.00e-02 2.50e+03 pdb=" N7 0IG A1201 " 0.085 2.00e-02 2.50e+03 pdb=" N8 0IG A1201 " 0.496 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG B1201 " -0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG B1201 " -0.075 2.00e-02 2.50e+03 pdb=" C12 0IG B1201 " -0.230 2.00e-02 2.50e+03 pdb=" C13 0IG B1201 " -0.082 2.00e-02 2.50e+03 pdb=" C14 0IG B1201 " 0.219 2.00e-02 2.50e+03 pdb=" C15 0IG B1201 " 0.373 2.00e-02 2.50e+03 pdb=" C16 0IG B1201 " 0.227 2.00e-02 2.50e+03 pdb=" N6 0IG B1201 " 0.371 2.00e-02 2.50e+03 pdb=" N7 0IG B1201 " -0.085 2.00e-02 2.50e+03 pdb=" N8 0IG B1201 " -0.496 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG C1201 " -0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG C1201 " -0.075 2.00e-02 2.50e+03 pdb=" C12 0IG C1201 " -0.230 2.00e-02 2.50e+03 pdb=" C13 0IG C1201 " -0.082 2.00e-02 2.50e+03 pdb=" C14 0IG C1201 " 0.219 2.00e-02 2.50e+03 pdb=" C15 0IG C1201 " 0.373 2.00e-02 2.50e+03 pdb=" C16 0IG C1201 " 0.227 2.00e-02 2.50e+03 pdb=" N6 0IG C1201 " 0.371 2.00e-02 2.50e+03 pdb=" N7 0IG C1201 " -0.085 2.00e-02 2.50e+03 pdb=" N8 0IG C1201 " -0.496 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3288 2.75 - 3.29: 18872 3.29 - 3.83: 30308 3.83 - 4.36: 37949 4.36 - 4.90: 65680 Nonbonded interactions: 156097 Sorted by model distance: nonbonded pdb=" ND2 ASN D 855 " pdb=" O 0IG D1202 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN A 855 " pdb=" O 0IG A1201 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN C 855 " pdb=" O 0IG C1201 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN B 855 " pdb=" O 0IG B1201 " model vdw 2.218 3.120 nonbonded pdb=" O ILE B 916 " pdb=" O HOH B1301 " model vdw 2.270 3.040 ... (remaining 156092 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 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'B' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'C' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'D' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) } 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.270 Find NCS groups from input model: 0.730 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.009 0.149 20248 Z= 0.414 Angle : 0.851 18.117 27448 Z= 0.401 Chirality : 0.354 5.032 3180 Planarity : 0.011 0.273 3296 Dihedral : 13.230 89.988 7360 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer: Outliers : 1.15 % Allowed : 6.99 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.16), residues: 2352 helix: -0.75 (0.12), residues: 1644 sheet: -0.42 (0.58), residues: 68 loop : -2.64 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 996 TYR 0.013 0.002 TYR C 456 PHE 0.012 0.002 PHE A 583 TRP 0.014 0.001 TRP C 832 HIS 0.004 0.001 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00919 / 0.41 (20236) covalent geometry : angle 0.84952 / 0.40 (27412) hydrogen bonds : bond 0.16156 / 11.08 ( 1145) hydrogen bonds : angle 5.14189 / 3.66 ( 3339) link_BETA1-4 : bond 0.00058 / 0.03 ( 4) link_BETA1-4 : angle 1.80335 / 1.18 ( 12) link_NAG-ASN : bond 0.00100 / 0.06 ( 8) link_NAG-ASN : angle 1.54539 / 1.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.746 Fit side-chains REVERT: A 809 TRP cc_start: 0.7826 (t60) cc_final: 0.7617 (t60) REVERT: A 912 MET cc_start: 0.8420 (ttm) cc_final: 0.8146 (ttp) REVERT: B 508 PHE cc_start: 0.9170 (m-80) cc_final: 0.8865 (m-80) REVERT: B 953 MET cc_start: 0.8561 (mmm) cc_final: 0.8354 (mmm) REVERT: C 862 MET cc_start: 0.8879 (mtt) cc_final: 0.8412 (mtt) REVERT: C 912 MET cc_start: 0.8473 (ttm) cc_final: 0.8252 (ttp) REVERT: D 912 MET cc_start: 0.8426 (ttm) cc_final: 0.8153 (ttp) outliers start: 24 outliers final: 9 residues processed: 211 average time/residue: 0.6252 time to fit residues: 148.8715 Evaluate side-chains 177 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A 664 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 619 ASN B 664 GLN B1008 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS C 619 ASN ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 664 GLN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.082249 restraints weight = 27507.049| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.61 r_work: 0.2897 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20248 Z= 0.133 Angle : 0.632 12.536 27448 Z= 0.293 Chirality : 0.045 0.600 3180 Planarity : 0.004 0.049 3296 Dihedral : 8.238 71.576 2835 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.77 % Allowed : 8.29 % Favored : 89.94 % 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: -0.14 (0.18), residues: 2352 helix: 0.59 (0.13), residues: 1664 sheet: 1.84 (0.57), residues: 60 loop : -2.04 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 996 TYR 0.010 0.001 TYR A 456 PHE 0.008 0.001 PHE C 879 TRP 0.012 0.001 TRP D 832 HIS 0.004 0.001 HIS C 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (20236) covalent geometry : angle 0.63019 / 0.29 (27412) hydrogen bonds : bond 0.05874 / 4.07 ( 1145) hydrogen bonds : angle 3.95296 / 2.80 ( 3339) link_BETA1-4 : bond 0.00408 / 0.20 ( 4) link_BETA1-4 : angle 1.18686 / 0.76 ( 12) link_NAG-ASN : bond 0.00233 / 0.16 ( 8) link_NAG-ASN : angle 1.39865 / 1.09 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.804 Fit side-chains REVERT: A 809 TRP cc_start: 0.8106 (t60) cc_final: 0.7875 (t60) REVERT: A 912 MET cc_start: 0.9088 (ttm) cc_final: 0.8852 (ttp) REVERT: A 996 ARG cc_start: 0.8866 (mmm-85) cc_final: 0.8644 (mmm-85) REVERT: B 508 PHE cc_start: 0.9180 (m-80) cc_final: 0.8901 (m-80) REVERT: B 608 CYS cc_start: 0.8967 (m) cc_final: 0.8695 (m) REVERT: B 651 CYS cc_start: 0.8443 (m) cc_final: 0.8166 (t) REVERT: C 912 MET cc_start: 0.9103 (ttm) cc_final: 0.8853 (ttp) REVERT: C 996 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8544 (mmm-85) REVERT: C 1063 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: D 912 MET cc_start: 0.9107 (ttm) cc_final: 0.8876 (ttp) REVERT: D 1063 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8152 (mp0) outliers start: 37 outliers final: 16 residues processed: 223 average time/residue: 0.5735 time to fit residues: 145.1779 Evaluate side-chains 193 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 1063 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 134 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 664 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN B1008 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN ** D1047 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 = 0.3553 r_free = 0.3553 target = 0.119584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.079179 restraints weight = 27728.799| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.54 r_work: 0.2783 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20248 Z= 0.224 Angle : 0.620 8.565 27448 Z= 0.303 Chirality : 0.043 0.184 3180 Planarity : 0.004 0.053 3296 Dihedral : 8.579 68.954 2833 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.83 % Allowed : 8.24 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2352 helix: 1.00 (0.13), residues: 1676 sheet: 0.96 (0.66), residues: 68 loop : -1.79 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 996 TYR 0.010 0.002 TYR B 456 PHE 0.012 0.002 PHE B 583 TRP 0.011 0.001 TRP D 832 HIS 0.004 0.001 HIS C 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.22 (20236) covalent geometry : angle 0.61797 / 0.30 (27412) hydrogen bonds : bond 0.06747 / 4.68 ( 1145) hydrogen bonds : angle 3.94624 / 2.80 ( 3339) link_BETA1-4 : bond 0.00328 / 0.17 ( 4) link_BETA1-4 : angle 1.37760 / 0.87 ( 12) link_NAG-ASN : bond 0.00141 / 0.10 ( 8) link_NAG-ASN : angle 1.39195 / 1.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.759 Fit side-chains REVERT: A 809 TRP cc_start: 0.8039 (t60) cc_final: 0.7800 (t60) REVERT: A 912 MET cc_start: 0.9116 (ttm) cc_final: 0.8859 (ttp) REVERT: A 992 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8662 (tm) REVERT: A 1063 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: B 608 CYS cc_start: 0.8927 (m) cc_final: 0.8695 (m) REVERT: B 651 CYS cc_start: 0.8467 (m) cc_final: 0.8180 (t) REVERT: B 996 ARG cc_start: 0.9002 (mmm-85) cc_final: 0.8730 (mmm-85) REVERT: B 1063 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: C 912 MET cc_start: 0.9111 (ttm) cc_final: 0.8847 (ttp) REVERT: C 992 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8619 (tm) REVERT: C 1063 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: D 651 CYS cc_start: 0.8239 (m) cc_final: 0.7920 (m) REVERT: D 912 MET cc_start: 0.9115 (ttm) cc_final: 0.8862 (ttp) REVERT: D 1063 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8080 (mp0) outliers start: 59 outliers final: 26 residues processed: 237 average time/residue: 0.5907 time to fit residues: 157.9810 Evaluate side-chains 218 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 1063 GLU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 875 VAL Chi-restraints excluded: chain D residue 1063 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 219 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1047 GLN B 664 GLN B1008 ASN B1047 GLN C1047 GLN D 664 GLN D1047 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.083024 restraints weight = 27471.692| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.53 r_work: 0.2894 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20248 Z= 0.110 Angle : 0.505 9.827 27448 Z= 0.249 Chirality : 0.038 0.182 3180 Planarity : 0.004 0.048 3296 Dihedral : 8.212 68.116 2833 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.16 % Allowed : 9.67 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2352 helix: 1.34 (0.13), residues: 1692 sheet: 2.50 (0.63), residues: 60 loop : -1.59 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1050 TYR 0.010 0.001 TYR A 456 PHE 0.008 0.001 PHE D 877 TRP 0.010 0.001 TRP D 832 HIS 0.004 0.001 HIS B 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (20236) covalent geometry : angle 0.50335 / 0.25 (27412) hydrogen bonds : bond 0.04810 / 3.34 ( 1145) hydrogen bonds : angle 3.67927 / 2.61 ( 3339) link_BETA1-4 : bond 0.00347 / 0.17 ( 4) link_BETA1-4 : angle 1.24385 / 0.79 ( 12) link_NAG-ASN : bond 0.00285 / 0.20 ( 8) link_NAG-ASN : angle 1.33331 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.789 Fit side-chains REVERT: A 607 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: A 992 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8718 (tm) REVERT: B 651 CYS cc_start: 0.8494 (m) cc_final: 0.8206 (t) REVERT: B 744 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8574 (mmm) REVERT: B 833 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: C 664 GLN cc_start: 0.8808 (pt0) cc_final: 0.8581 (pt0) REVERT: C 992 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8721 (tm) REVERT: C 996 ARG cc_start: 0.8894 (mmm-85) cc_final: 0.8686 (mmm-85) REVERT: D 607 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: D 651 CYS cc_start: 0.8315 (m) cc_final: 0.8011 (m) REVERT: D 920 GLU cc_start: 0.8724 (tt0) cc_final: 0.8109 (mp0) outliers start: 45 outliers final: 16 residues processed: 230 average time/residue: 0.5940 time to fit residues: 154.1924 Evaluate side-chains 203 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 833 GLN Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 18 optimal weight: 2.9990 chunk 219 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 221 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 HIS A 664 GLN B 494 HIS B 664 GLN C 494 HIS D 494 HIS D 664 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084255 restraints weight = 27413.360| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.53 r_work: 0.2924 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20248 Z= 0.102 Angle : 0.498 10.505 27448 Z= 0.243 Chirality : 0.038 0.181 3180 Planarity : 0.004 0.046 3296 Dihedral : 7.787 64.695 2833 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.16 % Allowed : 10.20 % Favored : 87.64 % 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: 1.35 (0.18), residues: 2352 helix: 1.65 (0.13), residues: 1676 sheet: 0.65 (0.57), residues: 100 loop : -1.31 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 996 TYR 0.011 0.001 TYR B 456 PHE 0.008 0.001 PHE B 877 TRP 0.008 0.001 TRP D 832 HIS 0.002 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (20236) covalent geometry : angle 0.49658 / 0.24 (27412) hydrogen bonds : bond 0.04319 / 3.00 ( 1145) hydrogen bonds : angle 3.50852 / 2.49 ( 3339) link_BETA1-4 : bond 0.00337 / 0.17 ( 4) link_BETA1-4 : angle 1.24635 / 0.81 ( 12) link_NAG-ASN : bond 0.00282 / 0.19 ( 8) link_NAG-ASN : angle 1.29580 / 1.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.748 Fit side-chains REVERT: A 607 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: A 992 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8620 (tm) REVERT: B 651 CYS cc_start: 0.8525 (m) cc_final: 0.8260 (t) REVERT: B 664 GLN cc_start: 0.8822 (pt0) cc_final: 0.7774 (pm20) REVERT: B 1059 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 664 GLN cc_start: 0.8802 (pt0) cc_final: 0.8571 (pt0) REVERT: C 920 GLU cc_start: 0.8685 (tt0) cc_final: 0.8153 (mp0) REVERT: C 992 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8708 (tm) REVERT: D 607 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: D 651 CYS cc_start: 0.8498 (m) cc_final: 0.8227 (m) REVERT: D 664 GLN cc_start: 0.8678 (pt0) cc_final: 0.8284 (pm20) REVERT: D 920 GLU cc_start: 0.8711 (tt0) cc_final: 0.8128 (mp0) outliers start: 45 outliers final: 18 residues processed: 225 average time/residue: 0.6457 time to fit residues: 163.7434 Evaluate side-chains 207 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 839 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 940 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.081403 restraints weight = 27402.982| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.51 r_work: 0.2872 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20248 Z= 0.163 Angle : 0.535 11.467 27448 Z= 0.262 Chirality : 0.040 0.179 3180 Planarity : 0.004 0.048 3296 Dihedral : 7.921 62.456 2831 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.01 % Allowed : 11.02 % Favored : 86.97 % 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: 1.36 (0.18), residues: 2352 helix: 1.60 (0.13), residues: 1696 sheet: 0.57 (0.57), residues: 100 loop : -1.21 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 996 TYR 0.012 0.001 TYR A 456 PHE 0.009 0.001 PHE B 841 TRP 0.009 0.001 TRP A 832 HIS 0.004 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 (20236) covalent geometry : angle 0.53314 / 0.26 (27412) hydrogen bonds : bond 0.05307 / 3.68 ( 1145) hydrogen bonds : angle 3.64831 / 2.59 ( 3339) link_BETA1-4 : bond 0.00273 / 0.14 ( 4) link_BETA1-4 : angle 1.28065 / 0.82 ( 12) link_NAG-ASN : bond 0.00193 / 0.13 ( 8) link_NAG-ASN : angle 1.20612 / 0.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.785 Fit side-chains REVERT: B 651 CYS cc_start: 0.8536 (m) cc_final: 0.8266 (t) REVERT: B 664 GLN cc_start: 0.8758 (pt0) cc_final: 0.7818 (pm20) REVERT: B 920 GLU cc_start: 0.8653 (tt0) cc_final: 0.8117 (mp0) REVERT: B 1059 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8298 (mt-10) REVERT: C 920 GLU cc_start: 0.8656 (tt0) cc_final: 0.8092 (mp0) REVERT: C 992 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8650 (tm) REVERT: D 651 CYS cc_start: 0.8390 (m) cc_final: 0.8086 (m) REVERT: D 664 GLN cc_start: 0.8696 (pt0) cc_final: 0.7832 (pm20) REVERT: D 920 GLU cc_start: 0.8674 (tt0) cc_final: 0.8132 (mp0) outliers start: 42 outliers final: 25 residues processed: 218 average time/residue: 0.6573 time to fit residues: 161.1985 Evaluate side-chains 212 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 864 GLU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 864 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 115 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 215 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084156 restraints weight = 27357.305| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.55 r_work: 0.2924 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20248 Z= 0.103 Angle : 0.493 11.244 27448 Z= 0.240 Chirality : 0.038 0.178 3180 Planarity : 0.004 0.046 3296 Dihedral : 7.589 60.927 2829 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.58 % Allowed : 11.83 % Favored : 86.59 % 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: 1.55 (0.18), residues: 2352 helix: 1.78 (0.13), residues: 1676 sheet: 0.63 (0.58), residues: 100 loop : -1.15 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 996 TYR 0.010 0.001 TYR A 456 PHE 0.008 0.001 PHE B 877 TRP 0.009 0.001 TRP D 832 HIS 0.002 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (20236) covalent geometry : angle 0.49101 / 0.24 (27412) hydrogen bonds : bond 0.04248 / 2.95 ( 1145) hydrogen bonds : angle 3.50561 / 2.49 ( 3339) link_BETA1-4 : bond 0.00339 / 0.17 ( 4) link_BETA1-4 : angle 1.21089 / 0.79 ( 12) link_NAG-ASN : bond 0.00297 / 0.20 ( 8) link_NAG-ASN : angle 1.19891 / 0.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.622 Fit side-chains REVERT: A 607 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: B 651 CYS cc_start: 0.8531 (m) cc_final: 0.8276 (t) REVERT: B 664 GLN cc_start: 0.8874 (pt0) cc_final: 0.8376 (pm20) REVERT: B 920 GLU cc_start: 0.8684 (tt0) cc_final: 0.8220 (mp0) REVERT: B 1059 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8399 (mt-10) REVERT: C 571 ASN cc_start: 0.8381 (m-40) cc_final: 0.8142 (t0) REVERT: C 920 GLU cc_start: 0.8701 (tt0) cc_final: 0.8176 (mp0) REVERT: D 651 CYS cc_start: 0.8482 (m) cc_final: 0.8221 (m) REVERT: D 664 GLN cc_start: 0.8785 (pt0) cc_final: 0.8414 (pm20) REVERT: D 920 GLU cc_start: 0.8716 (tt0) cc_final: 0.8192 (mp0) outliers start: 33 outliers final: 18 residues processed: 222 average time/residue: 0.6365 time to fit residues: 159.2824 Evaluate side-chains 202 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 864 GLU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 144 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082128 restraints weight = 27429.947| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.52 r_work: 0.2886 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20248 Z= 0.145 Angle : 0.525 11.758 27448 Z= 0.256 Chirality : 0.039 0.178 3180 Planarity : 0.004 0.046 3296 Dihedral : 7.649 58.587 2829 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.63 % Allowed : 12.31 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.18), residues: 2352 helix: 1.75 (0.13), residues: 1676 sheet: 0.61 (0.58), residues: 100 loop : -1.08 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1050 TYR 0.012 0.001 TYR C 456 PHE 0.008 0.001 PHE B 841 TRP 0.008 0.001 TRP D 832 HIS 0.004 0.001 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (20236) covalent geometry : angle 0.52394 / 0.26 (27412) hydrogen bonds : bond 0.05031 / 3.49 ( 1145) hydrogen bonds : angle 3.58839 / 2.55 ( 3339) link_BETA1-4 : bond 0.00275 / 0.14 ( 4) link_BETA1-4 : angle 1.26741 / 0.81 ( 12) link_NAG-ASN : bond 0.00206 / 0.14 ( 8) link_NAG-ASN : angle 1.16529 / 0.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: B 651 CYS cc_start: 0.8524 (m) cc_final: 0.8268 (t) REVERT: B 664 GLN cc_start: 0.8862 (pt0) cc_final: 0.7887 (pm20) REVERT: B 920 GLU cc_start: 0.8644 (tt0) cc_final: 0.8059 (mp0) REVERT: B 1059 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8142 (mt-10) REVERT: B 1063 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: C 571 ASN cc_start: 0.8451 (m-40) cc_final: 0.8175 (t0) REVERT: C 920 GLU cc_start: 0.8663 (tt0) cc_final: 0.8117 (mp0) REVERT: D 651 CYS cc_start: 0.8505 (m) cc_final: 0.8247 (m) REVERT: D 664 GLN cc_start: 0.8764 (pt0) cc_final: 0.8362 (pm20) REVERT: D 920 GLU cc_start: 0.8673 (tt0) cc_final: 0.8097 (mp0) outliers start: 34 outliers final: 26 residues processed: 211 average time/residue: 0.6771 time to fit residues: 160.5688 Evaluate side-chains 213 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 1063 GLU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 864 GLU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 193 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 131 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.0070 chunk 201 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 492 ASN D 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085082 restraints weight = 27258.719| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.54 r_work: 0.2935 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20248 Z= 0.098 Angle : 0.493 11.046 27448 Z= 0.239 Chirality : 0.038 0.176 3180 Planarity : 0.004 0.045 3296 Dihedral : 7.256 59.263 2829 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.44 % Allowed : 12.84 % Favored : 85.73 % 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: 1.70 (0.18), residues: 2352 helix: 1.87 (0.13), residues: 1676 sheet: 0.69 (0.59), residues: 100 loop : -1.02 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1050 TYR 0.010 0.001 TYR C 456 PHE 0.007 0.001 PHE C 877 TRP 0.009 0.001 TRP D 832 HIS 0.002 0.000 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (20236) covalent geometry : angle 0.49167 / 0.24 (27412) hydrogen bonds : bond 0.04002 / 2.78 ( 1145) hydrogen bonds : angle 3.45034 / 2.45 ( 3339) link_BETA1-4 : bond 0.00501 / 0.25 ( 4) link_BETA1-4 : angle 1.22927 / 0.78 ( 12) link_NAG-ASN : bond 0.00311 / 0.21 ( 8) link_NAG-ASN : angle 1.15907 / 0.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 571 ASN cc_start: 0.8689 (t0) cc_final: 0.8415 (t0) REVERT: A 607 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: A 996 ARG cc_start: 0.8938 (mmm-85) cc_final: 0.8139 (mpt-90) REVERT: B 571 ASN cc_start: 0.8705 (t0) cc_final: 0.8474 (t0) REVERT: B 651 CYS cc_start: 0.8517 (m) cc_final: 0.8290 (t) REVERT: B 664 GLN cc_start: 0.8829 (pt0) cc_final: 0.7947 (pm20) REVERT: B 920 GLU cc_start: 0.8680 (tt0) cc_final: 0.8206 (mp0) REVERT: B 1059 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8378 (mt-10) REVERT: C 571 ASN cc_start: 0.8258 (m-40) cc_final: 0.8017 (t0) REVERT: C 920 GLU cc_start: 0.8704 (tt0) cc_final: 0.8211 (mp0) REVERT: D 651 CYS cc_start: 0.8495 (m) cc_final: 0.8246 (m) REVERT: D 664 GLN cc_start: 0.8784 (pt0) cc_final: 0.8371 (pm20) REVERT: D 920 GLU cc_start: 0.8722 (tt0) cc_final: 0.8207 (mp0) outliers start: 30 outliers final: 21 residues processed: 214 average time/residue: 0.6130 time to fit residues: 148.4291 Evaluate side-chains 203 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 864 GLU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082366 restraints weight = 27461.544| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.52 r_work: 0.2891 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20248 Z= 0.144 Angle : 0.541 11.356 27448 Z= 0.260 Chirality : 0.039 0.174 3180 Planarity : 0.004 0.047 3296 Dihedral : 7.352 58.668 2829 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.29 % Allowed : 13.07 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.18), residues: 2352 helix: 1.83 (0.13), residues: 1676 sheet: 0.69 (0.59), residues: 100 loop : -0.96 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1050 TYR 0.011 0.001 TYR A 456 PHE 0.012 0.001 PHE D 877 TRP 0.009 0.001 TRP B 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (20236) covalent geometry : angle 0.53982 / 0.26 (27412) hydrogen bonds : bond 0.04915 / 3.41 ( 1145) hydrogen bonds : angle 3.55657 / 2.52 ( 3339) link_BETA1-4 : bond 0.00330 / 0.16 ( 4) link_BETA1-4 : angle 1.26708 / 0.81 ( 12) link_NAG-ASN : bond 0.00212 / 0.15 ( 8) link_NAG-ASN : angle 1.13722 / 0.92 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 571 ASN cc_start: 0.8728 (t0) cc_final: 0.8511 (t0) REVERT: B 651 CYS cc_start: 0.8531 (m) cc_final: 0.8310 (t) REVERT: B 664 GLN cc_start: 0.8844 (pt0) cc_final: 0.8393 (pm20) REVERT: B 920 GLU cc_start: 0.8663 (tt0) cc_final: 0.8115 (mp0) REVERT: B 1059 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8405 (mt-10) REVERT: C 571 ASN cc_start: 0.8333 (m-40) cc_final: 0.8103 (t0) REVERT: C 920 GLU cc_start: 0.8672 (tt0) cc_final: 0.8154 (mp0) REVERT: D 651 CYS cc_start: 0.8471 (m) cc_final: 0.8220 (m) REVERT: D 664 GLN cc_start: 0.8771 (pt0) cc_final: 0.8390 (pm20) REVERT: D 920 GLU cc_start: 0.8694 (tt0) cc_final: 0.8152 (mp0) outliers start: 27 outliers final: 22 residues processed: 206 average time/residue: 0.6920 time to fit residues: 160.2643 Evaluate side-chains 205 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 864 GLU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 130 optimal weight: 0.0020 chunk 179 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084455 restraints weight = 27474.434| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.55 r_work: 0.2934 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20248 Z= 0.101 Angle : 0.503 11.638 27448 Z= 0.242 Chirality : 0.038 0.173 3180 Planarity : 0.004 0.046 3296 Dihedral : 7.085 56.878 2829 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.25 % Allowed : 13.17 % Favored : 85.58 % 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: 1.79 (0.18), residues: 2352 helix: 1.90 (0.13), residues: 1680 sheet: 0.79 (0.60), residues: 100 loop : -0.87 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1050 TYR 0.011 0.001 TYR B 456 PHE 0.011 0.001 PHE D 877 TRP 0.010 0.001 TRP B 832 HIS 0.003 0.000 HIS C 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (20236) covalent geometry : angle 0.50153 / 0.24 (27412) hydrogen bonds : bond 0.04118 / 2.86 ( 1145) hydrogen bonds : angle 3.46537 / 2.46 ( 3339) link_BETA1-4 : bond 0.00373 / 0.19 ( 4) link_BETA1-4 : angle 1.19576 / 0.77 ( 12) link_NAG-ASN : bond 0.00292 / 0.20 ( 8) link_NAG-ASN : angle 1.14494 / 0.94 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7099.07 seconds wall clock time: 121 minutes 40.35 seconds (7300.35 seconds total)