Starting phenix.real_space_refine on Mon Jul 28 17:33:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oe2_12859/07_2025/7oe2_12859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oe2_12859/07_2025/7oe2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7oe2_12859/07_2025/7oe2_12859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oe2_12859/07_2025/7oe2_12859.map" model { file = "/net/cci-nas-00/data/ceres_data/7oe2_12859/07_2025/7oe2_12859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oe2_12859/07_2025/7oe2_12859.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D, 3, 2, 5, 4 Time building chain proxies: 7.20, per 1000 atoms: 0.68 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.38 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: 3.42 Time building geometry restraints manager: 2.98 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '2' selection = chain '5' selection = chain '4' } 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: 0.010 Normalize map: mean=0, sd=1: 11.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.770 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.002 TRP E 45 HIS 0.006 0.002 HIS C 121 PHE 0.018 0.004 PHE D 181 TYR 0.008 0.002 TYR B 168 ARG 0.008 0.001 ARG E 264 Details of bonding type rmsd hydrogen bonds : bond 0.15188 ( 480) hydrogen bonds : angle 7.58727 ( 1395) covalent geometry : bond 0.00639 (10650) covalent geometry : angle 0.68231 (14490) *********************** 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 : 1.252 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 152 average time/residue: 1.6205 time to fit residues: 261.0412 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 : 1.234 ------------------------------------------------------------------------------- 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 109 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.2967 r_free = 0.2967 target = 0.057963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.047248 restraints weight = 26937.369| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.91 r_work: 0.2543 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10650 Z= 0.136 Angle : 0.478 5.371 14490 Z= 0.255 Chirality : 0.043 0.128 1640 Planarity : 0.004 0.029 1920 Dihedral : 4.710 31.205 1501 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.82 % Allowed : 15.77 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1355 helix: 1.46 (0.26), residues: 445 sheet: 1.49 (0.29), residues: 345 loop : 0.09 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 45 HIS 0.001 0.000 HIS B 121 PHE 0.008 0.001 PHE B 82 TYR 0.009 0.001 TYR E 265 ARG 0.005 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 480) hydrogen bonds : angle 5.75057 ( 1395) covalent geometry : bond 0.00308 (10650) covalent geometry : angle 0.47809 (14490) *********************** 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 137 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.895 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 5 residues processed: 135 average time/residue: 2.1454 time to fit residues: 308.2551 Evaluate side-chains 107 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 120 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.047846 restraints weight = 27562.399| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.93 r_work: 0.2568 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2239 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= 0.101 Angle : 0.439 4.859 14490 Z= 0.231 Chirality : 0.042 0.130 1640 Planarity : 0.004 0.029 1920 Dihedral : 4.108 24.326 1495 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.16 % Allowed : 16.71 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1355 helix: 2.17 (0.26), residues: 415 sheet: 1.54 (0.31), residues: 310 loop : 0.20 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 45 HIS 0.001 0.000 HIS A 121 PHE 0.007 0.001 PHE B 82 TYR 0.021 0.001 TYR E 265 ARG 0.005 0.000 ARG E 264 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 480) hydrogen bonds : angle 5.29291 ( 1395) covalent geometry : bond 0.00228 (10650) covalent geometry : angle 0.43915 (14490) *********************** 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 138 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 241 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8467 (mmtp) REVERT: E 161 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8779 (mttt) outliers start: 23 outliers final: 7 residues processed: 133 average time/residue: 1.5678 time to fit residues: 221.9674 Evaluate side-chains 113 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 68 LYS 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 Chi-restraints excluded: chain E residue 161 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- 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 = 0.2960 r_free = 0.2960 target = 0.057443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.046700 restraints weight = 27291.346| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.96 r_work: 0.2538 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10650 Z= 0.139 Angle : 0.460 5.348 14490 Z= 0.240 Chirality : 0.042 0.131 1640 Planarity : 0.003 0.028 1920 Dihedral : 4.232 26.668 1495 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.16 % Allowed : 17.65 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1355 helix: 2.14 (0.26), residues: 415 sheet: 1.43 (0.31), residues: 310 loop : 0.26 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 45 HIS 0.001 0.000 HIS A 121 PHE 0.009 0.001 PHE A 181 TYR 0.005 0.001 TYR C 265 ARG 0.003 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 480) hydrogen bonds : angle 5.27734 ( 1395) covalent geometry : bond 0.00321 (10650) covalent geometry : angle 0.46012 (14490) *********************** 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 134 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 161 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8793 (mttt) REVERT: 2 918 SER cc_start: 0.9333 (p) cc_final: 0.9073 (p) outliers start: 23 outliers final: 10 residues processed: 130 average time/residue: 1.6335 time to fit residues: 226.1946 Evaluate side-chains 117 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 25 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 161 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.2937 r_free = 0.2937 target = 0.056471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.045611 restraints weight = 27664.040| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.98 r_work: 0.2506 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 10650 Z= 0.193 Angle : 0.487 5.593 14490 Z= 0.252 Chirality : 0.044 0.132 1640 Planarity : 0.004 0.028 1920 Dihedral : 4.425 29.106 1495 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.97 % Allowed : 17.56 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1355 helix: 2.08 (0.26), residues: 415 sheet: 1.25 (0.32), residues: 290 loop : 0.28 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 45 HIS 0.002 0.001 HIS C 121 PHE 0.010 0.001 PHE C 181 TYR 0.006 0.001 TYR C 265 ARG 0.002 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 480) hydrogen bonds : angle 5.34735 ( 1395) covalent geometry : bond 0.00447 (10650) covalent geometry : angle 0.48687 (14490) *********************** 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 125 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8737 (t0) REVERT: E 161 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8821 (mttt) REVERT: 2 918 SER cc_start: 0.9356 (p) cc_final: 0.9100 (p) outliers start: 21 outliers final: 11 residues processed: 121 average time/residue: 1.8126 time to fit residues: 232.7151 Evaluate side-chains 115 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 161 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN E 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.046604 restraints weight = 27597.699| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.98 r_work: 0.2535 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10650 Z= 0.132 Angle : 0.451 5.184 14490 Z= 0.235 Chirality : 0.042 0.131 1640 Planarity : 0.003 0.026 1920 Dihedral : 4.178 26.096 1495 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.35 % Allowed : 17.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1355 helix: 2.17 (0.26), residues: 415 sheet: 1.20 (0.32), residues: 280 loop : 0.32 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 45 HIS 0.001 0.000 HIS C 121 PHE 0.008 0.001 PHE D 82 TYR 0.005 0.001 TYR D 177 ARG 0.003 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 480) hydrogen bonds : angle 5.24315 ( 1395) covalent geometry : bond 0.00305 (10650) covalent geometry : angle 0.45075 (14490) *********************** 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 129 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 56 ARG cc_start: 0.8544 (ttm110) cc_final: 0.8281 (ttm110) REVERT: 2 918 SER cc_start: 0.9361 (p) cc_final: 0.9116 (p) outliers start: 25 outliers final: 11 residues processed: 125 average time/residue: 2.3121 time to fit residues: 307.8639 Evaluate side-chains 113 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG 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 68 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR 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 112 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 50 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.2967 r_free = 0.2967 target = 0.057755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.046887 restraints weight = 27748.205| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.95 r_work: 0.2544 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.2539 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= 0.122 Angle : 0.465 8.156 14490 Z= 0.237 Chirality : 0.042 0.131 1640 Planarity : 0.003 0.026 1920 Dihedral : 4.131 24.916 1495 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.41 % Allowed : 18.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1355 helix: 2.22 (0.26), residues: 415 sheet: 1.17 (0.32), residues: 280 loop : 0.27 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 45 HIS 0.001 0.000 HIS A 121 PHE 0.008 0.001 PHE A 82 TYR 0.005 0.001 TYR D 177 ARG 0.002 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 480) hydrogen bonds : angle 5.18096 ( 1395) covalent geometry : bond 0.00282 (10650) covalent geometry : angle 0.46525 (14490) *********************** 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 121 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 56 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8288 (ttm110) REVERT: E 103 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8671 (t0) REVERT: 2 918 SER cc_start: 0.9355 (p) cc_final: 0.9111 (p) outliers start: 15 outliers final: 10 residues processed: 118 average time/residue: 2.2357 time to fit residues: 279.5273 Evaluate side-chains 116 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG 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 68 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 103 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 106 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.2954 r_free = 0.2954 target = 0.057195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.046404 restraints weight = 27324.655| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.95 r_work: 0.2528 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10650 Z= 0.146 Angle : 0.482 8.784 14490 Z= 0.244 Chirality : 0.043 0.131 1640 Planarity : 0.003 0.026 1920 Dihedral : 4.226 26.108 1495 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.69 % Allowed : 18.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1355 helix: 2.21 (0.26), residues: 415 sheet: 1.14 (0.32), residues: 280 loop : 0.28 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 45 HIS 0.001 0.000 HIS C 121 PHE 0.009 0.001 PHE C 181 TYR 0.005 0.001 TYR A 222 ARG 0.002 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 480) hydrogen bonds : angle 5.21479 ( 1395) covalent geometry : bond 0.00336 (10650) covalent geometry : angle 0.48156 (14490) *********************** 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 123 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 ARG cc_start: 0.8560 (ttm110) cc_final: 0.8289 (ttm110) REVERT: E 103 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8707 (t0) REVERT: 2 918 SER cc_start: 0.9350 (p) cc_final: 0.9120 (p) outliers start: 18 outliers final: 13 residues processed: 121 average time/residue: 1.5378 time to fit residues: 198.3358 Evaluate side-chains 119 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 103 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.2966 r_free = 0.2966 target = 0.057654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.046888 restraints weight = 27710.527| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.93 r_work: 0.2544 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.2579 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= 0.124 Angle : 0.465 9.515 14490 Z= 0.237 Chirality : 0.042 0.130 1640 Planarity : 0.003 0.026 1920 Dihedral : 4.117 24.977 1495 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.78 % Allowed : 18.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1355 helix: 2.26 (0.26), residues: 415 sheet: 1.11 (0.32), residues: 280 loop : 0.29 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 45 HIS 0.001 0.000 HIS B 237 PHE 0.008 0.001 PHE B 82 TYR 0.005 0.001 TYR A 177 ARG 0.003 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 480) hydrogen bonds : angle 5.17323 ( 1395) covalent geometry : bond 0.00285 (10650) covalent geometry : angle 0.46468 (14490) *********************** 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 124 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6986 (ptm) cc_final: 0.6555 (mmp) REVERT: E 56 ARG cc_start: 0.8564 (ttm110) cc_final: 0.8291 (ttm110) REVERT: E 103 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8676 (t0) REVERT: E 241 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8439 (mmtp) REVERT: 2 918 SER cc_start: 0.9372 (p) cc_final: 0.9141 (p) REVERT: 4 918 SER cc_start: 0.9442 (p) cc_final: 0.9225 (p) outliers start: 19 outliers final: 14 residues processed: 121 average time/residue: 1.5649 time to fit residues: 201.1326 Evaluate side-chains 119 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 103 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.058469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.047736 restraints weight = 27460.700| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.92 r_work: 0.2572 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2722 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= 0.098 Angle : 0.450 9.397 14490 Z= 0.229 Chirality : 0.042 0.131 1640 Planarity : 0.003 0.027 1920 Dihedral : 3.935 23.007 1495 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.69 % Allowed : 18.50 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1355 helix: 2.32 (0.26), residues: 415 sheet: 1.12 (0.32), residues: 280 loop : 0.30 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 45 HIS 0.001 0.000 HIS B 237 PHE 0.008 0.001 PHE D 82 TYR 0.006 0.001 TYR A 177 ARG 0.003 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.02854 ( 480) hydrogen bonds : angle 5.08610 ( 1395) covalent geometry : bond 0.00225 (10650) covalent geometry : angle 0.44951 (14490) ********************** 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 131 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 GLN cc_start: 0.9536 (mp10) cc_final: 0.9286 (mp10) REVERT: E 56 ARG cc_start: 0.8564 (ttm110) cc_final: 0.8292 (ttm110) REVERT: 2 918 SER cc_start: 0.9363 (p) cc_final: 0.9126 (p) REVERT: 4 918 SER cc_start: 0.9435 (p) cc_final: 0.9218 (p) outliers start: 18 outliers final: 14 residues processed: 126 average time/residue: 1.5774 time to fit residues: 211.0494 Evaluate side-chains 125 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 97 THR 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 C residue 97 THR Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 = 0.2940 r_free = 0.2940 target = 0.056606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.045758 restraints weight = 27419.402| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.95 r_work: 0.2510 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 10650 Z= 0.194 Angle : 0.509 9.840 14490 Z= 0.258 Chirality : 0.044 0.133 1640 Planarity : 0.003 0.027 1920 Dihedral : 4.384 28.966 1495 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.31 % Allowed : 18.87 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.23), residues: 1355 helix: 2.17 (0.26), residues: 415 sheet: 1.12 (0.32), residues: 280 loop : 0.33 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 45 HIS 0.002 0.001 HIS D 30 PHE 0.011 0.001 PHE C 181 TYR 0.018 0.001 TYR B 265 ARG 0.003 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 480) hydrogen bonds : angle 5.27460 ( 1395) covalent geometry : bond 0.00449 (10650) covalent geometry : angle 0.50894 (14490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8594.45 seconds wall clock time: 156 minutes 18.25 seconds (9378.25 seconds total)