Starting phenix.real_space_refine on Wed Mar 4 03:36:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oe2_12859/03_2026/7oe2_12859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oe2_12859/03_2026/7oe2_12859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oe2_12859/03_2026/7oe2_12859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oe2_12859/03_2026/7oe2_12859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oe2_12859/03_2026/7oe2_12859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oe2_12859/03_2026/7oe2_12859.map" } resolution = 2.4 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= -0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 6615 2.51 5 N 1805 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10589 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2034 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain: "1" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 53 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, 2, 3, 4, 5 Time building chain proxies: 1.90, per 1000 atoms: 0.18 Number of scatterers: 10589 At special positions: 0 Unit cell: (95.192, 146.7, 134.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 2144 8.00 N 1805 7.00 C 6615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 633.2 milliseconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 25 sheets defined 42.2% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 12 through 31 removed outlier: 3.561A pdb=" N ILE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.644A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 101 through 122 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 162 Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 12 through 31 removed outlier: 3.561A pdb=" N ILE B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 3.645A pdb=" N LEU B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 101 through 122 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 162 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 12 through 31 removed outlier: 3.562A pdb=" N ILE C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.644A pdb=" N LEU C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 162 Processing helix chain 'C' and resid 173 through 183 Processing helix chain 'C' and resid 190 through 198 Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 12 through 31 removed outlier: 3.562A pdb=" N ILE D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.644A pdb=" N LEU D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 147 through 162 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 190 through 198 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 12 through 31 removed outlier: 3.562A pdb=" N ILE E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 removed outlier: 3.644A pdb=" N LEU E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 removed outlier: 4.036A pdb=" N VAL E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 101 through 122 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 147 through 162 Processing helix chain 'E' and resid 173 through 183 Processing helix chain 'E' and resid 190 through 198 Processing helix chain 'E' and resid 256 through 258 No H-bonds generated for 'chain 'E' and resid 256 through 258' Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP A 38 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 226 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG A 40 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP A 38 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 226 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG A 40 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE A 245 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR A 234 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA A 247 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 232 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 57 removed outlier: 7.280A pdb=" N THR A 52 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN A 73 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU A 54 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 removed outlier: 6.921A pdb=" N LEU A 140 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 204 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP B 38 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 226 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 40 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP B 38 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 226 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 40 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE B 245 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR B 234 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 247 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 232 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 57 removed outlier: 7.281A pdb=" N THR B 52 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN B 73 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU B 54 " --> pdb=" O GLN B 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 141 removed outlier: 6.921A pdb=" N LEU B 140 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 204 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 185 Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.275A pdb=" N ASP C 38 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 226 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG C 40 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.275A pdb=" N ASP C 38 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 226 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG C 40 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 245 " --> pdb=" O TYR C 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR C 234 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA C 247 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE C 232 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 49 through 57 removed outlier: 7.282A pdb=" N THR C 52 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN C 73 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU C 54 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 141 removed outlier: 6.921A pdb=" N LEU C 140 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 204 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB7, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP D 38 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 226 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG D 40 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP D 38 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 226 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG D 40 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE D 245 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR D 234 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA D 247 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE D 232 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 57 removed outlier: 7.282A pdb=" N THR D 52 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN D 73 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU D 54 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 140 through 141 removed outlier: 6.920A pdb=" N LEU D 140 " --> pdb=" O ARG D 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 204 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 184 through 185 Processing sheet with id=AC3, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP E 38 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL E 226 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG E 40 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.276A pdb=" N ASP E 38 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL E 226 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG E 40 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE E 245 " --> pdb=" O TYR E 234 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR E 234 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA E 247 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE E 232 " --> pdb=" O ALA E 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 49 through 57 removed outlier: 7.282A pdb=" N THR E 52 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN E 73 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU E 54 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 140 through 141 removed outlier: 6.920A pdb=" N LEU E 140 " --> pdb=" O ARG E 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 204 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 184 through 185 500 hydrogen bonds defined for protein. 1395 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: 1.89 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3566 1.34 - 1.46: 2099 1.46 - 1.58: 4935 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 10650 Sorted by residual: bond pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 1.515 1.496 0.019 1.43e-02 4.89e+03 1.75e+00 bond pdb=" CA GLY B 166 " pdb=" C GLY B 166 " ideal model delta sigma weight residual 1.515 1.497 0.018 1.43e-02 4.89e+03 1.58e+00 bond pdb=" CA GLY E 166 " pdb=" C GLY E 166 " ideal model delta sigma weight residual 1.515 1.497 0.018 1.43e-02 4.89e+03 1.56e+00 bond pdb=" CA GLY A 166 " pdb=" C GLY A 166 " ideal model delta sigma weight residual 1.515 1.497 0.018 1.43e-02 4.89e+03 1.55e+00 bond pdb=" CA GLY C 41 " pdb=" C GLY C 41 " ideal model delta sigma weight residual 1.515 1.497 0.018 1.43e-02 4.89e+03 1.54e+00 ... (remaining 10645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 13669 1.32 - 2.64: 671 2.64 - 3.97: 130 3.97 - 5.29: 10 5.29 - 6.61: 10 Bond angle restraints: 14490 Sorted by residual: angle pdb=" N GLY E 227 " pdb=" CA GLY E 227 " pdb=" C GLY E 227 " ideal model delta sigma weight residual 113.18 106.57 6.61 2.37e+00 1.78e-01 7.78e+00 angle pdb=" N GLY B 227 " pdb=" CA GLY B 227 " pdb=" C GLY B 227 " ideal model delta sigma weight residual 113.18 106.59 6.59 2.37e+00 1.78e-01 7.74e+00 angle pdb=" N GLY C 227 " pdb=" CA GLY C 227 " pdb=" C GLY C 227 " ideal model delta sigma weight residual 113.18 106.59 6.59 2.37e+00 1.78e-01 7.72e+00 angle pdb=" N GLY D 227 " pdb=" CA GLY D 227 " pdb=" C GLY D 227 " ideal model delta sigma weight residual 113.18 106.64 6.54 2.37e+00 1.78e-01 7.62e+00 angle pdb=" N GLY A 227 " pdb=" CA GLY A 227 " pdb=" C GLY A 227 " ideal model delta sigma weight residual 113.18 106.64 6.54 2.37e+00 1.78e-01 7.62e+00 ... (remaining 14485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5502 17.89 - 35.79: 618 35.79 - 53.68: 185 53.68 - 71.58: 20 71.58 - 89.47: 35 Dihedral angle restraints: 6360 sinusoidal: 2440 harmonic: 3920 Sorted by residual: dihedral pdb=" CA ARG D 264 " pdb=" C ARG D 264 " pdb=" N TYR D 265 " pdb=" CA TYR D 265 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG E 264 " pdb=" C ARG E 264 " pdb=" N TYR E 265 " pdb=" CA TYR E 265 " ideal model delta harmonic sigma weight residual 180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG B 264 " pdb=" C ARG B 264 " pdb=" N TYR B 265 " pdb=" CA TYR B 265 " ideal model delta harmonic sigma weight residual -180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 6357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 682 0.032 - 0.063: 566 0.063 - 0.095: 282 0.095 - 0.126: 84 0.126 - 0.158: 26 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CB VAL D 92 " pdb=" CA VAL D 92 " pdb=" CG1 VAL D 92 " pdb=" CG2 VAL D 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CB VAL A 92 " pdb=" CA VAL A 92 " pdb=" CG1 VAL A 92 " pdb=" CG2 VAL A 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CB VAL C 92 " pdb=" CA VAL C 92 " pdb=" CG1 VAL C 92 " pdb=" CG2 VAL C 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 1637 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 152 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C VAL D 152 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL D 152 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU D 153 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 152 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C VAL B 152 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL B 152 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 153 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 152 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C VAL A 152 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL A 152 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 153 " 0.010 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 564 2.72 - 3.27: 10100 3.27 - 3.81: 19178 3.81 - 4.36: 23739 4.36 - 4.90: 36477 Nonbonded interactions: 90058 Sorted by model distance: nonbonded pdb=" OE2 GLU D 115 " pdb=" O HOH D 301 " model vdw 2.179 3.040 nonbonded pdb=" OE2 GLU E 115 " pdb=" O HOH E 301 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR E 188 " pdb=" NH2 ARG E 196 " model vdw 2.324 3.120 nonbonded pdb=" OH TYR B 188 " pdb=" NH2 ARG B 196 " model vdw 2.324 3.120 nonbonded pdb=" OH TYR D 188 " pdb=" NH2 ARG D 196 " model vdw 2.325 3.120 ... (remaining 90053 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' } 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: 19.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.006 0.032 10650 Z= 0.297 Angle : 0.682 6.612 14490 Z= 0.386 Chirality : 0.054 0.158 1640 Planarity : 0.005 0.031 1920 Dihedral : 17.807 89.472 3840 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.44 % Allowed : 15.87 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1355 helix: 0.52 (0.25), residues: 415 sheet: 1.63 (0.30), residues: 315 loop : -0.03 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 264 TYR 0.008 0.002 TYR B 168 PHE 0.018 0.004 PHE D 181 TRP 0.010 0.002 TRP E 45 HIS 0.006 0.002 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00639 (10650) covalent geometry : angle 0.68231 (14490) hydrogen bonds : bond 0.15188 ( 480) hydrogen bonds : angle 7.58727 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.364 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 152 average time/residue: 0.8067 time to fit residues: 129.1379 Evaluate side-chains 107 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.060031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.049071 restraints weight = 27159.314| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.97 r_work: 0.2594 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10650 Z= 0.093 Angle : 0.458 4.794 14490 Z= 0.246 Chirality : 0.042 0.126 1640 Planarity : 0.004 0.029 1920 Dihedral : 4.571 29.408 1501 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.16 % Allowed : 16.15 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1355 helix: 1.52 (0.26), residues: 445 sheet: 1.53 (0.31), residues: 315 loop : 0.16 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 264 TYR 0.007 0.001 TYR D 265 PHE 0.007 0.001 PHE B 82 TRP 0.009 0.001 TRP C 45 HIS 0.001 0.000 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00197 (10650) covalent geometry : angle 0.45762 (14490) hydrogen bonds : bond 0.03147 ( 480) hydrogen bonds : angle 5.73352 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 103 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8785 (t0) outliers start: 23 outliers final: 6 residues processed: 135 average time/residue: 0.8346 time to fit residues: 118.7565 Evaluate side-chains 114 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 265 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 66 optimal weight: 0.0050 chunk 117 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.048834 restraints weight = 27517.497| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.96 r_work: 0.2598 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 10650 Z= 0.087 Angle : 0.428 4.621 14490 Z= 0.225 Chirality : 0.041 0.129 1640 Planarity : 0.003 0.029 1920 Dihedral : 4.005 23.565 1495 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.78 % Allowed : 17.00 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1355 helix: 1.70 (0.26), residues: 445 sheet: 1.50 (0.31), residues: 310 loop : 0.21 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 264 TYR 0.007 0.001 TYR C 177 PHE 0.007 0.001 PHE B 82 TRP 0.007 0.001 TRP E 45 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00192 (10650) covalent geometry : angle 0.42767 (14490) hydrogen bonds : bond 0.02987 ( 480) hydrogen bonds : angle 5.28657 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 241 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8420 (mmtp) REVERT: 2 918 SER cc_start: 0.9364 (p) cc_final: 0.9120 (p) outliers start: 19 outliers final: 6 residues processed: 133 average time/residue: 0.7368 time to fit residues: 103.8712 Evaluate side-chains 118 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 0.0040 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN D 73 GLN E 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.060020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.049222 restraints weight = 27711.369| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.97 r_work: 0.2612 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10650 Z= 0.081 Angle : 0.417 4.689 14490 Z= 0.217 Chirality : 0.041 0.129 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.797 21.936 1495 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.31 % Allowed : 17.65 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1355 helix: 2.23 (0.26), residues: 415 sheet: 1.03 (0.31), residues: 290 loop : 0.31 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 264 TYR 0.011 0.001 TYR E 265 PHE 0.007 0.001 PHE B 82 TRP 0.006 0.001 TRP A 45 HIS 0.001 0.000 HIS E 237 Details of bonding type rmsd covalent geometry : bond 0.00183 (10650) covalent geometry : angle 0.41715 (14490) hydrogen bonds : bond 0.02682 ( 480) hydrogen bonds : angle 5.10625 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 241 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8374 (mmtp) REVERT: 2 918 SER cc_start: 0.9283 (p) cc_final: 0.9046 (p) outliers start: 14 outliers final: 6 residues processed: 128 average time/residue: 0.7655 time to fit residues: 103.7156 Evaluate side-chains 119 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 1 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 49 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 66 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.058714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.047940 restraints weight = 27488.564| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.94 r_work: 0.2578 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10650 Z= 0.104 Angle : 0.430 5.022 14490 Z= 0.222 Chirality : 0.042 0.131 1640 Planarity : 0.003 0.026 1920 Dihedral : 3.897 23.181 1495 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.50 % Allowed : 18.12 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.23), residues: 1355 helix: 2.26 (0.26), residues: 415 sheet: 1.26 (0.32), residues: 280 loop : 0.29 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 264 TYR 0.021 0.001 TYR E 265 PHE 0.008 0.001 PHE A 82 TRP 0.005 0.001 TRP A 45 HIS 0.001 0.000 HIS E 262 Details of bonding type rmsd covalent geometry : bond 0.00239 (10650) covalent geometry : angle 0.43002 (14490) hydrogen bonds : bond 0.03004 ( 480) hydrogen bonds : angle 5.11601 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 241 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8459 (mmtp) REVERT: E 56 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8278 (ttm110) REVERT: 2 918 SER cc_start: 0.9309 (p) cc_final: 0.9060 (p) outliers start: 16 outliers final: 9 residues processed: 125 average time/residue: 0.7580 time to fit residues: 100.1841 Evaluate side-chains 117 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 0.0570 chunk 126 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 71 optimal weight: 0.0170 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.057371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.046566 restraints weight = 27720.300| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.95 r_work: 0.2534 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10650 Z= 0.160 Angle : 0.466 5.429 14490 Z= 0.240 Chirality : 0.043 0.133 1640 Planarity : 0.003 0.027 1920 Dihedral : 4.192 26.922 1495 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.69 % Allowed : 18.31 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1355 helix: 2.19 (0.26), residues: 415 sheet: 1.23 (0.32), residues: 280 loop : 0.32 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.020 0.001 TYR B 265 PHE 0.010 0.001 PHE C 181 TRP 0.005 0.001 TRP B 45 HIS 0.001 0.000 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00369 (10650) covalent geometry : angle 0.46628 (14490) hydrogen bonds : bond 0.03496 ( 480) hydrogen bonds : angle 5.24574 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.9011 (mttt) REVERT: C 241 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8561 (mmtt) REVERT: E 56 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8293 (ttm110) REVERT: 2 918 SER cc_start: 0.9342 (p) cc_final: 0.9062 (p) outliers start: 18 outliers final: 9 residues processed: 119 average time/residue: 0.7462 time to fit residues: 94.1631 Evaluate side-chains 115 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.047067 restraints weight = 27487.041| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.95 r_work: 0.2550 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10650 Z= 0.127 Angle : 0.442 5.052 14490 Z= 0.229 Chirality : 0.042 0.131 1640 Planarity : 0.003 0.026 1920 Dihedral : 4.061 25.100 1495 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.60 % Allowed : 18.50 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1355 helix: 2.23 (0.26), residues: 415 sheet: 1.17 (0.32), residues: 280 loop : 0.31 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 56 TYR 0.020 0.001 TYR B 265 PHE 0.008 0.001 PHE A 82 TRP 0.006 0.001 TRP A 45 HIS 0.001 0.000 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00293 (10650) covalent geometry : angle 0.44221 (14490) hydrogen bonds : bond 0.03184 ( 480) hydrogen bonds : angle 5.19025 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 241 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8445 (mmtp) REVERT: E 56 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8282 (ttm110) REVERT: 2 918 SER cc_start: 0.9340 (p) cc_final: 0.9058 (p) outliers start: 17 outliers final: 9 residues processed: 121 average time/residue: 0.7666 time to fit residues: 98.0037 Evaluate side-chains 116 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.048075 restraints weight = 27282.825| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.94 r_work: 0.2583 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10650 Z= 0.090 Angle : 0.440 8.578 14490 Z= 0.225 Chirality : 0.041 0.130 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.878 22.805 1495 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.03 % Allowed : 19.34 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.23), residues: 1355 helix: 2.32 (0.26), residues: 415 sheet: 1.16 (0.32), residues: 280 loop : 0.27 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 56 TYR 0.020 0.001 TYR B 265 PHE 0.007 0.001 PHE E 82 TRP 0.006 0.001 TRP A 45 HIS 0.001 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00207 (10650) covalent geometry : angle 0.44040 (14490) hydrogen bonds : bond 0.02788 ( 480) hydrogen bonds : angle 5.08635 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 241 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8442 (mmtp) REVERT: D 195 GLN cc_start: 0.9070 (mt0) cc_final: 0.8869 (mt0) REVERT: E 56 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8270 (ttm110) REVERT: 2 918 SER cc_start: 0.9318 (p) cc_final: 0.9049 (p) outliers start: 11 outliers final: 7 residues processed: 122 average time/residue: 0.7832 time to fit residues: 101.1574 Evaluate side-chains 120 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.057332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.046595 restraints weight = 27442.196| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.92 r_work: 0.2535 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10650 Z= 0.157 Angle : 0.480 8.934 14490 Z= 0.244 Chirality : 0.043 0.133 1640 Planarity : 0.003 0.026 1920 Dihedral : 4.188 26.685 1495 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.13 % Allowed : 19.44 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.23), residues: 1355 helix: 2.23 (0.26), residues: 415 sheet: 1.15 (0.32), residues: 280 loop : 0.30 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 56 TYR 0.023 0.001 TYR B 265 PHE 0.010 0.001 PHE C 181 TRP 0.005 0.001 TRP C 45 HIS 0.001 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00363 (10650) covalent geometry : angle 0.48017 (14490) hydrogen bonds : bond 0.03454 ( 480) hydrogen bonds : angle 5.21136 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: E 56 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8284 (ttm110) REVERT: 2 918 SER cc_start: 0.9359 (p) cc_final: 0.9098 (p) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 0.7840 time to fit residues: 96.1050 Evaluate side-chains 114 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.0470 chunk 57 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.059460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.048730 restraints weight = 27310.681| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.93 r_work: 0.2602 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10650 Z= 0.085 Angle : 0.443 9.494 14490 Z= 0.225 Chirality : 0.041 0.129 1640 Planarity : 0.003 0.026 1920 Dihedral : 3.828 22.017 1495 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.66 % Allowed : 20.19 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.23), residues: 1355 helix: 2.35 (0.26), residues: 415 sheet: 1.12 (0.31), residues: 280 loop : 0.27 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 264 TYR 0.024 0.001 TYR B 265 PHE 0.006 0.001 PHE B 82 TRP 0.007 0.001 TRP D 45 HIS 0.001 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00195 (10650) covalent geometry : angle 0.44255 (14490) hydrogen bonds : bond 0.02606 ( 480) hydrogen bonds : angle 5.05227 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: B 56 ARG cc_start: 0.8538 (ttm110) cc_final: 0.8262 (mtm110) REVERT: D 125 GLN cc_start: 0.9545 (mp10) cc_final: 0.9296 (mp10) REVERT: E 56 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8282 (ttm110) REVERT: 2 918 SER cc_start: 0.9327 (p) cc_final: 0.9066 (p) REVERT: 4 918 SER cc_start: 0.9256 (p) cc_final: 0.8940 (p) outliers start: 7 outliers final: 7 residues processed: 123 average time/residue: 0.8005 time to fit residues: 103.9007 Evaluate side-chains 122 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.058010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.047193 restraints weight = 27438.583| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.93 r_work: 0.2554 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10650 Z= 0.128 Angle : 0.473 9.845 14490 Z= 0.239 Chirality : 0.042 0.131 1640 Planarity : 0.003 0.025 1920 Dihedral : 4.031 24.561 1495 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.85 % Allowed : 20.00 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.23), residues: 1355 helix: 2.28 (0.26), residues: 415 sheet: 1.15 (0.32), residues: 280 loop : 0.31 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 56 TYR 0.026 0.001 TYR B 265 PHE 0.008 0.001 PHE A 82 TRP 0.005 0.001 TRP C 45 HIS 0.001 0.000 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00296 (10650) covalent geometry : angle 0.47315 (14490) hydrogen bonds : bond 0.03177 ( 480) hydrogen bonds : angle 5.12241 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4025.49 seconds wall clock time: 69 minutes 9.95 seconds (4149.95 seconds total)