Starting phenix.real_space_refine on Sat Jul 4 11:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7or1_13037/07_2026/7or1_13037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7or1_13037/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7or1_13037/07_2026/7or1_13037.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7or1_13037/07_2026/7or1_13037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7or1_13037/07_2026/7or1_13037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7or1_13037/07_2026/7or1_13037.map" model { file = "/net/cci-nas-00/data/ceres_data/7or1_13037/07_2026/7or1_13037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7or1_13037/07_2026/7or1_13037.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 32 5.49 5 S 144 5.16 5 C 12900 2.51 5 N 3168 2.21 5 O 3620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19869 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 174 Unusual residues: {' CA': 2, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 4.18, per 1000 atoms: 0.21 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: 1.66 Conformation dependent library (CDL) restraints added in 806.9 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: 0.39 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: 3.10 Time building geometry restraints manager: 2.13 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: 11672 34.46 - 68.91: 236 68.91 - 103.37: 16 103.37 - 137.83: 0 137.83 - 172.29: 4 Dihedral angle restraints: 11928 sinusoidal: 4900 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 11925 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: 1.420 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: 0.030 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.420 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 13.589 172.285 7360 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/Z covalent geometry : bond 0.00879 / 0.38 (20236) covalent geometry : angle 0.77832 / 0.39 (27412) hydrogen bonds : bond 0.16194 / 11.10 ( 1145) hydrogen bonds : angle 5.11778 / 3.64 ( 3339) link_BETA1-4 : bond 0.00047 / 0.02 ( 4) link_BETA1-4 : angle 1.76897 / 1.15 ( 12) link_NAG-ASN : bond 0.00088 / 0.05 ( 8) link_NAG-ASN : angle 1.42402 / 1.12 ( 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 : 0.731 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: 0.5930 time to fit residues: 147.6658 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 : 0.736 ------------------------------------------------------------------------------- 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... 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 = 0.3592 r_free = 0.3592 target = 0.122954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.082737 restraints weight = 27288.836| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.53 r_work: 0.2893 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20248 Z= 0.129 Angle : 0.624 13.571 27448 Z= 0.289 Chirality : 0.045 0.591 3180 Planarity : 0.004 0.051 3296 Dihedral : 9.875 163.122 2851 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.82 % Allowed : 8.57 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2352 helix: 0.61 (0.13), residues: 1664 sheet: 1.08 (0.63), residues: 60 loop : -2.01 (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 0.009 0.001 PHE C 879 TRP 0.012 0.001 TRP D 832 HIS 0.003 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (20236) covalent geometry : angle 0.62243 / 0.29 (27412) hydrogen bonds : bond 0.05734 / 3.97 ( 1145) hydrogen bonds : angle 3.91711 / 2.78 ( 3339) link_BETA1-4 : bond 0.00504 / 0.25 ( 4) link_BETA1-4 : angle 1.12640 / 0.73 ( 12) link_NAG-ASN : bond 0.00224 / 0.16 ( 8) link_NAG-ASN : angle 1.32623 / 1.04 ( 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 : 0.831 Fit side-chains REVERT: A 911 MET cc_start: 0.9027 (mtp) cc_final: 0.8796 (mtp) REVERT: A 1059 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 508 PHE cc_start: 0.9201 (m-80) cc_final: 0.8902 (m-80) REVERT: B 651 CYS cc_start: 0.8443 (m) cc_final: 0.8192 (t) REVERT: B 912 MET cc_start: 0.8974 (ttm) cc_final: 0.8692 (ttp) REVERT: C 862 MET cc_start: 0.9089 (mtt) cc_final: 0.8871 (mtt) REVERT: D 833 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8531 (pt0) REVERT: D 1059 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8382 (mt-10) outliers start: 38 outliers final: 21 residues processed: 222 average time/residue: 0.6082 time to fit residues: 153.0066 Evaluate side-chains 197 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 721 MET 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: 5.9990 chunk 135 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1047 GLN B 664 GLN B1047 GLN C 664 GLN C1047 GLN D 664 GLN D1047 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.080083 restraints weight = 27714.681| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.53 r_work: 0.2796 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20248 Z= 0.180 Angle : 0.577 8.567 27448 Z= 0.283 Chirality : 0.042 0.254 3180 Planarity : 0.004 0.053 3296 Dihedral : 9.853 156.037 2843 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.78 % Allowed : 9.10 % Favored : 88.12 % 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: 0.54 (0.18), residues: 2352 helix: 1.09 (0.13), residues: 1668 sheet: 0.50 (0.54), residues: 92 loop : -1.72 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 996 TYR 0.011 0.001 TYR C 655 PHE 0.010 0.001 PHE B 583 TRP 0.011 0.001 TRP D 832 HIS 0.004 0.001 HIS C 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (20236) covalent geometry : angle 0.57491 / 0.28 (27412) hydrogen bonds : bond 0.06159 / 4.28 ( 1145) hydrogen bonds : angle 3.82851 / 2.72 ( 3339) link_BETA1-4 : bond 0.00303 / 0.15 ( 4) link_BETA1-4 : angle 1.32918 / 0.87 ( 12) link_NAG-ASN : bond 0.00159 / 0.11 ( 8) link_NAG-ASN : angle 1.32329 / 1.04 ( 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 255 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 0.773 Fit side-chains REVERT: A 833 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8449 (pt0) REVERT: A 920 GLU cc_start: 0.8592 (tt0) cc_final: 0.7953 (mp0) REVERT: A 1059 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 1063 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: B 608 CYS cc_start: 0.8948 (m) cc_final: 0.8723 (m) REVERT: B 651 CYS cc_start: 0.8460 (m) cc_final: 0.8194 (t) REVERT: B 911 MET cc_start: 0.9055 (mtp) cc_final: 0.8767 (mtp) REVERT: B 912 MET cc_start: 0.9074 (ttm) cc_final: 0.8793 (ttp) REVERT: C 833 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: C 911 MET cc_start: 0.8995 (mtp) cc_final: 0.8720 (mtp) REVERT: D 651 CYS cc_start: 0.8253 (m) cc_final: 0.7930 (m) REVERT: D 920 GLU cc_start: 0.8640 (tt0) cc_final: 0.8055 (mp0) REVERT: D 1059 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8239 (mt-10) outliers start: 58 outliers final: 29 residues processed: 233 average time/residue: 0.6207 time to fit residues: 163.7532 Evaluate side-chains 222 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 721 MET 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 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: 2.9990 chunk 59 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 147 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 664 GLN B1008 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081382 restraints weight = 27685.207| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.53 r_work: 0.2821 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20248 Z= 0.142 Angle : 0.517 10.168 27448 Z= 0.256 Chirality : 0.040 0.195 3180 Planarity : 0.004 0.049 3296 Dihedral : 9.589 148.792 2840 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.01 % Allowed : 10.97 % Favored : 87.02 % 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: 0.95 (0.18), residues: 2352 helix: 1.37 (0.13), residues: 1672 sheet: 0.18 (0.55), residues: 100 loop : -1.43 (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 A 877 TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (20236) covalent geometry : angle 0.51578 / 0.26 (27412) hydrogen bonds : bond 0.05260 / 3.65 ( 1145) hydrogen bonds : angle 3.70944 / 2.63 ( 3339) link_BETA1-4 : bond 0.00431 / 0.22 ( 4) link_BETA1-4 : angle 1.26995 / 0.82 ( 12) link_NAG-ASN : bond 0.00221 / 0.15 ( 8) link_NAG-ASN : angle 1.24146 / 1.00 ( 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 238 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.798 Fit side-chains REVERT: A 920 GLU cc_start: 0.8630 (tt0) cc_final: 0.7967 (mp0) REVERT: A 1059 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8225 (mt-10) REVERT: B 651 CYS cc_start: 0.8484 (m) cc_final: 0.8192 (t) REVERT: B 911 MET cc_start: 0.8993 (mtp) cc_final: 0.8747 (mtp) REVERT: B 912 MET cc_start: 0.9059 (ttm) cc_final: 0.8777 (ttp) REVERT: C 996 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8623 (mmm-85) REVERT: D 651 CYS cc_start: 0.8332 (m) cc_final: 0.8020 (m) REVERT: D 833 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: D 920 GLU cc_start: 0.8652 (tt0) cc_final: 0.7973 (mp0) REVERT: D 1059 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8263 (mt-10) outliers start: 42 outliers final: 26 residues processed: 224 average time/residue: 0.6422 time to fit residues: 162.2519 Evaluate side-chains 211 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 839 VAL 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 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 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 839 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 785 TYR Chi-restraints excluded: chain D residue 833 GLN 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: 2.9990 chunk 219 optimal weight: 0.3980 chunk 155 optimal weight: 0.9980 chunk 96 optimal weight: 0.0040 chunk 233 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 154 optimal weight: 0.6980 chunk 221 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 HIS B 494 HIS B 664 GLN B1008 ASN C 492 ASN D 494 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084336 restraints weight = 27417.302| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.53 r_work: 0.2850 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20248 Z= 0.095 Angle : 0.481 10.851 27448 Z= 0.236 Chirality : 0.037 0.179 3180 Planarity : 0.004 0.048 3296 Dihedral : 9.124 141.580 2840 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.96 % Allowed : 11.45 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2352 helix: 1.65 (0.13), residues: 1676 sheet: 0.55 (0.57), residues: 100 loop : -1.29 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1050 TYR 0.010 0.001 TYR A 456 PHE 0.008 0.001 PHE D 877 TRP 0.009 0.001 TRP D 832 HIS 0.002 0.000 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (20236) covalent geometry : angle 0.47869 / 0.24 (27412) hydrogen bonds : bond 0.04150 / 2.88 ( 1145) hydrogen bonds : angle 3.50133 / 2.48 ( 3339) link_BETA1-4 : bond 0.00372 / 0.19 ( 4) link_BETA1-4 : angle 1.22325 / 0.80 ( 12) link_NAG-ASN : bond 0.00319 / 0.22 ( 8) link_NAG-ASN : angle 1.26068 / 1.02 ( 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 238 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.801 Fit side-chains REVERT: A 920 GLU cc_start: 0.8669 (tt0) cc_final: 0.8129 (mp0) REVERT: A 1059 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 651 CYS cc_start: 0.8479 (m) cc_final: 0.8209 (t) REVERT: B 920 GLU cc_start: 0.8696 (tt0) cc_final: 0.8146 (mp0) REVERT: D 651 CYS cc_start: 0.8494 (m) cc_final: 0.8213 (m) REVERT: D 920 GLU cc_start: 0.8671 (tt0) cc_final: 0.8060 (mp0) REVERT: D 1059 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8326 (mt-10) outliers start: 41 outliers final: 19 residues processed: 226 average time/residue: 0.6138 time to fit residues: 156.4777 Evaluate side-chains 197 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 912 MET Chi-restraints excluded: chain B residue 607 GLU 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 721 MET 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 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 664 GLN C 494 HIS D 664 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081865 restraints weight = 27442.906| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.51 r_work: 0.2834 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2109 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= 0.134 Angle : 0.505 10.372 27448 Z= 0.248 Chirality : 0.039 0.179 3180 Planarity : 0.004 0.046 3296 Dihedral : 9.165 140.824 2840 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.87 % Allowed : 12.31 % Favored : 85.82 % 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: 1.45 (0.18), residues: 2352 helix: 1.72 (0.13), residues: 1672 sheet: 0.54 (0.57), residues: 100 loop : -1.22 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 996 TYR 0.011 0.001 TYR D 456 PHE 0.010 0.001 PHE B 877 TRP 0.009 0.001 TRP D 832 HIS 0.004 0.001 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (20236) covalent geometry : angle 0.50359 / 0.25 (27412) hydrogen bonds : bond 0.04934 / 3.43 ( 1145) hydrogen bonds : angle 3.55944 / 2.53 ( 3339) link_BETA1-4 : bond 0.00343 / 0.17 ( 4) link_BETA1-4 : angle 1.26579 / 0.81 ( 12) link_NAG-ASN : bond 0.00228 / 0.16 ( 8) link_NAG-ASN : angle 1.18971 / 0.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.774 Fit side-chains REVERT: A 920 GLU cc_start: 0.8608 (tt0) cc_final: 0.7956 (mp0) REVERT: A 1059 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8264 (mt-10) REVERT: B 651 CYS cc_start: 0.8487 (m) cc_final: 0.8228 (t) REVERT: B 664 GLN cc_start: 0.8755 (pt0) cc_final: 0.8218 (pm20) REVERT: B 920 GLU cc_start: 0.8635 (tt0) cc_final: 0.8027 (mp0) REVERT: B 1059 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8180 (mt-10) REVERT: C 920 GLU cc_start: 0.8617 (tt0) cc_final: 0.8010 (mp0) REVERT: D 651 CYS cc_start: 0.8480 (m) cc_final: 0.8196 (m) REVERT: D 920 GLU cc_start: 0.8628 (tt0) cc_final: 0.8005 (mp0) REVERT: D 1059 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8266 (mt-10) outliers start: 39 outliers final: 25 residues processed: 213 average time/residue: 0.6636 time to fit residues: 159.2263 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 : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 721 MET 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 912 MET Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 115 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 215 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 940 GLN C 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.080007 restraints weight = 27655.363| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.51 r_work: 0.2801 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20248 Z= 0.193 Angle : 0.553 9.339 27448 Z= 0.272 Chirality : 0.041 0.178 3180 Planarity : 0.004 0.047 3296 Dihedral : 9.385 140.864 2840 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.82 % Allowed : 12.84 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2352 helix: 1.58 (0.13), residues: 1700 sheet: 0.44 (0.57), residues: 100 loop : -1.11 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 996 TYR 0.012 0.001 TYR A 456 PHE 0.009 0.001 PHE B 583 TRP 0.009 0.001 TRP D 832 HIS 0.004 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.19 (20236) covalent geometry : angle 0.55180 / 0.27 (27412) hydrogen bonds : bond 0.05748 / 3.99 ( 1145) hydrogen bonds : angle 3.71783 / 2.64 ( 3339) link_BETA1-4 : bond 0.00327 / 0.16 ( 4) link_BETA1-4 : angle 1.34285 / 0.86 ( 12) link_NAG-ASN : bond 0.00153 / 0.10 ( 8) link_NAG-ASN : angle 1.14540 / 0.92 ( 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 226 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.787 Fit side-chains REVERT: A 920 GLU cc_start: 0.8610 (tt0) cc_final: 0.7961 (mp0) REVERT: A 1059 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 651 CYS cc_start: 0.8500 (m) cc_final: 0.8241 (t) REVERT: B 664 GLN cc_start: 0.8820 (pt0) cc_final: 0.8254 (pm20) REVERT: B 920 GLU cc_start: 0.8625 (tt0) cc_final: 0.7971 (mp0) REVERT: B 1059 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 1063 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: C 920 GLU cc_start: 0.8604 (tt0) cc_final: 0.7974 (mp0) REVERT: D 651 CYS cc_start: 0.8477 (m) cc_final: 0.8191 (m) REVERT: D 920 GLU cc_start: 0.8628 (tt0) cc_final: 0.7968 (mp0) REVERT: D 1059 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8272 (mt-10) outliers start: 38 outliers final: 23 residues processed: 213 average time/residue: 0.6383 time to fit residues: 153.6575 Evaluate side-chains 208 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 864 GLU Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 992 LEU 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 B residue 1063 GLU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 839 VAL 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: 0.7980 chunk 193 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 152 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081437 restraints weight = 27509.611| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.52 r_work: 0.2878 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20248 Z= 0.130 Angle : 0.501 9.184 27448 Z= 0.248 Chirality : 0.039 0.177 3180 Planarity : 0.004 0.047 3296 Dihedral : 9.046 136.957 2833 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.63 % Allowed : 13.36 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.18), residues: 2352 helix: 1.74 (0.13), residues: 1672 sheet: 0.53 (0.57), residues: 100 loop : -1.14 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1050 TYR 0.011 0.001 TYR C 456 PHE 0.010 0.001 PHE B 877 TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (20236) covalent geometry : angle 0.49934 / 0.25 (27412) hydrogen bonds : bond 0.04895 / 3.40 ( 1145) hydrogen bonds : angle 3.62218 / 2.57 ( 3339) link_BETA1-4 : bond 0.00350 / 0.18 ( 4) link_BETA1-4 : angle 1.27227 / 0.82 ( 12) link_NAG-ASN : bond 0.00234 / 0.16 ( 8) link_NAG-ASN : angle 1.15250 / 0.95 ( 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 218 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.764 Fit side-chains REVERT: A 911 MET cc_start: 0.9152 (mtp) cc_final: 0.8813 (mtp) REVERT: A 920 GLU cc_start: 0.8642 (tt0) cc_final: 0.8085 (mp0) REVERT: A 1059 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8371 (mt-10) REVERT: B 651 CYS cc_start: 0.8604 (m) cc_final: 0.8282 (t) REVERT: B 664 GLN cc_start: 0.8842 (pt0) cc_final: 0.8361 (pm20) REVERT: B 920 GLU cc_start: 0.8679 (tt0) cc_final: 0.8140 (mp0) REVERT: B 1059 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 1063 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: C 920 GLU cc_start: 0.8670 (tt0) cc_final: 0.8127 (mp0) REVERT: D 651 CYS cc_start: 0.8509 (m) cc_final: 0.8243 (m) REVERT: D 920 GLU cc_start: 0.8681 (tt0) cc_final: 0.8106 (mp0) REVERT: D 1059 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8375 (mt-10) outliers start: 34 outliers final: 25 residues processed: 206 average time/residue: 0.5903 time to fit residues: 137.7511 Evaluate side-chains 205 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 824 VAL Chi-restraints excluded: chain A residue 864 GLU 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 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 B residue 1063 GLU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 721 MET 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 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: 4.9990 chunk 4 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083117 restraints weight = 27397.716| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.52 r_work: 0.2862 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2350 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 : 0.501 11.321 27448 Z= 0.244 Chirality : 0.038 0.176 3180 Planarity : 0.004 0.046 3296 Dihedral : 8.724 134.229 2830 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.25 % Allowed : 13.84 % 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: 1.64 (0.18), residues: 2352 helix: 1.84 (0.13), residues: 1672 sheet: 0.57 (0.58), residues: 100 loop : -1.06 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1050 TYR 0.011 0.001 TYR B 456 PHE 0.009 0.001 PHE B 877 TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20236) covalent geometry : angle 0.49990 / 0.24 (27412) hydrogen bonds : bond 0.04442 / 3.09 ( 1145) hydrogen bonds : angle 3.52518 / 2.50 ( 3339) link_BETA1-4 : bond 0.00329 / 0.17 ( 4) link_BETA1-4 : angle 1.25019 / 0.81 ( 12) link_NAG-ASN : bond 0.00271 / 0.19 ( 8) link_NAG-ASN : angle 1.14012 / 0.93 ( 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 213 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.799 Fit side-chains REVERT: A 664 GLN cc_start: 0.8751 (pt0) cc_final: 0.8424 (pt0) REVERT: A 920 GLU cc_start: 0.8623 (tt0) cc_final: 0.8006 (mp0) REVERT: A 996 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.8090 (mpt-90) REVERT: A 1059 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 651 CYS cc_start: 0.8559 (m) cc_final: 0.8218 (t) REVERT: B 664 GLN cc_start: 0.8799 (pt0) cc_final: 0.8297 (pm20) REVERT: B 920 GLU cc_start: 0.8652 (tt0) cc_final: 0.8018 (mp0) REVERT: B 1059 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8282 (mt-10) REVERT: C 920 GLU cc_start: 0.8619 (tt0) cc_final: 0.8023 (mp0) REVERT: D 651 CYS cc_start: 0.8475 (m) cc_final: 0.8199 (m) REVERT: D 920 GLU cc_start: 0.8652 (tt0) cc_final: 0.8038 (mp0) REVERT: D 1059 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8228 (mt-10) outliers start: 26 outliers final: 21 residues processed: 202 average time/residue: 0.6116 time to fit residues: 140.0460 Evaluate side-chains 203 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 824 VAL Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 721 MET 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 785 TYR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 912 MET 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: 0.9980 chunk 189 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.082674 restraints weight = 27503.295| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.52 r_work: 0.2819 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2358 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= 0.122 Angle : 0.502 11.977 27448 Z= 0.247 Chirality : 0.039 0.175 3180 Planarity : 0.004 0.046 3296 Dihedral : 8.647 133.876 2827 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.10 % Allowed : 14.03 % Favored : 84.87 % 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: 1.69 (0.18), residues: 2352 helix: 1.87 (0.13), residues: 1672 sheet: 0.59 (0.58), residues: 100 loop : -0.99 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1050 TYR 0.012 0.001 TYR D 456 PHE 0.011 0.001 PHE B 877 TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (20236) covalent geometry : angle 0.50032 / 0.25 (27412) hydrogen bonds : bond 0.04649 / 3.23 ( 1145) hydrogen bonds : angle 3.53599 / 2.51 ( 3339) link_BETA1-4 : bond 0.00322 / 0.16 ( 4) link_BETA1-4 : angle 1.26146 / 0.81 ( 12) link_NAG-ASN : bond 0.00244 / 0.17 ( 8) link_NAG-ASN : angle 1.12458 / 0.92 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.788 Fit side-chains REVERT: A 920 GLU cc_start: 0.8643 (tt0) cc_final: 0.8052 (mp0) REVERT: A 1059 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 651 CYS cc_start: 0.8564 (m) cc_final: 0.8249 (t) REVERT: B 664 GLN cc_start: 0.8818 (pt0) cc_final: 0.8336 (pm20) REVERT: B 920 GLU cc_start: 0.8687 (tt0) cc_final: 0.8117 (mp0) REVERT: B 1059 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8342 (mt-10) REVERT: C 920 GLU cc_start: 0.8654 (tt0) cc_final: 0.8098 (mp0) REVERT: D 651 CYS cc_start: 0.8480 (m) cc_final: 0.8212 (m) REVERT: D 920 GLU cc_start: 0.8680 (tt0) cc_final: 0.8109 (mp0) REVERT: D 1059 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8304 (mt-10) outliers start: 23 outliers final: 20 residues processed: 201 average time/residue: 0.6220 time to fit residues: 141.1279 Evaluate side-chains 207 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 824 VAL Chi-restraints excluded: chain A residue 912 MET 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 721 MET 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 785 TYR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 912 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083123 restraints weight = 27578.776| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.53 r_work: 0.2826 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20248 Z= 0.114 Angle : 0.502 11.762 27448 Z= 0.245 Chirality : 0.038 0.174 3180 Planarity : 0.004 0.045 3296 Dihedral : 8.501 132.674 2827 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.20 % Allowed : 14.18 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.18), residues: 2352 helix: 1.90 (0.13), residues: 1672 sheet: 0.65 (0.59), residues: 100 loop : -0.94 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1050 TYR 0.011 0.001 TYR C 456 PHE 0.011 0.001 PHE B 877 TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (20236) covalent geometry : angle 0.50101 / 0.24 (27412) hydrogen bonds : bond 0.04457 / 3.10 ( 1145) hydrogen bonds : angle 3.51349 / 2.49 ( 3339) link_BETA1-4 : bond 0.00339 / 0.17 ( 4) link_BETA1-4 : angle 1.24301 / 0.80 ( 12) link_NAG-ASN : bond 0.00258 / 0.18 ( 8) link_NAG-ASN : angle 1.11263 / 0.91 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7118.71 seconds wall clock time: 122 minutes 4.22 seconds (7324.22 seconds total)