Starting phenix.real_space_refine on Sun Aug 9 02:34:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ov5_70890/08_2026/9ov5_70890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ov5_70890/08_2026/9ov5_70890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ov5_70890/08_2026/9ov5_70890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ov5_70890/08_2026/9ov5_70890.map" model { file = "/net/cci-nas-00/data/ceres_data/9ov5_70890/08_2026/9ov5_70890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ov5_70890/08_2026/9ov5_70890.cif" } resolution = 3.34 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 10161 2.51 5 N 2830 2.21 5 O 2890 1.98 5 H 15580 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31509 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1976 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1976 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1945 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1984 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1976 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1977 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1970 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1976 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1969 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1977 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "K" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1952 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1960 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "M" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1961 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "N" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1967 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "O" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1976 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "P" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1967 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 5.24, per 1000 atoms: 0.17 Number of scatterers: 31509 At special positions: 0 Unit cell: (100.43, 100.43, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 2890 8.00 N 2830 7.00 C 10161 6.00 H 15580 1.00 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 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 936.6 milliseconds 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 58.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid -12 through 25 removed outlier: 4.405A pdb=" N GLN A -8 " --> pdb=" O MET A -12 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A -2 " --> pdb=" O ILE A -6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 48 Processing helix chain 'A' and resid 50 through 69 removed outlier: 4.195A pdb=" N TYR A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) Processing helix chain 'B' and resid -11 through 24 removed outlier: 4.278A pdb=" N ASN B -7 " --> pdb=" O THR B -11 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 49 removed outlier: 4.129A pdb=" N ARG B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 69 Processing helix chain 'C' and resid -11 through 23 removed outlier: 3.822A pdb=" N ARG C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 49 Processing helix chain 'C' and resid 53 through 69 removed outlier: 4.120A pdb=" N TYR C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'D' and resid -11 through 24 Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.941A pdb=" N GLY D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 69 Processing helix chain 'E' and resid -11 through 25 removed outlier: 4.266A pdb=" N GLU E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 19 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 24 " --> pdb=" O GLU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.773A pdb=" N GLY E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY E 47 " --> pdb=" O MET E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 69 Processing helix chain 'F' and resid -11 through 22 removed outlier: 3.648A pdb=" N MET F -2 " --> pdb=" O ILE F -6 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 49 Processing helix chain 'F' and resid 50 through 69 Processing helix chain 'G' and resid -11 through 23 removed outlier: 3.742A pdb=" N GLU G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 49 Processing helix chain 'G' and resid 50 through 69 removed outlier: 3.652A pdb=" N LYS G 67 " --> pdb=" O GLN G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 102 Processing helix chain 'H' and resid -11 through 24 removed outlier: 3.745A pdb=" N GLU H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 49 Processing helix chain 'H' and resid 52 through 69 Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'I' and resid -11 through 23 removed outlier: 3.836A pdb=" N GLU I 18 " --> pdb=" O ARG I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 49 removed outlier: 3.584A pdb=" N GLY I 47 " --> pdb=" O MET I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 69 Processing helix chain 'J' and resid -10 through 25 removed outlier: 3.776A pdb=" N VAL J -3 " --> pdb=" O ASN J -7 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET J -2 " --> pdb=" O ILE J -6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE J 0 " --> pdb=" O ALA J -4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG J 14 " --> pdb=" O ARG J 10 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU J 17 " --> pdb=" O GLU J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 49 Processing helix chain 'J' and resid 52 through 69 removed outlier: 3.899A pdb=" N TYR J 56 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR J 57 " --> pdb=" O GLU J 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS J 67 " --> pdb=" O GLN J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 102 removed outlier: 3.883A pdb=" N LEU J 101 " --> pdb=" O PRO J 98 " (cutoff:3.500A) Processing helix chain 'K' and resid -11 through 24 removed outlier: 3.630A pdb=" N ASN K -7 " --> pdb=" O THR K -11 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU K 18 " --> pdb=" O ARG K 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 49 removed outlier: 3.615A pdb=" N GLY K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 69 removed outlier: 3.628A pdb=" N GLU K 64 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS K 67 " --> pdb=" O GLN K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 102 removed outlier: 3.638A pdb=" N LEU K 101 " --> pdb=" O PRO K 98 " (cutoff:3.500A) Processing helix chain 'L' and resid -11 through 24 removed outlier: 4.358A pdb=" N ASN L -7 " --> pdb=" O THR L -11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG L 14 " --> pdb=" O ARG L 10 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 49 removed outlier: 3.947A pdb=" N GLY L 47 " --> pdb=" O MET L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 69 Processing helix chain 'L' and resid 100 through 102 No H-bonds generated for 'chain 'L' and resid 100 through 102' Processing helix chain 'M' and resid -11 through 25 removed outlier: 3.686A pdb=" N GLU M 17 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG M 25 " --> pdb=" O ARG M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 49 removed outlier: 3.864A pdb=" N GLY M 47 " --> pdb=" O MET M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 69 removed outlier: 3.546A pdb=" N LYS M 67 " --> pdb=" O GLN M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'N' and resid -11 through 25 removed outlier: 3.877A pdb=" N GLU N 17 " --> pdb=" O GLU N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 49 removed outlier: 3.523A pdb=" N GLY N 47 " --> pdb=" O MET N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 69 Processing helix chain 'O' and resid -11 through 24 removed outlier: 3.934A pdb=" N GLU O 17 " --> pdb=" O GLU O 13 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 49 removed outlier: 3.722A pdb=" N ARG O 34 " --> pdb=" O GLY O 30 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY O 47 " --> pdb=" O MET O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 69 removed outlier: 3.542A pdb=" N GLU O 64 " --> pdb=" O LYS O 60 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS O 67 " --> pdb=" O GLN O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid -11 through 24 removed outlier: 3.750A pdb=" N GLU P 17 " --> pdb=" O GLU P 13 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU P 18 " --> pdb=" O ARG P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 49 removed outlier: 4.389A pdb=" N ARG P 34 " --> pdb=" O GLY P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 69 removed outlier: 3.850A pdb=" N LYS P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 73 through 75 removed outlier: 4.075A pdb=" N ILE G 78 " --> pdb=" O LEU H 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 73 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 105 removed outlier: 5.266A pdb=" N VAL E 104 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 88 through 89 Processing sheet with id=AA7, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AA8, first strand: chain 'L' and resid 119 through 121 removed outlier: 3.637A pdb=" N PHE K 80 " --> pdb=" O ALA L 117 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY N 120 " --> pdb=" O SER N 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU P 119 " --> pdb=" O ILE O 78 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY J 112 " --> pdb=" O SER J 81 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER J 81 " --> pdb=" O GLY J 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 88 through 89 removed outlier: 3.546A pdb=" N GLY P 92 " --> pdb=" O VAL I 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 104 through 105 removed outlier: 5.148A pdb=" N ILE M 89 " --> pdb=" O THR N 106 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL N 104 " --> pdb=" O ASP M 91 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3510 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: 8.16 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15580 1.03 - 1.22: 2 1.22 - 1.42: 6694 1.42 - 1.62: 9409 1.62 - 1.81: 96 Bond restraints: 31781 Sorted by residual: bond pdb=" CB GLU D 53 " pdb=" CG GLU D 53 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" N GLU D 53 " pdb=" H GLU D 53 " ideal model delta sigma weight residual 0.860 0.833 0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C LEU C 88 " pdb=" N ILE C 89 " ideal model delta sigma weight residual 1.334 1.317 0.016 1.24e-02 6.50e+03 1.71e+00 bond pdb=" CA GLU D 53 " pdb=" CB GLU D 53 " ideal model delta sigma weight residual 1.528 1.546 -0.018 1.66e-02 3.63e+03 1.13e+00 bond pdb=" C LEU N 88 " pdb=" N ILE N 89 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.24e-02 6.50e+03 1.08e+00 ... (remaining 31776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 55725 1.45 - 2.90: 1426 2.90 - 4.35: 124 4.35 - 5.80: 8 5.80 - 7.25: 3 Bond angle restraints: 57286 Sorted by residual: angle pdb=" CA GLU D 53 " pdb=" CB GLU D 53 " pdb=" CG GLU D 53 " ideal model delta sigma weight residual 114.10 120.29 -6.19 2.00e+00 2.50e-01 9.57e+00 angle pdb=" C PHE G 99 " pdb=" CA PHE G 99 " pdb=" CB PHE G 99 " ideal model delta sigma weight residual 115.89 111.92 3.97 1.32e+00 5.74e-01 9.03e+00 angle pdb=" C LEU I 59 " pdb=" N LYS I 60 " pdb=" CA LYS I 60 " ideal model delta sigma weight residual 120.29 116.54 3.75 1.42e+00 4.96e-01 6.99e+00 angle pdb=" CA PRO O 107 " pdb=" C PRO O 107 " pdb=" N ASN O 108 " ideal model delta sigma weight residual 115.12 118.33 -3.21 1.25e+00 6.40e-01 6.61e+00 angle pdb=" CB GLU D 53 " pdb=" CG GLU D 53 " pdb=" CD GLU D 53 " ideal model delta sigma weight residual 112.60 116.67 -4.07 1.70e+00 3.46e-01 5.73e+00 ... (remaining 57281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 13062 17.62 - 35.25: 1181 35.25 - 52.87: 485 52.87 - 70.50: 123 70.50 - 88.12: 26 Dihedral angle restraints: 14877 sinusoidal: 8114 harmonic: 6763 Sorted by residual: dihedral pdb=" CA SER M 81 " pdb=" C SER M 81 " pdb=" N TYR M 82 " pdb=" CA TYR M 82 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE O 94 " pdb=" C ILE O 94 " pdb=" N THR O 95 " pdb=" CA THR O 95 " ideal model delta harmonic sigma weight residual 180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASN O 108 " pdb=" C ASN O 108 " pdb=" N LEU O 109 " pdb=" CA LEU O 109 " ideal model delta harmonic sigma weight residual 180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 14874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1649 0.032 - 0.064: 594 0.064 - 0.096: 146 0.096 - 0.128: 78 0.128 - 0.160: 22 Chirality restraints: 2489 Sorted by residual: chirality pdb=" CA PRO D 51 " pdb=" N PRO D 51 " pdb=" C PRO D 51 " pdb=" CB PRO D 51 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE L 105 " pdb=" N ILE L 105 " pdb=" C ILE L 105 " pdb=" CB ILE L 105 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE H 105 " pdb=" N ILE H 105 " pdb=" C ILE H 105 " pdb=" CB ILE H 105 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 2486 not shown) Planarity restraints: 4831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 50 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO K 51 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO K 51 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 51 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG O 96 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO O 97 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO O 97 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO O 97 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 96 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO F 97 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 97 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 97 " -0.028 5.00e-02 4.00e+02 ... (remaining 4828 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 8456 2.32 - 2.89: 72093 2.89 - 3.46: 83678 3.46 - 4.03: 113463 4.03 - 4.60: 174649 Nonbonded interactions: 452339 Sorted by model distance: nonbonded pdb=" OE1 GLU D 53 " pdb=" H GLU D 53 " model vdw 1.755 2.450 nonbonded pdb=" HG1 THR F 84 " pdb=" H VAL G 113 " model vdw 1.771 2.100 nonbonded pdb=" H GLU M 53 " pdb=" HG2 GLU M 53 " model vdw 1.824 2.270 nonbonded pdb=" HG3 ARG L 10 " pdb="HH11 ARG L 10 " model vdw 1.840 2.270 nonbonded pdb=" HB2 LYS F 60 " pdb=" HZ3 LYS F 60 " model vdw 1.841 2.270 ... (remaining 452334 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 -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 121)) \ selection = (chain 'B' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'C' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 17 or (resid 18 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 19 through 20 or (resid 21 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 22 through 24 or resid 30 through 63 o \ r (resid 64 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 65 through 121)) selection = (chain 'D' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'E' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 through 20 or (resid 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'F' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'G' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 or (resid 66 through 68 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 69 through 121)) selection = (chain 'H' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 17 or (resid 18 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 19 or (resid 20 through 21 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 22 t \ hrough 24 or resid 30 through 52 or (resid 53 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 54 through 63 or (resid 64 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 65 through 121)) selection = (chain 'I' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 through 20 or (resid 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'J' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'K' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'L' and (resid -12 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 14 through 16 or (resid \ 17 through 18 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 19 or (resid 20 through 21 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 22 through 24 or resid 3 \ 0 through 52 or (resid 53 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 54 through 121)) selection = (chain 'M' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 through 20 or (resid 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'N' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) selection = (chain 'O' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 121)) \ selection = (chain 'P' and (resid -12 through 5 or (resid 6 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 7 through 12 or (resid 13 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 14 through 16 or (resid 17 through 18 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 19 or (resid 20 through 21 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 24 or resid 30 through 52 or (resid 53 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 54 through 63 or \ (resid 64 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 65 through 121)) } 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: 3.320 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: 0.210 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 30.490 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.003 0.047 16201 Z= 0.163 Angle : 0.596 7.251 21944 Z= 0.337 Chirality : 0.040 0.160 2489 Planarity : 0.005 0.056 2870 Dihedral : 15.546 88.124 5912 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.47 % Allowed : 15.78 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.74 (0.18), residues: 2025 helix: 1.41 (0.14), residues: 1134 sheet: 0.42 (0.28), residues: 316 loop : -1.30 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 10 TYR 0.015 0.001 TYR M 82 PHE 0.015 0.001 PHE J 99 TRP 0.019 0.002 TRP C 72 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (16201) covalent geometry : angle 0.59556 / 0.34 (21944) hydrogen bonds : bond 0.14860 / 9.94 ( 1224) hydrogen bonds : angle 5.98867 / 4.27 ( 3510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 474 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 451 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7680 (tp30) cc_final: 0.7192 (tp30) REVERT: A 103 SER cc_start: 0.7789 (m) cc_final: 0.7392 (t) REVERT: A 116 SER cc_start: 0.7980 (t) cc_final: 0.7563 (m) REVERT: B 39 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7741 (tt) REVERT: C -2 MET cc_start: 0.7302 (mmm) cc_final: 0.6955 (mmm) REVERT: D 14 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7714 (mtm180) REVERT: D 64 GLU cc_start: 0.6948 (tt0) cc_final: 0.6692 (tt0) REVERT: D 116 SER cc_start: 0.8208 (m) cc_final: 0.7358 (t) REVERT: E 64 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7149 (mm-30) REVERT: H 32 LEU cc_start: 0.8054 (tp) cc_final: 0.7820 (tt) REVERT: H 80 PHE cc_start: 0.7970 (t80) cc_final: 0.7452 (t80) REVERT: J 45 TYR cc_start: 0.8036 (m-80) cc_final: 0.6943 (m-10) REVERT: K 78 ILE cc_start: 0.7997 (mp) cc_final: 0.7586 (mt) REVERT: L 9 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6875 (mpp80) REVERT: M -11 THR cc_start: 0.8212 (p) cc_final: 0.7907 (t) REVERT: M 48 SER cc_start: 0.8159 (m) cc_final: 0.7778 (t) REVERT: N 20 GLU cc_start: 0.7019 (tp30) cc_final: 0.6547 (tp30) REVERT: P 103 SER cc_start: 0.7814 (p) cc_final: 0.7288 (p) outliers start: 23 outliers final: 17 residues processed: 467 average time/residue: 0.3973 time to fit residues: 255.3555 Evaluate side-chains 456 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 437 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123485 restraints weight = 60470.626| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.70 r_work: 0.3485 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16201 Z= 0.176 Angle : 0.561 7.555 21944 Z= 0.305 Chirality : 0.039 0.170 2489 Planarity : 0.005 0.056 2870 Dihedral : 5.876 56.141 2349 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.49 % Allowed : 15.40 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.01 (0.18), residues: 2025 helix: 1.66 (0.14), residues: 1133 sheet: 0.45 (0.27), residues: 320 loop : -1.20 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.013 0.001 TYR P 44 PHE 0.014 0.001 PHE J 99 TRP 0.008 0.001 TRP C 72 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (16201) covalent geometry : angle 0.56115 / 0.31 (21944) hydrogen bonds : bond 0.05872 / 3.89 ( 1224) hydrogen bonds : angle 4.91799 / 3.53 ( 3510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 429 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7637 (tp30) cc_final: 0.7055 (tp30) REVERT: A 103 SER cc_start: 0.7835 (m) cc_final: 0.7476 (t) REVERT: A 116 SER cc_start: 0.7905 (t) cc_final: 0.7484 (m) REVERT: B 39 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7816 (tt) REVERT: C -2 MET cc_start: 0.7276 (mmm) cc_final: 0.6853 (mmm) REVERT: D 14 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7746 (mtp85) REVERT: D 64 GLU cc_start: 0.6866 (tt0) cc_final: 0.6594 (tt0) REVERT: E 60 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7949 (ttmm) REVERT: E 64 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7050 (mm-30) REVERT: G -2 MET cc_start: 0.7693 (mmt) cc_final: 0.7378 (mmt) REVERT: I 103 SER cc_start: 0.8237 (t) cc_final: 0.7842 (p) REVERT: L 9 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6900 (mpp80) REVERT: M 14 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7905 (tpp-160) REVERT: M 48 SER cc_start: 0.8180 (m) cc_final: 0.7884 (t) REVERT: P 103 SER cc_start: 0.7611 (p) cc_final: 0.7103 (p) outliers start: 39 outliers final: 30 residues processed: 455 average time/residue: 0.3950 time to fit residues: 249.1425 Evaluate side-chains 454 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 422 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E -7 ASN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121357 restraints weight = 61065.549| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.71 r_work: 0.3463 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16201 Z= 0.257 Angle : 0.593 5.576 21944 Z= 0.327 Chirality : 0.041 0.170 2489 Planarity : 0.006 0.062 2870 Dihedral : 5.699 58.104 2339 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.03 % Allowed : 15.21 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.71 (0.17), residues: 2025 helix: 1.38 (0.14), residues: 1132 sheet: 0.46 (0.27), residues: 320 loop : -1.31 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 16 TYR 0.014 0.002 TYR I 56 PHE 0.020 0.002 PHE A 80 TRP 0.010 0.002 TRP I 72 HIS 0.006 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.26 (16201) covalent geometry : angle 0.59339 / 0.33 (21944) hydrogen bonds : bond 0.06157 / 4.09 ( 1224) hydrogen bonds : angle 4.87349 / 3.51 ( 3510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 516 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 453 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7637 (tp30) cc_final: 0.7296 (tp30) REVERT: A 116 SER cc_start: 0.8005 (t) cc_final: 0.7586 (m) REVERT: B 39 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7801 (tt) REVERT: B 114 SER cc_start: 0.8129 (t) cc_final: 0.7596 (p) REVERT: C -2 MET cc_start: 0.7280 (mmm) cc_final: 0.6900 (mmm) REVERT: D 14 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7756 (mtp85) REVERT: D 64 GLU cc_start: 0.6897 (tt0) cc_final: 0.6665 (tt0) REVERT: D 116 SER cc_start: 0.8123 (m) cc_final: 0.7349 (t) REVERT: E 60 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7948 (ttmm) REVERT: E 64 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7100 (mm-30) REVERT: F 14 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7188 (mtt-85) REVERT: G -2 MET cc_start: 0.7682 (mmt) cc_final: 0.7471 (mmt) REVERT: I 103 SER cc_start: 0.8279 (t) cc_final: 0.7869 (p) REVERT: J 21 ARG cc_start: 0.6995 (ttp80) cc_final: 0.6777 (ttp80) REVERT: L 9 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6908 (mpp80) REVERT: M 14 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7922 (tpp-160) REVERT: M 48 SER cc_start: 0.8169 (m) cc_final: 0.7882 (t) REVERT: M 93 ASP cc_start: 0.7637 (t0) cc_final: 0.7383 (t0) REVERT: O 19 ILE cc_start: 0.7338 (tp) cc_final: 0.7057 (tt) REVERT: P 103 SER cc_start: 0.7681 (p) cc_final: 0.7181 (p) REVERT: P 113 VAL cc_start: 0.8335 (p) cc_final: 0.8075 (m) outliers start: 63 outliers final: 44 residues processed: 488 average time/residue: 0.4037 time to fit residues: 271.2466 Evaluate side-chains 497 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 450 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 88 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118833 restraints weight = 61442.070| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.80 r_work: 0.3409 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16201 Z= 0.233 Angle : 0.572 5.874 21944 Z= 0.312 Chirality : 0.040 0.165 2489 Planarity : 0.006 0.062 2870 Dihedral : 5.687 59.837 2339 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.09 % Allowed : 16.81 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.80 (0.17), residues: 2025 helix: 1.44 (0.14), residues: 1132 sheet: 0.57 (0.27), residues: 321 loop : -1.31 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 16 TYR 0.012 0.001 TYR I 56 PHE 0.017 0.002 PHE A 80 TRP 0.009 0.002 TRP I 72 HIS 0.005 0.001 HIS J 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (16201) covalent geometry : angle 0.57234 / 0.31 (21944) hydrogen bonds : bond 0.05731 / 3.81 ( 1224) hydrogen bonds : angle 4.73713 / 3.41 ( 3510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 512 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 448 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7709 (tp30) cc_final: 0.7372 (tp30) REVERT: A 116 SER cc_start: 0.7987 (t) cc_final: 0.7588 (m) REVERT: B 39 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7817 (tt) REVERT: B 104 VAL cc_start: 0.8283 (m) cc_final: 0.8062 (p) REVERT: B 114 SER cc_start: 0.8106 (t) cc_final: 0.7561 (p) REVERT: C -2 MET cc_start: 0.7324 (mmm) cc_final: 0.6941 (mmm) REVERT: D 14 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7832 (mtp85) REVERT: D 64 GLU cc_start: 0.7136 (tt0) cc_final: 0.6874 (tt0) REVERT: E -11 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7677 (m) REVERT: E -5 GLN cc_start: 0.7891 (tp40) cc_final: 0.7651 (tp40) REVERT: E 60 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7950 (ttmm) REVERT: E 64 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7169 (mm-30) REVERT: F 14 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7217 (mtt-85) REVERT: H 80 PHE cc_start: 0.8045 (t80) cc_final: 0.7519 (t80) REVERT: I 103 SER cc_start: 0.8163 (t) cc_final: 0.7868 (p) REVERT: L 9 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6852 (mpp80) REVERT: M 14 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7951 (tpp-160) REVERT: M 48 SER cc_start: 0.8128 (m) cc_final: 0.7877 (t) REVERT: O 6 GLU cc_start: 0.7233 (tp30) cc_final: 0.6952 (tp30) REVERT: O 19 ILE cc_start: 0.7345 (tp) cc_final: 0.7095 (tt) REVERT: P 103 SER cc_start: 0.7652 (p) cc_final: 0.7165 (p) REVERT: P 110 PHE cc_start: 0.8354 (m-80) cc_final: 0.8002 (m-80) REVERT: P 113 VAL cc_start: 0.8309 (p) cc_final: 0.8047 (m) outliers start: 64 outliers final: 50 residues processed: 484 average time/residue: 0.4015 time to fit residues: 267.0270 Evaluate side-chains 507 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 453 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue -11 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 88 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 92 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118301 restraints weight = 61402.135| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.78 r_work: 0.3403 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16201 Z= 0.255 Angle : 0.580 6.045 21944 Z= 0.318 Chirality : 0.040 0.166 2489 Planarity : 0.006 0.064 2870 Dihedral : 5.719 59.315 2339 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.41 % Allowed : 16.93 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.77 (0.17), residues: 2025 helix: 1.41 (0.14), residues: 1133 sheet: 0.63 (0.27), residues: 321 loop : -1.36 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 16 TYR 0.012 0.002 TYR N 44 PHE 0.019 0.002 PHE A 80 TRP 0.008 0.002 TRP L 72 HIS 0.006 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.26 (16201) covalent geometry : angle 0.57968 / 0.32 (21944) hydrogen bonds : bond 0.05815 / 3.86 ( 1224) hydrogen bonds : angle 4.71723 / 3.40 ( 3510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 510 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 441 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7707 (tp30) cc_final: 0.7381 (tp30) REVERT: A 15 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7270 (mp) REVERT: A 116 SER cc_start: 0.8038 (t) cc_final: 0.7593 (m) REVERT: B 39 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7813 (tt) REVERT: B 104 VAL cc_start: 0.8310 (m) cc_final: 0.8098 (p) REVERT: B 114 SER cc_start: 0.8130 (t) cc_final: 0.7631 (p) REVERT: C -2 MET cc_start: 0.7283 (mmm) cc_final: 0.6878 (mmm) REVERT: C 83 THR cc_start: 0.8485 (m) cc_final: 0.8206 (p) REVERT: D -12 MET cc_start: 0.7715 (mmm) cc_final: 0.7468 (mmm) REVERT: D 14 ARG cc_start: 0.8129 (mtm180) cc_final: 0.7849 (mtp85) REVERT: D 64 GLU cc_start: 0.7192 (tt0) cc_final: 0.6911 (tt0) REVERT: D 116 SER cc_start: 0.8035 (m) cc_final: 0.7254 (t) REVERT: E -5 GLN cc_start: 0.7845 (tp40) cc_final: 0.7611 (tp40) REVERT: E 60 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7941 (ttmm) REVERT: F -2 MET cc_start: 0.8123 (mmm) cc_final: 0.7672 (mmp) REVERT: F 14 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7196 (mtt-85) REVERT: I 103 SER cc_start: 0.8195 (t) cc_final: 0.7802 (p) REVERT: L 9 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6821 (mpp80) REVERT: M 48 SER cc_start: 0.8120 (m) cc_final: 0.7885 (t) REVERT: O 19 ILE cc_start: 0.7378 (tp) cc_final: 0.7123 (tt) REVERT: P 10 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7485 (mtp180) REVERT: P 103 SER cc_start: 0.7603 (p) cc_final: 0.7134 (p) REVERT: P 110 PHE cc_start: 0.8347 (m-80) cc_final: 0.7980 (m-80) outliers start: 69 outliers final: 56 residues processed: 478 average time/residue: 0.3828 time to fit residues: 254.3417 Evaluate side-chains 496 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 435 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue -12 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 88 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 50 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C -7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118518 restraints weight = 61366.718| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.78 r_work: 0.3405 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16201 Z= 0.229 Angle : 0.564 6.863 21944 Z= 0.308 Chirality : 0.040 0.162 2489 Planarity : 0.006 0.067 2870 Dihedral : 5.670 58.975 2339 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.60 % Allowed : 17.38 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.84 (0.17), residues: 2025 helix: 1.47 (0.14), residues: 1132 sheet: 0.66 (0.27), residues: 321 loop : -1.33 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 10 TYR 0.012 0.001 TYR N 44 PHE 0.017 0.002 PHE A 80 TRP 0.008 0.001 TRP L 72 HIS 0.005 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (16201) covalent geometry : angle 0.56389 / 0.31 (21944) hydrogen bonds : bond 0.05634 / 3.75 ( 1224) hydrogen bonds : angle 4.64701 / 3.35 ( 3510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 500 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 428 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7652 (tp30) cc_final: 0.7325 (tp30) REVERT: A 15 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7284 (mp) REVERT: A 116 SER cc_start: 0.7998 (t) cc_final: 0.7615 (m) REVERT: B 39 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7810 (tt) REVERT: B 104 VAL cc_start: 0.8337 (m) cc_final: 0.8128 (p) REVERT: B 114 SER cc_start: 0.8164 (t) cc_final: 0.7641 (p) REVERT: C -2 MET cc_start: 0.7283 (mmm) cc_final: 0.6886 (mmm) REVERT: C 83 THR cc_start: 0.8487 (m) cc_final: 0.8244 (p) REVERT: D -12 MET cc_start: 0.7757 (mmm) cc_final: 0.7546 (mmm) REVERT: D 14 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7842 (mtp85) REVERT: D 64 GLU cc_start: 0.7193 (tt0) cc_final: 0.6938 (tt0) REVERT: D 116 SER cc_start: 0.8065 (m) cc_final: 0.7288 (t) REVERT: E -11 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7633 (m) REVERT: E 60 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7963 (ttmm) REVERT: F 14 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7185 (mtt-85) REVERT: F 15 LEU cc_start: 0.7710 (mt) cc_final: 0.7491 (tt) REVERT: H 80 PHE cc_start: 0.8006 (t80) cc_final: 0.7509 (t80) REVERT: I 103 SER cc_start: 0.8164 (t) cc_final: 0.7833 (p) REVERT: J 60 LYS cc_start: 0.8081 (tttt) cc_final: 0.7859 (tttt) REVERT: L 9 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6818 (mpp80) REVERT: L 103 SER cc_start: 0.6742 (OUTLIER) cc_final: 0.6482 (t) REVERT: O 19 ILE cc_start: 0.7391 (tp) cc_final: 0.7139 (tt) REVERT: P 10 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7492 (mtp180) REVERT: P 103 SER cc_start: 0.7615 (p) cc_final: 0.7145 (p) REVERT: P 110 PHE cc_start: 0.8354 (m-80) cc_final: 0.8018 (m-80) outliers start: 72 outliers final: 58 residues processed: 469 average time/residue: 0.3762 time to fit residues: 246.3377 Evaluate side-chains 491 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 426 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue -12 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue -11 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 14 ARG Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue -12 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 88 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 195 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C -7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119660 restraints weight = 61376.223| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.79 r_work: 0.3424 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16201 Z= 0.157 Angle : 0.524 7.197 21944 Z= 0.281 Chirality : 0.039 0.152 2489 Planarity : 0.006 0.066 2870 Dihedral : 5.445 56.534 2337 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.09 % Allowed : 17.70 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.28 (0.18), residues: 2025 helix: 1.88 (0.14), residues: 1132 sheet: 0.75 (0.27), residues: 321 loop : -1.22 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 10 TYR 0.012 0.001 TYR M 82 PHE 0.012 0.001 PHE A 80 TRP 0.010 0.001 TRP G 72 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (16201) covalent geometry : angle 0.52403 / 0.28 (21944) hydrogen bonds : bond 0.05077 / 3.37 ( 1224) hydrogen bonds : angle 4.41461 / 3.18 ( 3510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 427 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7552 (tp30) cc_final: 0.7295 (tp30) REVERT: A 15 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7208 (mp) REVERT: A 116 SER cc_start: 0.7966 (t) cc_final: 0.7560 (m) REVERT: B 114 SER cc_start: 0.8153 (t) cc_final: 0.7654 (p) REVERT: C -2 MET cc_start: 0.7292 (mmm) cc_final: 0.6861 (mmm) REVERT: C 83 THR cc_start: 0.8504 (m) cc_final: 0.8226 (p) REVERT: D -12 MET cc_start: 0.7761 (mmm) cc_final: 0.7542 (mmm) REVERT: D 14 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7791 (mtp85) REVERT: D 64 GLU cc_start: 0.7195 (tt0) cc_final: 0.6906 (tt0) REVERT: E -11 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7593 (m) REVERT: E 60 LYS cc_start: 0.8297 (mtpp) cc_final: 0.7967 (ttmm) REVERT: F -2 MET cc_start: 0.8155 (mmm) cc_final: 0.7686 (mmp) REVERT: F 15 LEU cc_start: 0.7682 (mt) cc_final: 0.7353 (tt) REVERT: H 80 PHE cc_start: 0.8012 (t80) cc_final: 0.7539 (t80) REVERT: I 103 SER cc_start: 0.8130 (t) cc_final: 0.7815 (p) REVERT: J 60 LYS cc_start: 0.8054 (tttt) cc_final: 0.7830 (tttt) REVERT: L 88 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7586 (pp) REVERT: L 103 SER cc_start: 0.6676 (OUTLIER) cc_final: 0.6429 (t) REVERT: N 20 GLU cc_start: 0.6963 (tp30) cc_final: 0.6530 (tp30) REVERT: O 19 ILE cc_start: 0.7372 (tp) cc_final: 0.7118 (tt) REVERT: P 10 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7161 (mtp180) REVERT: P 103 SER cc_start: 0.7585 (p) cc_final: 0.7126 (p) REVERT: P 110 PHE cc_start: 0.8342 (m-80) cc_final: 0.8052 (m-80) outliers start: 64 outliers final: 44 residues processed: 465 average time/residue: 0.3736 time to fit residues: 241.4279 Evaluate side-chains 470 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 421 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue -11 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue -12 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 86 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 169 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.129756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119564 restraints weight = 61447.001| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.79 r_work: 0.3421 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16201 Z= 0.181 Angle : 0.534 7.632 21944 Z= 0.286 Chirality : 0.039 0.152 2489 Planarity : 0.005 0.062 2870 Dihedral : 5.254 55.515 2331 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.09 % Allowed : 18.15 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.28 (0.18), residues: 2025 helix: 1.88 (0.14), residues: 1132 sheet: 0.80 (0.27), residues: 321 loop : -1.24 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.011 0.001 TYR M 82 PHE 0.015 0.001 PHE A 80 TRP 0.007 0.001 TRP L 72 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (16201) covalent geometry : angle 0.53401 / 0.29 (21944) hydrogen bonds : bond 0.05107 / 3.40 ( 1224) hydrogen bonds : angle 4.40629 / 3.18 ( 3510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 496 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 432 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7543 (tp30) cc_final: 0.7305 (tp30) REVERT: A 15 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7199 (mp) REVERT: A 116 SER cc_start: 0.8005 (t) cc_final: 0.7592 (m) REVERT: B 114 SER cc_start: 0.8148 (t) cc_final: 0.7665 (p) REVERT: D 14 ARG cc_start: 0.8113 (mtm180) cc_final: 0.7849 (mtp85) REVERT: D 64 GLU cc_start: 0.7190 (tt0) cc_final: 0.6905 (tt0) REVERT: E -11 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7572 (m) REVERT: E 60 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7971 (ttmm) REVERT: F -2 MET cc_start: 0.8130 (mmm) cc_final: 0.7652 (mmp) REVERT: H 80 PHE cc_start: 0.8003 (t80) cc_final: 0.7519 (t80) REVERT: I 103 SER cc_start: 0.8144 (t) cc_final: 0.7814 (p) REVERT: J 60 LYS cc_start: 0.8053 (tttt) cc_final: 0.7825 (tttt) REVERT: L 88 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7570 (pp) REVERT: L 103 SER cc_start: 0.6655 (OUTLIER) cc_final: 0.6393 (t) REVERT: N 20 GLU cc_start: 0.6945 (tp30) cc_final: 0.6518 (tp30) REVERT: O 19 ILE cc_start: 0.7378 (tp) cc_final: 0.7115 (tt) REVERT: P 10 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7152 (mtp180) REVERT: P 103 SER cc_start: 0.7565 (p) cc_final: 0.7064 (p) REVERT: P 110 PHE cc_start: 0.8348 (m-80) cc_final: 0.8052 (m-80) outliers start: 64 outliers final: 53 residues processed: 467 average time/residue: 0.3968 time to fit residues: 256.4168 Evaluate side-chains 483 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 425 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue -11 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue -12 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 86 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 112 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 153 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.130374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120189 restraints weight = 61204.193| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.80 r_work: 0.3427 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16201 Z= 0.152 Angle : 0.521 8.378 21944 Z= 0.276 Chirality : 0.039 0.148 2489 Planarity : 0.006 0.064 2870 Dihedral : 5.167 53.715 2331 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.77 % Allowed : 19.04 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.51 (0.18), residues: 2025 helix: 2.08 (0.14), residues: 1132 sheet: 0.90 (0.27), residues: 321 loop : -1.19 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 14 TYR 0.011 0.001 TYR M 82 PHE 0.012 0.001 PHE A 80 TRP 0.008 0.001 TRP G 72 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16201) covalent geometry : angle 0.52145 / 0.28 (21944) hydrogen bonds : bond 0.04858 / 3.23 ( 1224) hydrogen bonds : angle 4.28529 / 3.09 ( 3510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 494 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 435 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7151 (mp) REVERT: A 116 SER cc_start: 0.7985 (t) cc_final: 0.7585 (m) REVERT: B 114 SER cc_start: 0.8152 (t) cc_final: 0.7662 (p) REVERT: D 14 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7838 (mtp85) REVERT: D 64 GLU cc_start: 0.7209 (tt0) cc_final: 0.6883 (tt0) REVERT: E -11 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7550 (m) REVERT: E 60 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7966 (ttmm) REVERT: F -2 MET cc_start: 0.8124 (mmm) cc_final: 0.7629 (mmp) REVERT: F 15 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7610 (tt) REVERT: H 80 PHE cc_start: 0.8004 (t80) cc_final: 0.7496 (t80) REVERT: I 103 SER cc_start: 0.8113 (t) cc_final: 0.7811 (p) REVERT: J 60 LYS cc_start: 0.8040 (tttt) cc_final: 0.7809 (tttt) REVERT: L 88 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7534 (pp) REVERT: L 103 SER cc_start: 0.6549 (OUTLIER) cc_final: 0.6301 (t) REVERT: N 20 GLU cc_start: 0.6960 (tp30) cc_final: 0.6523 (tp30) REVERT: O 19 ILE cc_start: 0.7391 (tp) cc_final: 0.7127 (tt) REVERT: P 10 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7116 (mtp180) REVERT: P 13 GLU cc_start: 0.7637 (tt0) cc_final: 0.7416 (tt0) REVERT: P 103 SER cc_start: 0.7547 (p) cc_final: 0.7046 (p) outliers start: 59 outliers final: 47 residues processed: 471 average time/residue: 0.3419 time to fit residues: 223.7897 Evaluate side-chains 481 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 428 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue -11 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue -12 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 17 GLU Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.128789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118682 restraints weight = 61480.115| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.79 r_work: 0.3417 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16201 Z= 0.193 Angle : 0.547 8.595 21944 Z= 0.291 Chirality : 0.039 0.157 2489 Planarity : 0.006 0.059 2870 Dihedral : 5.211 52.780 2331 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.45 % Allowed : 19.81 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.38 (0.18), residues: 2025 helix: 1.95 (0.14), residues: 1132 sheet: 0.92 (0.27), residues: 321 loop : -1.24 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 16 TYR 0.011 0.001 TYR M 82 PHE 0.016 0.002 PHE A 80 TRP 0.008 0.001 TRP K 72 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (16201) covalent geometry : angle 0.54655 / 0.29 (21944) hydrogen bonds : bond 0.05038 / 3.35 ( 1224) hydrogen bonds : angle 4.34697 / 3.14 ( 3510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 494 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 440 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7152 (mp) REVERT: A 116 SER cc_start: 0.7999 (t) cc_final: 0.7544 (m) REVERT: B 114 SER cc_start: 0.8148 (t) cc_final: 0.7670 (p) REVERT: D 14 ARG cc_start: 0.8119 (mtm180) cc_final: 0.7837 (mtp85) REVERT: D 64 GLU cc_start: 0.7233 (tt0) cc_final: 0.6955 (tt0) REVERT: E -11 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7562 (m) REVERT: E 60 LYS cc_start: 0.8285 (mtpp) cc_final: 0.7969 (ttmm) REVERT: F -2 MET cc_start: 0.8111 (mmm) cc_final: 0.7610 (mmp) REVERT: I 103 SER cc_start: 0.8120 (t) cc_final: 0.7816 (p) REVERT: J 59 LEU cc_start: 0.7714 (mm) cc_final: 0.7418 (mp) REVERT: J 60 LYS cc_start: 0.8051 (tttt) cc_final: 0.7823 (tttt) REVERT: L 88 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7814 (pp) REVERT: L 103 SER cc_start: 0.6511 (OUTLIER) cc_final: 0.6260 (t) REVERT: N 20 GLU cc_start: 0.6943 (tp30) cc_final: 0.6518 (tp30) REVERT: O 19 ILE cc_start: 0.7376 (tp) cc_final: 0.7120 (tt) REVERT: P 103 SER cc_start: 0.7544 (p) cc_final: 0.7052 (p) REVERT: P 110 PHE cc_start: 0.8299 (m-80) cc_final: 0.7823 (m-80) outliers start: 54 outliers final: 46 residues processed: 469 average time/residue: 0.3852 time to fit residues: 250.7910 Evaluate side-chains 483 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 433 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue -11 THR Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue -12 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain L residue -3 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 44 TYR Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.0970 chunk 189 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.130713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120490 restraints weight = 61138.626| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.81 r_work: 0.3433 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16201 Z= 0.133 Angle : 0.514 7.988 21944 Z= 0.270 Chirality : 0.039 0.149 2489 Planarity : 0.005 0.057 2870 Dihedral : 4.958 51.219 2329 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.00 % Allowed : 20.19 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.18), residues: 2025 helix: 2.26 (0.14), residues: 1132 sheet: 0.98 (0.27), residues: 321 loop : -1.17 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 14 TYR 0.013 0.001 TYR L 44 PHE 0.011 0.001 PHE A 80 TRP 0.015 0.001 TRP M 72 HIS 0.002 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16201) covalent geometry : angle 0.51430 / 0.27 (21944) hydrogen bonds : bond 0.04643 / 3.09 ( 1224) hydrogen bonds : angle 4.18617 / 3.02 ( 3510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7485.20 seconds wall clock time: 127 minutes 37.80 seconds (7657.80 seconds total)