Starting phenix.real_space_refine on Thu Mar 5 07:34:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7or0_13036/03_2026/7or0_13036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7or0_13036/03_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_13036/03_2026/7or0_13036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7or0_13036/03_2026/7or0_13036.map" model { file = "/net/cci-nas-00/data/ceres_data/7or0_13036/03_2026/7or0_13036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7or0_13036/03_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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: 18 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: 18 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: 18 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: 18 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: 4.82, per 1000 atoms: 0.24 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: 1.59 Conformation dependent library (CDL) restraints added in 956.5 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: 0.76 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: 3.46 Time building geometry restraints manager: 2.02 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 - 23.95: 11726 23.95 - 47.90: 514 47.90 - 71.86: 88 71.86 - 95.81: 20 95.81 - 119.76: 48 Dihedral angle restraints: 12396 sinusoidal: 5368 harmonic: 7028 Sorted by residual: dihedral pdb=" C4 IHP D1201 " pdb=" C2 IHP D1201 " pdb=" C3 IHP D1201 " pdb=" O12 IHP D1201 " ideal model delta sinusoidal sigma weight residual 60.90 -179.34 -119.76 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C4 IHP C1206 " pdb=" C2 IHP C1206 " pdb=" C3 IHP C1206 " pdb=" O12 IHP C1206 " ideal model delta sinusoidal sigma weight residual 60.90 -179.35 -119.75 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C6 IHP D1201 " pdb=" C1 IHP D1201 " pdb=" C2 IHP D1201 " pdb=" O12 IHP D1201 " ideal model delta sinusoidal sigma weight residual 61.05 -179.20 -119.75 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 12393 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.360 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 16.304 119.760 7828 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 covalent geometry : bond 0.00919 (20236) covalent geometry : angle 0.84952 (27412) hydrogen bonds : bond 0.16156 ( 1145) hydrogen bonds : angle 5.14189 ( 3339) link_BETA1-4 : bond 0.00058 ( 4) link_BETA1-4 : angle 1.80335 ( 12) link_NAG-ASN : bond 0.00100 ( 8) link_NAG-ASN : angle 1.54539 ( 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 : 0.681 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: 0.6621 time to fit residues: 156.5789 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 : 0.735 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3596 r_free = 0.3596 target = 0.123185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082918 restraints weight = 27230.742| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.53 r_work: 0.2873 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1074 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= 0.135 Angle : 0.625 12.158 27448 Z= 0.292 Chirality : 0.044 0.498 3180 Planarity : 0.004 0.049 3296 Dihedral : 9.534 74.035 3303 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.72 % Allowed : 8.43 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2352 helix: 0.58 (0.13), residues: 1664 sheet: 1.82 (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 covalent geometry : bond 0.00283 (20236) covalent geometry : angle 0.62402 (27412) hydrogen bonds : bond 0.05878 ( 1145) hydrogen bonds : angle 3.95653 ( 3339) link_BETA1-4 : bond 0.00351 ( 4) link_BETA1-4 : angle 1.00170 ( 12) link_NAG-ASN : bond 0.00225 ( 8) link_NAG-ASN : angle 1.38314 ( 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 236 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.646 Fit side-chains REVERT: A 809 TRP cc_start: 0.8082 (t60) cc_final: 0.7850 (t60) REVERT: A 912 MET cc_start: 0.9081 (ttm) cc_final: 0.8846 (ttp) REVERT: A 996 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8613 (mmm-85) REVERT: B 508 PHE cc_start: 0.9177 (m-80) cc_final: 0.8898 (m-80) REVERT: B 608 CYS cc_start: 0.8946 (m) cc_final: 0.8667 (m) REVERT: B 651 CYS cc_start: 0.8433 (m) cc_final: 0.8149 (t) REVERT: C 912 MET cc_start: 0.9097 (ttm) cc_final: 0.8848 (ttp) REVERT: C 996 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8515 (mmm-85) REVERT: C 1063 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: D 912 MET cc_start: 0.9100 (ttm) cc_final: 0.8869 (ttp) REVERT: D 1063 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8134 (mp0) outliers start: 36 outliers final: 16 residues processed: 222 average time/residue: 0.6081 time to fit residues: 152.2916 Evaluate side-chains 195 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 6.9990 chunk 135 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 211 optimal weight: 0.4980 chunk 200 optimal weight: 0.0010 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN A1047 GLN B 664 GLN B1047 GLN C 664 GLN C1047 GLN D 664 GLN D1047 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081706 restraints weight = 27583.846| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.53 r_work: 0.2872 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1518 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= 0.151 Angle : 0.551 8.953 27448 Z= 0.270 Chirality : 0.041 0.188 3180 Planarity : 0.004 0.051 3296 Dihedral : 8.837 71.166 3301 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.49 % Allowed : 8.62 % Favored : 88.89 % 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: 0.60 (0.18), residues: 2352 helix: 1.15 (0.13), residues: 1668 sheet: 2.31 (0.62), residues: 60 loop : -1.83 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 996 TYR 0.010 0.001 TYR A 456 PHE 0.009 0.001 PHE B 583 TRP 0.011 0.001 TRP D 832 HIS 0.003 0.001 HIS C 983 Details of bonding type rmsd covalent geometry : bond 0.00363 (20236) covalent geometry : angle 0.54951 (27412) hydrogen bonds : bond 0.05610 ( 1145) hydrogen bonds : angle 3.76931 ( 3339) link_BETA1-4 : bond 0.00315 ( 4) link_BETA1-4 : angle 1.22037 ( 12) link_NAG-ASN : bond 0.00225 ( 8) link_NAG-ASN : angle 1.36555 ( 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 248 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 0.764 Fit side-chains REVERT: A 809 TRP cc_start: 0.8127 (t60) cc_final: 0.7896 (t60) REVERT: A 912 MET cc_start: 0.9119 (ttm) cc_final: 0.8900 (ttp) REVERT: A 920 GLU cc_start: 0.8687 (tt0) cc_final: 0.8161 (mp0) REVERT: A 996 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8774 (mmm-85) REVERT: B 608 CYS cc_start: 0.8936 (m) cc_final: 0.8704 (m) REVERT: B 651 CYS cc_start: 0.8473 (m) cc_final: 0.8211 (t) REVERT: B 721 MET cc_start: 0.8259 (mmp) cc_final: 0.8028 (mmt) REVERT: C 992 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8748 (tm) REVERT: C 1063 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: D 651 CYS cc_start: 0.8299 (m) cc_final: 0.7994 (m) REVERT: D 912 MET cc_start: 0.9108 (ttm) cc_final: 0.8888 (ttp) REVERT: D 1059 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8327 (mt-10) REVERT: D 1063 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8132 (mp0) outliers start: 52 outliers final: 21 residues processed: 235 average time/residue: 0.6101 time to fit residues: 162.0921 Evaluate side-chains 209 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 839 VAL 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 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: 1.9990 chunk 59 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 147 optimal weight: 0.0170 chunk 116 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 206 optimal weight: 0.0770 chunk 104 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS B 494 HIS B 664 GLN B1008 ASN C 494 HIS C 664 GLN D 494 HIS D 664 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083566 restraints weight = 27523.616| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.53 r_work: 0.2908 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20248 Z= 0.114 Angle : 0.497 10.377 27448 Z= 0.245 Chirality : 0.038 0.190 3180 Planarity : 0.004 0.048 3296 Dihedral : 8.427 68.417 3301 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: 1.08 (0.18), residues: 2352 helix: 1.48 (0.13), residues: 1668 sheet: 2.50 (0.63), residues: 60 loop : -1.59 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 996 TYR 0.011 0.001 TYR A 456 PHE 0.008 0.001 PHE D 877 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd covalent geometry : bond 0.00259 (20236) covalent geometry : angle 0.49502 (27412) hydrogen bonds : bond 0.04650 ( 1145) hydrogen bonds : angle 3.58775 ( 3339) link_BETA1-4 : bond 0.00382 ( 4) link_BETA1-4 : angle 1.16667 ( 12) link_NAG-ASN : bond 0.00310 ( 8) link_NAG-ASN : angle 1.32611 ( 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 244 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.730 Fit side-chains REVERT: A 920 GLU cc_start: 0.8705 (tt0) cc_final: 0.8092 (mp0) REVERT: B 651 CYS cc_start: 0.8458 (m) cc_final: 0.8220 (t) REVERT: B 721 MET cc_start: 0.8254 (mmp) cc_final: 0.7993 (mmt) REVERT: C 996 ARG cc_start: 0.8919 (mmm-85) cc_final: 0.8718 (mmm-85) REVERT: C 1042 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7040 (ppp) REVERT: D 607 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: D 651 CYS cc_start: 0.8352 (m) cc_final: 0.8043 (m) REVERT: D 920 GLU cc_start: 0.8691 (tt0) cc_final: 0.8156 (mp0) outliers start: 45 outliers final: 17 residues processed: 232 average time/residue: 0.6229 time to fit residues: 162.5413 Evaluate side-chains 200 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR 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 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1042 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 18 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 155 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 221 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 664 GLN B1008 ASN D 664 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084315 restraints weight = 27444.214| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.54 r_work: 0.2871 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2035 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= 0.105 Angle : 0.501 10.700 27448 Z= 0.243 Chirality : 0.038 0.190 3180 Planarity : 0.004 0.046 3296 Dihedral : 8.095 65.480 3299 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.01 % Allowed : 10.54 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.18), residues: 2352 helix: 1.70 (0.13), residues: 1668 sheet: 1.54 (0.69), residues: 68 loop : -1.38 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 996 TYR 0.011 0.001 TYR B 456 PHE 0.008 0.001 PHE D 877 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS B 481 Details of bonding type rmsd covalent geometry : bond 0.00232 (20236) covalent geometry : angle 0.49889 (27412) hydrogen bonds : bond 0.04370 ( 1145) hydrogen bonds : angle 3.50032 ( 3339) link_BETA1-4 : bond 0.00409 ( 4) link_BETA1-4 : angle 1.20667 ( 12) link_NAG-ASN : bond 0.00306 ( 8) link_NAG-ASN : angle 1.30504 ( 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 234 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.715 Fit side-chains REVERT: A 607 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: A 920 GLU cc_start: 0.8643 (tt0) cc_final: 0.7983 (mp0) REVERT: B 651 CYS cc_start: 0.8441 (m) cc_final: 0.8215 (t) REVERT: B 664 GLN cc_start: 0.8819 (pt0) cc_final: 0.7713 (pm20) REVERT: C 664 GLN cc_start: 0.8759 (pt0) cc_final: 0.8482 (pt0) REVERT: C 992 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8621 (tm) REVERT: C 1042 MET cc_start: 0.7268 (ptt) cc_final: 0.7036 (ppp) REVERT: D 651 CYS cc_start: 0.8439 (m) cc_final: 0.8150 (m) REVERT: D 664 GLN cc_start: 0.8733 (pt0) cc_final: 0.8162 (pm20) REVERT: D 920 GLU cc_start: 0.8663 (tt0) cc_final: 0.8036 (mp0) outliers start: 42 outliers final: 18 residues processed: 223 average time/residue: 0.6383 time to fit residues: 159.8282 Evaluate side-chains 200 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 912 MET 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 992 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081837 restraints weight = 27389.848| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.52 r_work: 0.2878 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20248 Z= 0.149 Angle : 0.521 10.339 27448 Z= 0.256 Chirality : 0.039 0.189 3180 Planarity : 0.004 0.047 3296 Dihedral : 8.191 63.036 3299 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.01 % Allowed : 10.92 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2352 helix: 1.68 (0.13), residues: 1672 sheet: 0.53 (0.57), residues: 100 loop : -1.27 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 996 TYR 0.011 0.001 TYR A 456 PHE 0.008 0.001 PHE D 583 TRP 0.009 0.001 TRP D 832 HIS 0.004 0.001 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00365 (20236) covalent geometry : angle 0.51947 (27412) hydrogen bonds : bond 0.05181 ( 1145) hydrogen bonds : angle 3.61073 ( 3339) link_BETA1-4 : bond 0.00339 ( 4) link_BETA1-4 : angle 1.25275 ( 12) link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 1.23228 ( 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 232 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.776 Fit side-chains REVERT: A 920 GLU cc_start: 0.8662 (tt0) cc_final: 0.8117 (mp0) REVERT: B 651 CYS cc_start: 0.8534 (m) cc_final: 0.8270 (t) REVERT: B 664 GLN cc_start: 0.8844 (pt0) cc_final: 0.8340 (pm20) REVERT: B 920 GLU cc_start: 0.8677 (tt0) cc_final: 0.8222 (mp0) REVERT: B 1059 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 1063 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: C 920 GLU cc_start: 0.8651 (tt0) cc_final: 0.8112 (mp0) REVERT: C 992 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8681 (tm) REVERT: D 651 CYS cc_start: 0.8496 (m) cc_final: 0.8222 (m) REVERT: D 664 GLN cc_start: 0.8838 (pt0) cc_final: 0.8374 (pm20) REVERT: D 920 GLU cc_start: 0.8666 (tt0) cc_final: 0.8141 (mp0) outliers start: 42 outliers final: 25 residues processed: 218 average time/residue: 0.6293 time to fit residues: 154.5113 Evaluate side-chains 211 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 A residue 864 GLU Chi-restraints excluded: chain A residue 875 VAL 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 912 MET Chi-restraints excluded: chain B residue 1063 GLU 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 875 VAL Chi-restraints excluded: chain C residue 992 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083012 restraints weight = 27350.692| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.51 r_work: 0.2897 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20248 Z= 0.119 Angle : 0.501 9.311 27448 Z= 0.246 Chirality : 0.038 0.187 3180 Planarity : 0.004 0.046 3296 Dihedral : 8.043 61.403 3299 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.77 % Allowed : 11.69 % Favored : 86.54 % 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: 1.50 (0.18), residues: 2352 helix: 1.78 (0.13), residues: 1668 sheet: 0.55 (0.58), residues: 100 loop : -1.25 (0.26), residues: 584 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 0.008 0.001 PHE B 877 TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00277 (20236) covalent geometry : angle 0.49946 (27412) hydrogen bonds : bond 0.04647 ( 1145) hydrogen bonds : angle 3.55941 ( 3339) link_BETA1-4 : bond 0.00350 ( 4) link_BETA1-4 : angle 1.24249 ( 12) link_NAG-ASN : bond 0.00281 ( 8) link_NAG-ASN : angle 1.23348 ( 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 228 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.758 Fit side-chains REVERT: A 607 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: A 920 GLU cc_start: 0.8693 (tt0) cc_final: 0.8151 (mp0) REVERT: B 651 CYS cc_start: 0.8528 (m) cc_final: 0.8278 (t) REVERT: B 664 GLN cc_start: 0.8845 (pt0) cc_final: 0.7891 (pm20) REVERT: B 920 GLU cc_start: 0.8672 (tt0) cc_final: 0.8213 (mp0) REVERT: B 1059 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 571 ASN cc_start: 0.8440 (m-40) cc_final: 0.8185 (t0) REVERT: C 721 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7957 (mmt) REVERT: C 920 GLU cc_start: 0.8668 (tt0) cc_final: 0.8136 (mp0) REVERT: D 651 CYS cc_start: 0.8517 (m) cc_final: 0.8255 (m) REVERT: D 664 GLN cc_start: 0.8860 (pt0) cc_final: 0.8396 (pm20) REVERT: D 920 GLU cc_start: 0.8695 (tt0) cc_final: 0.8145 (mp0) outliers start: 37 outliers final: 21 residues processed: 218 average time/residue: 0.6458 time to fit residues: 157.5549 Evaluate side-chains 208 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 562 LYS 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 912 MET 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 721 MET Chi-restraints excluded: chain C residue 785 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 144 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 940 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.081896 restraints weight = 27419.281| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.52 r_work: 0.2884 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20248 Z= 0.144 Angle : 0.519 11.930 27448 Z= 0.255 Chirality : 0.039 0.185 3180 Planarity : 0.004 0.047 3296 Dihedral : 8.027 58.926 3297 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.44 % Allowed : 12.12 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.18), residues: 2352 helix: 1.73 (0.13), residues: 1676 sheet: 0.57 (0.58), residues: 100 loop : -1.12 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1050 TYR 0.012 0.001 TYR B 456 PHE 0.009 0.001 PHE B 877 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS C 983 Details of bonding type rmsd covalent geometry : bond 0.00350 (20236) covalent geometry : angle 0.51712 (27412) hydrogen bonds : bond 0.05065 ( 1145) hydrogen bonds : angle 3.60918 ( 3339) link_BETA1-4 : bond 0.00237 ( 4) link_BETA1-4 : angle 1.27505 ( 12) link_NAG-ASN : bond 0.00240 ( 8) link_NAG-ASN : angle 1.19767 ( 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 222 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.739 Fit side-chains REVERT: A 920 GLU cc_start: 0.8672 (tt0) cc_final: 0.8107 (mp0) REVERT: B 651 CYS cc_start: 0.8522 (m) cc_final: 0.8270 (t) REVERT: B 664 GLN cc_start: 0.8834 (pt0) cc_final: 0.7867 (pm20) REVERT: B 920 GLU cc_start: 0.8643 (tt0) cc_final: 0.8072 (mp0) REVERT: B 1059 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8301 (mt-10) REVERT: C 571 ASN cc_start: 0.8480 (m-40) cc_final: 0.8219 (t0) REVERT: C 920 GLU cc_start: 0.8654 (tt0) cc_final: 0.8101 (mp0) REVERT: C 1063 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: D 651 CYS cc_start: 0.8472 (m) cc_final: 0.8205 (m) REVERT: D 664 GLN cc_start: 0.8842 (pt0) cc_final: 0.8366 (pm20) REVERT: D 920 GLU cc_start: 0.8676 (tt0) cc_final: 0.8112 (mp0) outliers start: 30 outliers final: 21 residues processed: 213 average time/residue: 0.6533 time to fit residues: 156.0603 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 : 0.784 ------------------------------------------------------------------------------- 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 A residue 839 VAL 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 785 TYR Chi-restraints excluded: chain B residue 912 MET 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 1063 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.083623 restraints weight = 27287.319| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.53 r_work: 0.2911 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20248 Z= 0.113 Angle : 0.510 10.706 27448 Z= 0.248 Chirality : 0.038 0.184 3180 Planarity : 0.004 0.045 3296 Dihedral : 7.862 59.176 3297 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.44 % Allowed : 12.60 % Favored : 85.97 % 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: 1.60 (0.18), residues: 2352 helix: 1.81 (0.13), residues: 1672 sheet: 0.61 (0.58), residues: 100 loop : -1.10 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1050 TYR 0.011 0.001 TYR A 456 PHE 0.008 0.001 PHE C 877 TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00262 (20236) covalent geometry : angle 0.50892 (27412) hydrogen bonds : bond 0.04458 ( 1145) hydrogen bonds : angle 3.53550 ( 3339) link_BETA1-4 : bond 0.00206 ( 4) link_BETA1-4 : angle 1.23618 ( 12) link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 1.20682 ( 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 219 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.733 Fit side-chains REVERT: A 920 GLU cc_start: 0.8702 (tt0) cc_final: 0.8194 (mp0) REVERT: B 651 CYS cc_start: 0.8534 (m) cc_final: 0.8306 (t) REVERT: B 664 GLN cc_start: 0.8832 (pt0) cc_final: 0.8357 (pm20) REVERT: B 920 GLU cc_start: 0.8676 (tt0) cc_final: 0.8138 (mp0) REVERT: B 1059 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8420 (mt-10) REVERT: C 571 ASN cc_start: 0.8349 (m-40) cc_final: 0.8122 (t0) REVERT: C 920 GLU cc_start: 0.8708 (tt0) cc_final: 0.8194 (mp0) REVERT: C 1063 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: D 651 CYS cc_start: 0.8505 (m) cc_final: 0.8258 (m) REVERT: D 664 GLN cc_start: 0.8822 (pt0) cc_final: 0.8380 (pm20) REVERT: D 920 GLU cc_start: 0.8705 (tt0) cc_final: 0.8168 (mp0) outliers start: 30 outliers final: 17 residues processed: 210 average time/residue: 0.6479 time to fit residues: 153.0059 Evaluate side-chains 203 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 912 MET 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 839 VAL 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: 0.9990 chunk 189 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 235 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 940 GLN D 940 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082402 restraints weight = 27402.187| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.52 r_work: 0.2893 rms_B_bonded: 3.04 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: 0.8282 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20248 Z= 0.132 Angle : 0.520 11.890 27448 Z= 0.254 Chirality : 0.039 0.182 3180 Planarity : 0.004 0.046 3296 Dihedral : 7.843 59.726 3297 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.01 % Allowed : 13.07 % Favored : 85.92 % 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: 1.62 (0.18), residues: 2352 helix: 1.80 (0.13), residues: 1676 sheet: 0.61 (0.58), residues: 100 loop : -1.02 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1050 TYR 0.011 0.001 TYR A 456 PHE 0.008 0.001 PHE B 877 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd covalent geometry : bond 0.00316 (20236) covalent geometry : angle 0.51886 (27412) hydrogen bonds : bond 0.04836 ( 1145) hydrogen bonds : angle 3.57279 ( 3339) link_BETA1-4 : bond 0.00308 ( 4) link_BETA1-4 : angle 1.30759 ( 12) link_NAG-ASN : bond 0.00256 ( 8) link_NAG-ASN : angle 1.17363 ( 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 204 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.767 Fit side-chains REVERT: A 920 GLU cc_start: 0.8674 (tt0) cc_final: 0.8123 (mp0) REVERT: B 651 CYS cc_start: 0.8527 (m) cc_final: 0.8312 (t) REVERT: B 664 GLN cc_start: 0.8832 (pt0) cc_final: 0.7874 (pm20) REVERT: B 920 GLU cc_start: 0.8650 (tt0) cc_final: 0.8097 (mp0) REVERT: B 1059 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8380 (mt-10) REVERT: C 571 ASN cc_start: 0.8367 (m-40) cc_final: 0.8122 (t0) REVERT: C 920 GLU cc_start: 0.8680 (tt0) cc_final: 0.8134 (mp0) REVERT: C 1063 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: D 651 CYS cc_start: 0.8498 (m) cc_final: 0.8249 (m) REVERT: D 664 GLN cc_start: 0.8836 (pt0) cc_final: 0.8400 (pm20) REVERT: D 920 GLU cc_start: 0.8687 (tt0) cc_final: 0.8145 (mp0) REVERT: D 1063 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8163 (mp0) outliers start: 21 outliers final: 17 residues processed: 197 average time/residue: 0.6646 time to fit residues: 146.5869 Evaluate side-chains 200 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 912 MET 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 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 839 VAL Chi-restraints excluded: chain D residue 1063 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 0.0060 chunk 214 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 130 optimal weight: 0.4980 chunk 179 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN B 492 ASN C 492 ASN D 492 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086005 restraints weight = 27415.931| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.53 r_work: 0.2942 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2505 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= 0.096 Angle : 0.497 11.678 27448 Z= 0.241 Chirality : 0.038 0.183 3180 Planarity : 0.004 0.045 3296 Dihedral : 7.490 59.861 3297 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.05 % Allowed : 13.51 % Favored : 85.44 % 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: 1.76 (0.18), residues: 2352 helix: 1.91 (0.13), residues: 1676 sheet: 0.72 (0.59), residues: 100 loop : -0.96 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1050 TYR 0.011 0.001 TYR C 714 PHE 0.008 0.001 PHE C 877 TRP 0.010 0.001 TRP D 832 HIS 0.002 0.000 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00206 (20236) covalent geometry : angle 0.49531 (27412) hydrogen bonds : bond 0.03898 ( 1145) hydrogen bonds : angle 3.45249 ( 3339) link_BETA1-4 : bond 0.00445 ( 4) link_BETA1-4 : angle 1.24714 ( 12) link_NAG-ASN : bond 0.00358 ( 8) link_NAG-ASN : angle 1.17977 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7142.61 seconds wall clock time: 121 minutes 56.99 seconds (7316.99 seconds total)