Starting phenix.real_space_refine on Thu Mar 5 07:33:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7or1_13037/03_2026/7or1_13037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7or1_13037/03_2026/7or1_13037.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 { model { file = "/net/cci-nas-00/data/ceres_data/7or1_13037/03_2026/7or1_13037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7or1_13037/03_2026/7or1_13037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7or1_13037/03_2026/7or1_13037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7or1_13037/03_2026/7or1_13037.map" } 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: 4.46, per 1000 atoms: 0.22 Number of scatterers: 19869 At special positions: 0 Unit cell: (113.36, 114.45, 148.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 144 16.00 P 32 15.00 O 3620 8.00 N 3168 7.00 C 12900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1205 " - " ASN A 753 " " NAG B1205 " - " ASN B 753 " " NAG C1205 " - " ASN C 753 " " NAG D1206 " - " ASN D 753 " " NAG E 1 " - " ASN A 747 " " NAG F 1 " - " ASN B 747 " " NAG G 1 " - " ASN C 747 " " NAG H 1 " - " ASN D 747 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 863.7 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, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 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: 3.562A 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: 6.210A pdb=" N PHE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 4.292A 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: 4.033A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.906A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 872 removed outlier: 3.620A 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: 4.027A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 988 removed outlier: 3.600A 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: 3.562A 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: 6.210A pdb=" N PHE B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 722 " --> pdb=" O ALA B 718 " (cutoff:3.500A) removed outlier: 4.292A 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: 4.033A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 817 " --> pdb=" O THR B 813 " (cutoff:3.500A) removed outlier: 3.627A 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: 3.906A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 872 removed outlier: 3.620A 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: 4.026A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 988 removed outlier: 3.600A 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: 3.562A 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: 3.688A 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: 6.209A pdb=" N PHE C 716 " --> pdb=" O LEU C 712 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN C 722 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 4.292A 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: 4.033A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 817 " --> pdb=" O THR C 813 " (cutoff:3.500A) removed outlier: 3.627A 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: 3.905A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.760A 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: 4.199A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.611A 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: 3.621A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 892 removed outlier: 3.682A 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: 4.027A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 988 removed outlier: 3.600A 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: 3.562A 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: 6.210A pdb=" N PHE D 716 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.293A 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: 4.033A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 817 " --> pdb=" O THR D 813 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.906A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 4.002A 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: 4.611A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 872 removed outlier: 3.621A 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: 4.027A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 988 removed outlier: 3.599A 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 643 Processing sheet with id=AA2, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.225A 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 643 Processing sheet with id=AA4, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.225A 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 643 Processing sheet with id=AA6, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.225A 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 643 Processing sheet with id=AA8, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.224A 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: 2.64 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 3044 1.27 - 1.41: 4916 1.41 - 1.54: 11966 1.54 - 1.67: 78 1.67 - 1.81: 232 Bond restraints: 20236 Sorted by residual: bond pdb=" N6 0IG A1201 " pdb=" N7 0IG A1201 " ideal model delta sigma weight residual 1.161 1.283 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" N6 0IG C1201 " pdb=" N7 0IG C1201 " ideal model delta sigma weight residual 1.161 1.283 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" N6 0IG D1202 " pdb=" N7 0IG D1202 " ideal model delta sigma weight residual 1.161 1.283 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" N6 0IG B1201 " pdb=" N7 0IG B1201 " ideal model delta sigma weight residual 1.161 1.283 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C5 IHP C1206 " pdb=" O15 IHP C1206 " ideal model delta sigma weight residual 1.389 1.469 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 20231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 26938 2.42 - 4.83: 394 4.83 - 7.25: 64 7.25 - 9.66: 8 9.66 - 12.08: 8 Bond angle restraints: 27412 Sorted by residual: angle pdb=" C14 0IG D1202 " pdb=" N6 0IG D1202 " pdb=" N7 0IG D1202 " ideal model delta sigma weight residual 130.27 118.19 12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C14 0IG A1201 " pdb=" N6 0IG A1201 " pdb=" N7 0IG A1201 " ideal model delta sigma weight residual 130.27 118.23 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C14 0IG C1201 " pdb=" N6 0IG C1201 " pdb=" N7 0IG C1201 " ideal model delta sigma weight residual 130.27 118.23 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C14 0IG B1201 " pdb=" N6 0IG B1201 " pdb=" N7 0IG B1201 " ideal model delta sigma weight residual 130.27 118.23 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N6 0IG D1202 " pdb=" N7 0IG D1202 " pdb=" N8 0IG D1202 " ideal model delta sigma weight residual 168.86 179.62 -10.76 3.00e+00 1.11e-01 1.29e+01 ... (remaining 27407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 12036 34.46 - 68.91: 288 68.91 - 103.37: 20 103.37 - 137.83: 48 137.83 - 172.29: 4 Dihedral angle restraints: 12396 sinusoidal: 5368 harmonic: 7028 Sorted by residual: dihedral pdb=" N 0IG B1201 " pdb=" C 0IG B1201 " pdb=" C1 0IG B1201 " pdb=" O 0IG B1201 " ideal model delta sinusoidal sigma weight residual 203.70 31.41 172.29 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N 0IG C1201 " pdb=" C 0IG C1201 " pdb=" C1 0IG C1201 " pdb=" O 0IG C1201 " ideal model delta sinusoidal sigma weight residual 203.70 31.46 172.24 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N 0IG D1202 " pdb=" C 0IG D1202 " pdb=" C1 0IG D1202 " pdb=" O 0IG D1202 " ideal model delta sinusoidal sigma weight residual 203.70 31.51 172.19 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 3164 1.006 - 2.012: 0 2.012 - 3.019: 0 3.019 - 4.025: 0 4.025 - 5.031: 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 2.61 -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 C1206 " pdb=" C4 IHP C1206 " pdb=" C6 IHP C1206 " pdb=" O15 IHP C1206 " 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 C1201 " -0.143 2.00e-02 2.50e+03 1.69e-01 7.12e+02 pdb=" C11 0IG C1201 " -0.043 2.00e-02 2.50e+03 pdb=" C12 0IG C1201 " -0.144 2.00e-02 2.50e+03 pdb=" C13 0IG C1201 " -0.055 2.00e-02 2.50e+03 pdb=" C14 0IG C1201 " 0.136 2.00e-02 2.50e+03 pdb=" C15 0IG C1201 " 0.243 2.00e-02 2.50e+03 pdb=" C16 0IG C1201 " 0.155 2.00e-02 2.50e+03 pdb=" N6 0IG C1201 " 0.209 2.00e-02 2.50e+03 pdb=" N7 0IG C1201 " -0.060 2.00e-02 2.50e+03 pdb=" N8 0IG C1201 " -0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG D1202 " 0.142 2.00e-02 2.50e+03 1.69e-01 7.12e+02 pdb=" C11 0IG D1202 " 0.042 2.00e-02 2.50e+03 pdb=" C12 0IG D1202 " 0.145 2.00e-02 2.50e+03 pdb=" C13 0IG D1202 " 0.055 2.00e-02 2.50e+03 pdb=" C14 0IG D1202 " -0.136 2.00e-02 2.50e+03 pdb=" C15 0IG D1202 " -0.244 2.00e-02 2.50e+03 pdb=" C16 0IG D1202 " -0.154 2.00e-02 2.50e+03 pdb=" N6 0IG D1202 " -0.209 2.00e-02 2.50e+03 pdb=" N7 0IG D1202 " 0.059 2.00e-02 2.50e+03 pdb=" N8 0IG D1202 " 0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG B1201 " -0.143 2.00e-02 2.50e+03 1.69e-01 7.11e+02 pdb=" C11 0IG B1201 " -0.042 2.00e-02 2.50e+03 pdb=" C12 0IG B1201 " -0.144 2.00e-02 2.50e+03 pdb=" C13 0IG B1201 " -0.055 2.00e-02 2.50e+03 pdb=" C14 0IG B1201 " 0.136 2.00e-02 2.50e+03 pdb=" C15 0IG B1201 " 0.243 2.00e-02 2.50e+03 pdb=" C16 0IG B1201 " 0.154 2.00e-02 2.50e+03 pdb=" N6 0IG B1201 " 0.209 2.00e-02 2.50e+03 pdb=" N7 0IG B1201 " -0.059 2.00e-02 2.50e+03 pdb=" N8 0IG B1201 " -0.299 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4813 2.79 - 3.32: 18554 3.32 - 3.84: 30282 3.84 - 4.37: 37754 4.37 - 4.90: 64491 Nonbonded interactions: 155894 Sorted by model distance: nonbonded pdb=" O ILE B 916 " pdb=" O HOH B1301 " model vdw 2.262 3.040 nonbonded pdb=" O ILE C 916 " pdb=" O HOH C1301 " model vdw 2.288 3.040 nonbonded pdb=" OG SER C 887 " pdb=" OE1 GLN C 940 " model vdw 2.321 3.040 nonbonded pdb=" OG SER A 887 " pdb=" OE1 GLN A 940 " model vdw 2.321 3.040 nonbonded pdb=" OG SER D 887 " pdb=" OE1 GLN D 940 " model vdw 2.321 3.040 ... (remaining 155889 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: 1.280 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.870 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 0.122 20248 Z= 0.384 Angle : 0.780 12.076 27448 Z= 0.387 Chirality : 0.354 5.031 3180 Planarity : 0.007 0.169 3296 Dihedral : 16.579 172.285 7828 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.95 % Favored : 93.71 % Rotamer: Outliers : 1.72 % Allowed : 6.90 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.16), residues: 2352 helix: -0.75 (0.12), residues: 1644 sheet: -0.04 (0.62), residues: 60 loop : -2.71 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 464 TYR 0.013 0.002 TYR A 456 PHE 0.013 0.002 PHE A 583 TRP 0.014 0.001 TRP D 832 HIS 0.003 0.001 HIS C 983 Details of bonding type rmsd covalent geometry : bond 0.00879 (20236) covalent geometry : angle 0.77832 (27412) hydrogen bonds : bond 0.16194 ( 1145) hydrogen bonds : angle 5.11778 ( 3339) link_BETA1-4 : bond 0.00047 ( 4) link_BETA1-4 : angle 1.76897 ( 12) link_NAG-ASN : bond 0.00088 ( 8) link_NAG-ASN : angle 1.42402 ( 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 230 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.705 Fit side-chains REVERT: B 953 MET cc_start: 0.8611 (mmm) cc_final: 0.8344 (mmm) REVERT: B 978 MET cc_start: 0.8081 (mtm) cc_final: 0.7876 (mtp) REVERT: C 862 MET cc_start: 0.8898 (mtt) cc_final: 0.8660 (mtt) REVERT: C 1063 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: D 911 MET cc_start: 0.9088 (mtp) cc_final: 0.8653 (mtp) REVERT: D 912 MET cc_start: 0.8388 (ttm) cc_final: 0.8168 (ttp) REVERT: D 1059 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7508 (mt-10) REVERT: D 1063 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7547 (mp0) outliers start: 36 outliers final: 12 residues processed: 221 average time/residue: 0.6660 time to fit residues: 164.2987 Evaluate side-chains 191 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 611 ILE 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 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 1063 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 619 ASN B 664 GLN B1008 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 664 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082500 restraints weight = 27294.722| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.52 r_work: 0.2868 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1047 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= 0.132 Angle : 0.604 11.921 27448 Z= 0.284 Chirality : 0.045 0.549 3180 Planarity : 0.004 0.051 3296 Dihedral : 10.747 163.669 3319 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.82 % Allowed : 8.62 % Favored : 89.56 % 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: -0.15 (0.18), residues: 2352 helix: 0.61 (0.13), residues: 1664 sheet: 1.04 (0.63), residues: 60 loop : -2.04 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1050 TYR 0.017 0.001 TYR A 655 PHE 0.008 0.001 PHE C 879 TRP 0.013 0.001 TRP D 832 HIS 0.004 0.001 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00284 (20236) covalent geometry : angle 0.60305 (27412) hydrogen bonds : bond 0.05880 ( 1145) hydrogen bonds : angle 3.93632 ( 3339) link_BETA1-4 : bond 0.00418 ( 4) link_BETA1-4 : angle 1.08517 ( 12) link_NAG-ASN : bond 0.00220 ( 8) link_NAG-ASN : angle 1.29884 ( 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 233 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.641 Fit side-chains REVERT: A 1059 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8247 (mt-10) REVERT: B 508 PHE cc_start: 0.9190 (m-80) cc_final: 0.8903 (m-80) REVERT: B 651 CYS cc_start: 0.8432 (m) cc_final: 0.8171 (t) REVERT: B 664 GLN cc_start: 0.8861 (pt0) cc_final: 0.8656 (pt0) REVERT: C 862 MET cc_start: 0.9055 (mtt) cc_final: 0.8837 (mtt) REVERT: C 996 ARG cc_start: 0.8943 (mmt90) cc_final: 0.8732 (mmm-85) REVERT: D 833 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: D 1059 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8344 (mt-10) outliers start: 38 outliers final: 20 residues processed: 222 average time/residue: 0.5952 time to fit residues: 148.8665 Evaluate side-chains 197 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 607 GLU 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 833 GLN 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 785 TYR Chi-restraints excluded: chain D residue 833 GLN Chi-restraints excluded: chain D residue 839 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 134 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 0.0980 chunk 211 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.079289 restraints weight = 27796.996| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.53 r_work: 0.2754 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20248 Z= 0.204 Angle : 0.592 8.653 27448 Z= 0.292 Chirality : 0.042 0.261 3180 Planarity : 0.004 0.054 3296 Dihedral : 10.299 157.624 3311 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.02 % Allowed : 8.52 % Favored : 88.46 % 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: 0.52 (0.18), residues: 2352 helix: 1.09 (0.13), residues: 1676 sheet: -0.18 (0.54), residues: 100 loop : -1.67 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 996 TYR 0.011 0.001 TYR B 456 PHE 0.011 0.002 PHE B 583 TRP 0.011 0.001 TRP D 832 HIS 0.005 0.001 HIS C 983 Details of bonding type rmsd covalent geometry : bond 0.00509 (20236) covalent geometry : angle 0.59020 (27412) hydrogen bonds : bond 0.06426 ( 1145) hydrogen bonds : angle 3.89121 ( 3339) link_BETA1-4 : bond 0.00275 ( 4) link_BETA1-4 : angle 1.38480 ( 12) link_NAG-ASN : bond 0.00155 ( 8) link_NAG-ASN : angle 1.27921 ( 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 262 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 199 time to evaluate : 0.576 Fit side-chains REVERT: A 833 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8489 (pt0) REVERT: A 920 GLU cc_start: 0.8643 (tt0) cc_final: 0.8080 (mp0) REVERT: A 996 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8699 (mmm-85) REVERT: A 1059 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8019 (mt-10) REVERT: A 1063 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 608 CYS cc_start: 0.8968 (m) cc_final: 0.8753 (m) REVERT: B 651 CYS cc_start: 0.8464 (m) cc_final: 0.8198 (t) REVERT: B 664 GLN cc_start: 0.8721 (pt0) cc_final: 0.8520 (pt0) REVERT: B 911 MET cc_start: 0.9119 (mtp) cc_final: 0.8862 (mtp) REVERT: B 996 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8739 (mmm-85) REVERT: C 833 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: D 651 CYS cc_start: 0.8258 (m) cc_final: 0.7936 (m) REVERT: D 996 ARG cc_start: 0.9009 (mmm-85) cc_final: 0.8805 (mmm-85) REVERT: D 1059 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8308 (mt-10) outliers start: 63 outliers final: 29 residues processed: 235 average time/residue: 0.6051 time to fit residues: 159.9282 Evaluate side-chains 224 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 912 MET 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 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 875 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 219 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN B1008 ASN B1047 GLN C1047 GLN D1047 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082793 restraints weight = 27612.666| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.53 r_work: 0.2890 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20248 Z= 0.111 Angle : 0.486 8.276 27448 Z= 0.242 Chirality : 0.038 0.191 3180 Planarity : 0.004 0.049 3296 Dihedral : 9.695 148.579 3308 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 10.82 % Favored : 87.31 % 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: 1.03 (0.18), residues: 2352 helix: 1.44 (0.13), residues: 1672 sheet: 0.17 (0.55), residues: 100 loop : -1.44 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1050 TYR 0.016 0.001 TYR A 655 PHE 0.008 0.001 PHE B 879 TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00245 (20236) covalent geometry : angle 0.48413 (27412) hydrogen bonds : bond 0.04769 ( 1145) hydrogen bonds : angle 3.64044 ( 3339) link_BETA1-4 : bond 0.00355 ( 4) link_BETA1-4 : angle 1.23496 ( 12) link_NAG-ASN : bond 0.00306 ( 8) link_NAG-ASN : angle 1.27022 ( 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 234 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.683 Fit side-chains REVERT: A 920 GLU cc_start: 0.8693 (tt0) cc_final: 0.8084 (mp0) REVERT: A 1059 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 651 CYS cc_start: 0.8487 (m) cc_final: 0.8228 (t) REVERT: B 744 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8567 (mmm) REVERT: B 911 MET cc_start: 0.9016 (mtp) cc_final: 0.8783 (mtp) REVERT: D 651 CYS cc_start: 0.8373 (m) cc_final: 0.8082 (m) REVERT: D 911 MET cc_start: 0.9069 (mtp) cc_final: 0.8793 (mtp) REVERT: D 1059 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8344 (mt-10) outliers start: 39 outliers final: 21 residues processed: 220 average time/residue: 0.6244 time to fit residues: 154.2487 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 : 0.643 ------------------------------------------------------------------------------- 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 912 MET 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 721 MET Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 912 MET 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 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 912 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 18 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 B1008 ASN C 494 HIS D 494 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083115 restraints weight = 27516.668| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.52 r_work: 0.2855 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2011 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 : 0.495 10.154 27448 Z= 0.243 Chirality : 0.038 0.189 3180 Planarity : 0.004 0.047 3296 Dihedral : 9.385 143.155 3305 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.82 % Allowed : 11.64 % 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: 1.33 (0.18), residues: 2352 helix: 1.65 (0.13), residues: 1672 sheet: 0.47 (0.56), residues: 100 loop : -1.31 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 996 TYR 0.014 0.001 TYR C 655 PHE 0.007 0.001 PHE C 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 0.00258 (20236) covalent geometry : angle 0.49284 (27412) hydrogen bonds : bond 0.04628 ( 1145) hydrogen bonds : angle 3.55968 ( 3339) link_BETA1-4 : bond 0.00321 ( 4) link_BETA1-4 : angle 1.25996 ( 12) link_NAG-ASN : bond 0.00288 ( 8) link_NAG-ASN : angle 1.25041 ( 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 229 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.769 Fit side-chains REVERT: A 920 GLU cc_start: 0.8617 (tt0) cc_final: 0.7990 (mp0) REVERT: A 1059 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8245 (mt-10) REVERT: B 651 CYS cc_start: 0.8485 (m) cc_final: 0.8206 (t) REVERT: B 911 MET cc_start: 0.8888 (mtp) cc_final: 0.8641 (mtp) REVERT: B 920 GLU cc_start: 0.8647 (tt0) cc_final: 0.8076 (mp0) REVERT: C 920 GLU cc_start: 0.8600 (tt0) cc_final: 0.8018 (mp0) REVERT: D 651 CYS cc_start: 0.8482 (m) cc_final: 0.8200 (m) REVERT: D 911 MET cc_start: 0.8984 (mtp) cc_final: 0.8675 (mtp) REVERT: D 1059 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8259 (mt-10) outliers start: 38 outliers final: 22 residues processed: 216 average time/residue: 0.6224 time to fit residues: 151.4484 Evaluate side-chains 207 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 864 GLU Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 912 MET 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 864 GLU Chi-restraints excluded: chain D residue 912 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 91 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.122778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.082458 restraints weight = 27379.275| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.52 r_work: 0.2883 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2112 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= 0.122 Angle : 0.492 11.601 27448 Z= 0.242 Chirality : 0.039 0.188 3180 Planarity : 0.004 0.046 3296 Dihedral : 9.238 139.557 3305 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.77 % Allowed : 12.21 % Favored : 86.02 % 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: 1.48 (0.18), residues: 2352 helix: 1.75 (0.13), residues: 1672 sheet: 0.59 (0.57), residues: 100 loop : -1.22 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 996 TYR 0.015 0.001 TYR C 655 PHE 0.008 0.001 PHE C 877 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00290 (20236) covalent geometry : angle 0.48995 (27412) hydrogen bonds : bond 0.04741 ( 1145) hydrogen bonds : angle 3.56760 ( 3339) link_BETA1-4 : bond 0.00311 ( 4) link_BETA1-4 : angle 1.27139 ( 12) link_NAG-ASN : bond 0.00273 ( 8) link_NAG-ASN : angle 1.22451 ( 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 230 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.746 Fit side-chains REVERT: A 920 GLU cc_start: 0.8666 (tt0) cc_final: 0.8184 (mp0) REVERT: A 1059 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 651 CYS cc_start: 0.8504 (m) cc_final: 0.8258 (t) REVERT: B 911 MET cc_start: 0.9090 (mtp) cc_final: 0.8872 (mtp) REVERT: B 920 GLU cc_start: 0.8702 (tt0) cc_final: 0.8197 (mp0) REVERT: B 1059 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8353 (mt-10) REVERT: C 920 GLU cc_start: 0.8671 (tt0) cc_final: 0.8186 (mp0) REVERT: D 651 CYS cc_start: 0.8527 (m) cc_final: 0.8267 (m) REVERT: D 911 MET cc_start: 0.9139 (mtp) cc_final: 0.8843 (mtp) REVERT: D 1059 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8423 (mt-10) outliers start: 37 outliers final: 20 residues processed: 216 average time/residue: 0.6330 time to fit residues: 154.0861 Evaluate side-chains 205 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 ASP 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 912 MET Chi-restraints excluded: chain B residue 562 LYS 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 C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain 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 864 GLU Chi-restraints excluded: chain D residue 912 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 115 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 chunk 215 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.122996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082586 restraints weight = 27431.442| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.53 r_work: 0.2888 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2194 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= 0.118 Angle : 0.492 10.584 27448 Z= 0.242 Chirality : 0.038 0.186 3180 Planarity : 0.004 0.046 3296 Dihedral : 9.062 137.283 3303 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.58 % Allowed : 12.74 % Favored : 85.68 % 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: 1.58 (0.18), residues: 2352 helix: 1.81 (0.13), residues: 1672 sheet: 0.64 (0.58), residues: 100 loop : -1.15 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 996 TYR 0.015 0.001 TYR A 655 PHE 0.008 0.001 PHE D 877 TRP 0.009 0.001 TRP D 832 HIS 0.004 0.001 HIS C 481 Details of bonding type rmsd covalent geometry : bond 0.00277 (20236) covalent geometry : angle 0.48995 (27412) hydrogen bonds : bond 0.04600 ( 1145) hydrogen bonds : angle 3.53171 ( 3339) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 1.28511 ( 12) link_NAG-ASN : bond 0.00278 ( 8) link_NAG-ASN : angle 1.19814 ( 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 222 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.706 Fit side-chains REVERT: A 920 GLU cc_start: 0.8674 (tt0) cc_final: 0.8176 (mp0) REVERT: A 1059 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 651 CYS cc_start: 0.8599 (m) cc_final: 0.8277 (t) REVERT: B 920 GLU cc_start: 0.8697 (tt0) cc_final: 0.8190 (mp0) REVERT: B 1059 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8372 (mt-10) REVERT: C 920 GLU cc_start: 0.8665 (tt0) cc_final: 0.8168 (mp0) REVERT: D 651 CYS cc_start: 0.8509 (m) cc_final: 0.8246 (m) REVERT: D 1059 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8416 (mt-10) outliers start: 33 outliers final: 21 residues processed: 209 average time/residue: 0.6370 time to fit residues: 149.5082 Evaluate side-chains 205 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 912 MET 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 721 MET Chi-restraints excluded: chain B residue 785 TYR 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 483 MET 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 864 GLU Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 144 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.121751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.081109 restraints weight = 27508.563| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.53 r_work: 0.2792 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2203 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= 0.146 Angle : 0.506 11.111 27448 Z= 0.252 Chirality : 0.040 0.184 3180 Planarity : 0.004 0.046 3296 Dihedral : 9.068 136.941 3298 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.58 % Allowed : 12.93 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 2352 helix: 1.77 (0.13), residues: 1676 sheet: 0.53 (0.57), residues: 100 loop : -1.08 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1050 TYR 0.013 0.001 TYR A 655 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 0.00358 (20236) covalent geometry : angle 0.50488 (27412) hydrogen bonds : bond 0.05110 ( 1145) hydrogen bonds : angle 3.61616 ( 3339) link_BETA1-4 : bond 0.00276 ( 4) link_BETA1-4 : angle 1.32364 ( 12) link_NAG-ASN : bond 0.00232 ( 8) link_NAG-ASN : angle 1.16223 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.747 Fit side-chains REVERT: A 920 GLU cc_start: 0.8623 (tt0) cc_final: 0.8007 (mp0) REVERT: A 1059 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8266 (mt-10) REVERT: B 651 CYS cc_start: 0.8568 (m) cc_final: 0.8245 (t) REVERT: B 920 GLU cc_start: 0.8645 (tt0) cc_final: 0.7986 (mp0) REVERT: B 1059 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8219 (mt-10) REVERT: C 920 GLU cc_start: 0.8620 (tt0) cc_final: 0.8019 (mp0) REVERT: D 523 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8025 (tpp) REVERT: D 651 CYS cc_start: 0.8460 (m) cc_final: 0.8181 (m) REVERT: D 1059 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8273 (mt-10) outliers start: 33 outliers final: 24 residues processed: 208 average time/residue: 0.6019 time to fit residues: 141.5144 Evaluate side-chains 207 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 824 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 839 VAL 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 C residue 839 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 523 MET 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 864 GLU Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 193 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 0.0000 chunk 201 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.123953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083638 restraints weight = 27344.229| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.52 r_work: 0.2903 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20248 Z= 0.104 Angle : 0.490 10.905 27448 Z= 0.240 Chirality : 0.038 0.184 3180 Planarity : 0.004 0.045 3296 Dihedral : 8.793 133.491 3295 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.48 % Allowed : 13.46 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.18), residues: 2352 helix: 1.89 (0.13), residues: 1672 sheet: 0.61 (0.58), residues: 100 loop : -1.02 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1050 TYR 0.014 0.001 TYR A 655 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 0.00231 (20236) covalent geometry : angle 0.48858 (27412) hydrogen bonds : bond 0.04281 ( 1145) hydrogen bonds : angle 3.50424 ( 3339) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 1.26689 ( 12) link_NAG-ASN : bond 0.00314 ( 8) link_NAG-ASN : angle 1.18131 ( 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 222 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.769 Fit side-chains REVERT: A 664 GLN cc_start: 0.8825 (pt0) cc_final: 0.8515 (pt0) REVERT: A 920 GLU cc_start: 0.8675 (tt0) cc_final: 0.8188 (mp0) REVERT: A 1059 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8401 (mt-10) REVERT: B 571 ASN cc_start: 0.8732 (t0) cc_final: 0.8505 (t0) REVERT: B 651 CYS cc_start: 0.8592 (m) cc_final: 0.8293 (t) REVERT: B 920 GLU cc_start: 0.8699 (tt0) cc_final: 0.8214 (mp0) REVERT: B 1059 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8449 (mt-10) REVERT: C 920 GLU cc_start: 0.8668 (tt0) cc_final: 0.8210 (mp0) REVERT: D 523 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8081 (tpp) REVERT: D 651 CYS cc_start: 0.8499 (m) cc_final: 0.8189 (t) REVERT: D 1059 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8385 (mt-10) outliers start: 31 outliers final: 19 residues processed: 208 average time/residue: 0.5951 time to fit residues: 139.9243 Evaluate side-chains 204 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 824 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 721 MET 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 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=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: 0.9980 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.123906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083596 restraints weight = 27433.219| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.52 r_work: 0.2835 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20248 Z= 0.109 Angle : 0.491 11.687 27448 Z= 0.241 Chirality : 0.038 0.182 3180 Planarity : 0.004 0.045 3296 Dihedral : 8.699 133.176 3295 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.05 % Allowed : 14.03 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2352 helix: 1.90 (0.13), residues: 1680 sheet: 0.64 (0.58), residues: 100 loop : -1.01 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1050 TYR 0.013 0.001 TYR A 655 PHE 0.007 0.001 PHE D 583 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd covalent geometry : bond 0.00249 (20236) covalent geometry : angle 0.48935 (27412) hydrogen bonds : bond 0.04354 ( 1145) hydrogen bonds : angle 3.48521 ( 3339) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 1.27328 ( 12) link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 1.16024 ( 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 210 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.720 Fit side-chains REVERT: A 664 GLN cc_start: 0.8747 (pt0) cc_final: 0.8434 (pt0) REVERT: A 920 GLU cc_start: 0.8642 (tt0) cc_final: 0.8064 (mp0) REVERT: B 571 ASN cc_start: 0.8808 (t0) cc_final: 0.8580 (t0) REVERT: B 651 CYS cc_start: 0.8565 (m) cc_final: 0.8245 (t) REVERT: B 920 GLU cc_start: 0.8661 (tt0) cc_final: 0.8069 (mp0) REVERT: B 1059 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8359 (mt-10) REVERT: C 920 GLU cc_start: 0.8645 (tt0) cc_final: 0.8102 (mp0) REVERT: D 523 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8058 (tpp) REVERT: D 571 ASN cc_start: 0.8737 (t0) cc_final: 0.8478 (t0) REVERT: D 651 CYS cc_start: 0.8490 (m) cc_final: 0.8206 (t) outliers start: 22 outliers final: 18 residues processed: 200 average time/residue: 0.6055 time to fit residues: 136.2403 Evaluate side-chains 204 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 824 VAL Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 785 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 215 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.123773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083315 restraints weight = 27496.200| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.53 r_work: 0.2902 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2404 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= 0.111 Angle : 0.502 11.547 27448 Z= 0.244 Chirality : 0.038 0.181 3180 Planarity : 0.004 0.045 3296 Dihedral : 8.620 132.701 3295 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.34 % Allowed : 13.98 % Favored : 84.67 % 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: 1.78 (0.18), residues: 2352 helix: 1.92 (0.13), residues: 1680 sheet: 0.70 (0.59), residues: 100 loop : -0.96 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1050 TYR 0.014 0.001 TYR A 655 PHE 0.009 0.001 PHE C 877 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00258 (20236) covalent geometry : angle 0.50057 (27412) hydrogen bonds : bond 0.04340 ( 1145) hydrogen bonds : angle 3.48173 ( 3339) link_BETA1-4 : bond 0.00324 ( 4) link_BETA1-4 : angle 1.26284 ( 12) link_NAG-ASN : bond 0.00299 ( 8) link_NAG-ASN : angle 1.15027 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7036.54 seconds wall clock time: 120 minutes 10.00 seconds (7210.00 seconds total)