Starting phenix.real_space_refine on Fri Oct 23 01:22:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c9c_30311/10_2026/7c9c_30311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9c_30311/10_2026/7c9c_30311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7c9c_30311/10_2026/7c9c_30311.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c9c_30311/10_2026/7c9c_30311.cif" model { file = "/net/cci-nas-00/data/ceres_data/7c9c_30311/10_2026/7c9c_30311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9c_30311/10_2026/7c9c_30311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c9c_30311/10_2026/7c9c_30311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9c_30311/10_2026/7c9c_30311.map" } resolution = 3.33 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 18 5.49 5 S 33 5.16 5 C 4656 2.51 5 N 1293 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7452 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.67, per 1000 atoms: 0.22 Number of scatterers: 7452 At special positions: 0 Unit cell: (72.24, 113.4, 112.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 33 16.00 P 18 15.00 O 1449 8.00 N 1293 7.00 C 4656 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 390.5 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 46.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 4.096A pdb=" N LEU A 26 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 27 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 28 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.861A pdb=" N ILE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 52' Processing helix chain 'A' and resid 56 through 64 removed outlier: 4.242A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.713A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.574A pdb=" N ASP A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.609A pdb=" N CYS A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.829A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 removed outlier: 3.722A pdb=" N VAL A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 removed outlier: 4.152A pdb=" N LEU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.680A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.571A pdb=" N ALA A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 removed outlier: 4.094A pdb=" N LEU B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 27 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.860A pdb=" N ILE B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 52' Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.711A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.574A pdb=" N ASP B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.609A pdb=" N CYS B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.828A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 removed outlier: 3.722A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 213 removed outlier: 4.153A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.679A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.570A pdb=" N ALA B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 31 removed outlier: 4.094A pdb=" N LEU C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 27 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 28 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.860A pdb=" N ILE C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 52' Processing helix chain 'C' and resid 56 through 64 removed outlier: 4.242A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.714A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET C 97 " --> pdb=" O LYS C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 97' Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.575A pdb=" N ASP C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 143 removed outlier: 3.608A pdb=" N CYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.828A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 3.721A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 removed outlier: 4.152A pdb=" N LEU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.681A pdb=" N PHE C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.570A pdb=" N ALA C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.521A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 268 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 126 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS A 155 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 221 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 157 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 156 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA A 191 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 158 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 removed outlier: 3.546A pdb=" N GLY A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.520A pdb=" N ALA B 313 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 268 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 126 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 155 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE B 221 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 157 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA B 191 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 158 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 331 removed outlier: 3.545A pdb=" N GLY B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.629A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA C 191 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE C 158 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS C 155 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE C 221 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 157 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN C 268 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 126 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 313 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AB3, first strand: chain 'C' and resid 330 through 331 removed outlier: 3.547A pdb=" N GLY C 334 " --> pdb=" O THR C 331 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 600 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: 0.97 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1654 1.33 - 1.45: 1544 1.45 - 1.57: 4302 1.57 - 1.69: 26 1.69 - 1.81: 57 Bond restraints: 7583 Sorted by residual: bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 1.700 1.545 0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 7578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 10152 3.84 - 7.68: 83 7.68 - 11.52: 12 11.52 - 15.36: 0 15.36 - 19.20: 3 Bond angle restraints: 10250 Sorted by residual: angle pdb=" PB ANP C 402 " pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 126.95 107.75 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 107.76 19.19 3.00e+00 1.11e-01 4.09e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 107.77 19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" N3 DT D 2 " pdb=" C4 DT D 2 " pdb=" O4 DT D 2 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 ... (remaining 10245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.10: 4227 26.10 - 52.20: 249 52.20 - 78.30: 42 78.30 - 104.40: 12 104.40 - 130.50: 3 Dihedral angle restraints: 4533 sinusoidal: 1908 harmonic: 2625 Sorted by residual: dihedral pdb=" CA GLU A 82 " pdb=" C GLU A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA GLU C 82 " pdb=" C GLU C 82 " pdb=" N PRO C 83 " pdb=" CA PRO C 83 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU B 82 " pdb=" C GLU B 82 " pdb=" N PRO B 83 " pdb=" CA PRO B 83 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 909 0.062 - 0.124: 214 0.124 - 0.186: 25 0.186 - 0.248: 4 0.248 - 0.310: 3 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C3' ANP C 402 " pdb=" C2' ANP C 402 " pdb=" C4' ANP C 402 " pdb=" O3' ANP C 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1152 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 128 " -0.009 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE B 128 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 128 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 128 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 128 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 128 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 128 " -0.009 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE C 128 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 128 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 128 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 128 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 128 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 128 " 0.008 2.00e-02 2.50e+03 1.49e-02 3.88e+00 pdb=" CG PHE A 128 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 128 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 128 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 128 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 128 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 128 " -0.001 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 4 1.97 - 2.70: 235 2.70 - 3.43: 9286 3.43 - 4.17: 16840 4.17 - 4.90: 31357 Nonbonded interactions: 57722 Sorted by model distance: nonbonded pdb=" NH1 ARG C 56 " pdb=" OD1 ASP C 71 " model vdw 1.232 3.120 nonbonded pdb="CA CA B 401 " pdb=" O1G ANP B 402 " model vdw 1.678 2.510 nonbonded pdb="CA CA C 401 " pdb=" O1G ANP C 402 " model vdw 1.763 2.510 nonbonded pdb=" CZ ARG C 56 " pdb=" OD1 ASP C 71 " model vdw 1.789 3.270 nonbonded pdb="CA CA A 401 " pdb=" O1G ANP A 402 " model vdw 1.989 2.510 ... (remaining 57717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.156 7586 Z= 0.423 Angle : 1.046 19.200 10250 Z= 0.566 Chirality : 0.056 0.310 1155 Planarity : 0.005 0.041 1278 Dihedral : 17.281 130.497 2847 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.79 % Allowed : 6.98 % Favored : 92.23 % 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: -5.45 (0.20), residues: 912 helix: -5.12 (0.06), residues: 351 sheet: -1.95 (0.38), residues: 156 loop : -2.68 (0.24), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.014 0.002 TYR A 316 PHE 0.033 0.003 PHE C 128 HIS 0.009 0.002 HIS C 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.42 ( 7583) covalent geometry : angle 1.04561 / 0.57 (10250) hydrogen bonds : bond 0.30424 / 31.69 ( 217) hydrogen bonds : angle 9.83353 / 8.82 ( 600) Misc. bond : bond 0.02966 / 1.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7771 (p0) cc_final: 0.7493 (m-30) REVERT: A 252 ARG cc_start: 0.8046 (tpt-90) cc_final: 0.7747 (ttt90) REVERT: B 41 LYS cc_start: 0.6961 (mttt) cc_final: 0.6394 (mttm) REVERT: B 171 ARG cc_start: 0.7424 (tpt170) cc_final: 0.7139 (mtt90) REVERT: C 36 ASP cc_start: 0.6220 (m-30) cc_final: 0.6009 (m-30) REVERT: C 41 LYS cc_start: 0.6410 (mttt) cc_final: 0.5726 (tptt) REVERT: C 285 LYS cc_start: 0.8990 (mttt) cc_final: 0.8372 (mmmt) outliers start: 6 outliers final: 3 residues processed: 177 average time/residue: 0.1251 time to fit residues: 27.5061 Evaluate side-chains 116 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 78 ASN A 198 HIS A 199 GLN A 248 GLN B 30 HIS B 61 ASN B 78 ASN B 198 HIS B 199 GLN B 295 HIS C 61 ASN C 78 ASN C 187 ASN C 198 HIS C 199 GLN C 243 GLN ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.132226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.098793 restraints weight = 9103.318| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.77 r_work: 0.2838 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7586 Z= 0.139 Angle : 0.571 6.586 10250 Z= 0.304 Chirality : 0.043 0.137 1155 Planarity : 0.005 0.067 1278 Dihedral : 14.829 165.428 1100 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.45 % Allowed : 12.91 % Favored : 85.64 % 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: -4.33 (0.23), residues: 912 helix: -3.79 (0.15), residues: 378 sheet: -1.91 (0.36), residues: 189 loop : -1.96 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 169 TYR 0.005 0.001 TYR C 260 PHE 0.018 0.001 PHE A 128 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 7583) covalent geometry : angle 0.57134 / 0.30 (10250) hydrogen bonds : bond 0.04205 / 4.35 ( 217) hydrogen bonds : angle 5.13102 / 4.53 ( 600) Misc. bond : bond 0.00270 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 102 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8641 (t) REVERT: A 168 ASP cc_start: 0.8311 (p0) cc_final: 0.7681 (m-30) REVERT: A 252 ARG cc_start: 0.8499 (tpt-90) cc_final: 0.8295 (ttt90) REVERT: B 41 LYS cc_start: 0.6556 (mttt) cc_final: 0.5836 (mttm) REVERT: B 171 ARG cc_start: 0.6962 (tpt170) cc_final: 0.6227 (mtt-85) REVERT: B 325 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8514 (mt-10) REVERT: C 41 LYS cc_start: 0.6088 (mttt) cc_final: 0.5425 (tptt) REVERT: C 102 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8939 (t) REVERT: C 285 LYS cc_start: 0.8937 (mttt) cc_final: 0.7905 (mmmt) outliers start: 11 outliers final: 3 residues processed: 125 average time/residue: 0.1110 time to fit residues: 17.6649 Evaluate side-chains 112 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [20, 31, 25, 62, 34, 44, 24, 73, 41, 19, 8] chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN C 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.131204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.096829 restraints weight = 9077.729| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.84 r_work: 0.2783 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7586 Z= 0.125 Angle : 0.509 6.646 10250 Z= 0.270 Chirality : 0.042 0.133 1155 Planarity : 0.006 0.136 1278 Dihedral : 14.268 164.805 1089 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.58 % Allowed : 13.04 % Favored : 85.38 % 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: -3.68 (0.24), residues: 912 helix: -2.79 (0.20), residues: 402 sheet: -1.66 (0.37), residues: 189 loop : -2.08 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 169 TYR 0.007 0.001 TYR C 316 PHE 0.017 0.001 PHE A 128 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7583) covalent geometry : angle 0.50914 / 0.27 (10250) hydrogen bonds : bond 0.03597 / 3.64 ( 217) hydrogen bonds : angle 4.22892 / 3.75 ( 600) Misc. bond : bond 0.00191 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.275 Fit side-chains REVERT: A 168 ASP cc_start: 0.8294 (p0) cc_final: 0.7813 (m-30) REVERT: A 252 ARG cc_start: 0.8600 (tpt-90) cc_final: 0.8396 (ttt90) REVERT: B 41 LYS cc_start: 0.6592 (mttt) cc_final: 0.5877 (mttm) REVERT: B 171 ARG cc_start: 0.7004 (tpt170) cc_final: 0.6250 (mtt-85) REVERT: B 180 ASP cc_start: 0.7432 (m-30) cc_final: 0.6713 (t0) REVERT: B 186 ASP cc_start: 0.8384 (m-30) cc_final: 0.7741 (m-30) REVERT: B 325 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8578 (mt-10) REVERT: C 41 LYS cc_start: 0.6069 (mttt) cc_final: 0.5421 (tptt) REVERT: C 102 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8948 (t) REVERT: C 285 LYS cc_start: 0.9012 (mttt) cc_final: 0.8035 (mmmt) outliers start: 12 outliers final: 6 residues processed: 122 average time/residue: 0.0917 time to fit residues: 15.1044 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [30, 88, 37, 26, 90, 15, 78, 1, 60, 59, 33] chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.0020 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.129436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.092829 restraints weight = 9281.209| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.07 r_work: 0.2736 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7586 Z= 0.140 Angle : 0.499 6.344 10250 Z= 0.266 Chirality : 0.043 0.173 1155 Planarity : 0.005 0.095 1278 Dihedral : 14.400 176.478 1089 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.24 % Allowed : 14.23 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.26), residues: 912 helix: -2.04 (0.23), residues: 396 sheet: -1.43 (0.38), residues: 189 loop : -1.72 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 169 TYR 0.014 0.001 TYR B 316 PHE 0.015 0.001 PHE A 128 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 7583) covalent geometry : angle 0.49911 / 0.27 (10250) hydrogen bonds : bond 0.03161 / 3.18 ( 217) hydrogen bonds : angle 4.01282 / 3.54 ( 600) Misc. bond : bond 0.00217 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.259 Fit side-chains REVERT: A 168 ASP cc_start: 0.8328 (p0) cc_final: 0.8021 (m-30) REVERT: A 241 GLU cc_start: 0.8670 (tt0) cc_final: 0.8452 (tt0) REVERT: A 252 ARG cc_start: 0.8736 (tpt-90) cc_final: 0.8525 (ttt90) REVERT: B 41 LYS cc_start: 0.6581 (mttt) cc_final: 0.5825 (mttm) REVERT: B 186 ASP cc_start: 0.8465 (m-30) cc_final: 0.7832 (m-30) REVERT: B 325 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8626 (mt-10) REVERT: C 36 ASP cc_start: 0.6769 (m-30) cc_final: 0.6558 (m-30) REVERT: C 41 LYS cc_start: 0.6143 (mttt) cc_final: 0.5476 (tptt) REVERT: C 285 LYS cc_start: 0.9083 (mttt) cc_final: 0.8120 (mmmt) outliers start: 17 outliers final: 6 residues processed: 115 average time/residue: 0.0911 time to fit residues: 14.2027 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [63, 10, 75, 6, 72, 45, 40, 62, 67, 46, 68] chunk 63 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 72 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.093659 restraints weight = 9266.704| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.13 r_work: 0.2725 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7586 Z= 0.160 Angle : 0.513 5.846 10250 Z= 0.270 Chirality : 0.043 0.159 1155 Planarity : 0.006 0.143 1278 Dihedral : 14.480 179.094 1089 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.77 % Allowed : 14.62 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.27), residues: 912 helix: -1.58 (0.25), residues: 396 sheet: -1.29 (0.38), residues: 189 loop : -1.65 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 169 TYR 0.015 0.001 TYR B 316 PHE 0.015 0.001 PHE A 128 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 7583) covalent geometry : angle 0.51265 / 0.27 (10250) hydrogen bonds : bond 0.03298 / 3.32 ( 217) hydrogen bonds : angle 3.98764 / 3.53 ( 600) Misc. bond : bond 0.00228 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.208 Fit side-chains REVERT: A 168 ASP cc_start: 0.8240 (p0) cc_final: 0.8021 (m-30) REVERT: A 241 GLU cc_start: 0.8710 (tt0) cc_final: 0.8477 (tt0) REVERT: B 41 LYS cc_start: 0.6589 (mttt) cc_final: 0.5841 (mttm) REVERT: B 186 ASP cc_start: 0.8466 (m-30) cc_final: 0.7993 (m-30) REVERT: B 325 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8636 (mt-10) REVERT: C 36 ASP cc_start: 0.6861 (m-30) cc_final: 0.6612 (m-30) REVERT: C 41 LYS cc_start: 0.6059 (mttt) cc_final: 0.5448 (tptt) outliers start: 21 outliers final: 12 residues processed: 113 average time/residue: 0.0880 time to fit residues: 13.4690 Evaluate side-chains 107 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [14, 9, 74, 37, 33, 75, 44, 22, 54, 38, 4] chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 144 GLN C 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.131262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.096822 restraints weight = 9182.540| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.09 r_work: 0.2751 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7586 Z= 0.105 Angle : 0.456 6.399 10250 Z= 0.243 Chirality : 0.042 0.132 1155 Planarity : 0.004 0.101 1278 Dihedral : 14.399 179.257 1089 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.58 % Allowed : 16.21 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.27), residues: 912 helix: -1.18 (0.26), residues: 396 sheet: -1.23 (0.37), residues: 189 loop : -1.56 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 169 TYR 0.009 0.001 TYR B 316 PHE 0.014 0.001 PHE A 128 HIS 0.002 0.000 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7583) covalent geometry : angle 0.45588 / 0.24 (10250) hydrogen bonds : bond 0.02707 / 2.74 ( 217) hydrogen bonds : angle 3.79039 / 3.38 ( 600) Misc. bond : bond 0.00183 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.304 Fit side-chains REVERT: A 168 ASP cc_start: 0.8101 (p0) cc_final: 0.7896 (m-30) REVERT: A 241 GLU cc_start: 0.8573 (tt0) cc_final: 0.8295 (tt0) REVERT: B 41 LYS cc_start: 0.6519 (mttt) cc_final: 0.5788 (mttm) REVERT: B 186 ASP cc_start: 0.8452 (m-30) cc_final: 0.7955 (m-30) REVERT: B 197 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8153 (mp0) REVERT: B 226 MET cc_start: 0.8921 (mmm) cc_final: 0.8586 (mmm) REVERT: B 325 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8611 (mt-10) REVERT: C 36 ASP cc_start: 0.6866 (m-30) cc_final: 0.6604 (m-30) REVERT: C 41 LYS cc_start: 0.5963 (mttt) cc_final: 0.5378 (tptt) REVERT: C 201 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7282 (tt0) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.0959 time to fit residues: 13.2341 Evaluate side-chains 102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [16, 80, 72, 38, 78, 88, 74, 4, 76, 48, 14] chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.130162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.093982 restraints weight = 9191.684| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.03 r_work: 0.2723 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7586 Z= 0.127 Angle : 0.468 5.864 10250 Z= 0.249 Chirality : 0.042 0.128 1155 Planarity : 0.006 0.177 1278 Dihedral : 14.415 179.073 1089 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.11 % Allowed : 15.68 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.27), residues: 912 helix: -1.02 (0.26), residues: 402 sheet: -1.13 (0.37), residues: 189 loop : -1.65 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 169 TYR 0.010 0.001 TYR B 316 PHE 0.014 0.001 PHE A 128 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7583) covalent geometry : angle 0.46834 / 0.25 (10250) hydrogen bonds : bond 0.02900 / 2.92 ( 217) hydrogen bonds : angle 3.78067 / 3.37 ( 600) Misc. bond : bond 0.00372 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.342 Fit side-chains REVERT: A 241 GLU cc_start: 0.8690 (tt0) cc_final: 0.8436 (tt0) REVERT: B 41 LYS cc_start: 0.6592 (mttt) cc_final: 0.5808 (mttm) REVERT: B 186 ASP cc_start: 0.8500 (m-30) cc_final: 0.8025 (m-30) REVERT: B 197 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8229 (mp0) REVERT: B 273 ASP cc_start: 0.8666 (t0) cc_final: 0.8406 (t0) REVERT: B 325 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8618 (mt-10) REVERT: C 36 ASP cc_start: 0.6967 (m-30) cc_final: 0.6717 (m-30) REVERT: C 41 LYS cc_start: 0.6087 (mttt) cc_final: 0.5458 (tptt) REVERT: C 201 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7403 (tt0) outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 0.0914 time to fit residues: 13.6236 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [57, 66, 18, 32, 89, 56, 52, 51, 80, 63, 83] chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.089119 restraints weight = 9291.033| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.06 r_work: 0.2674 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7586 Z= 0.212 Angle : 0.558 4.934 10250 Z= 0.294 Chirality : 0.045 0.181 1155 Planarity : 0.007 0.158 1278 Dihedral : 14.488 177.282 1089 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.98 % Allowed : 16.34 % 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: -2.16 (0.27), residues: 912 helix: -1.10 (0.25), residues: 411 sheet: -1.04 (0.38), residues: 189 loop : -1.88 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 169 TYR 0.018 0.001 TYR B 316 PHE 0.016 0.002 PHE A 128 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 ( 7583) covalent geometry : angle 0.55760 / 0.29 (10250) hydrogen bonds : bond 0.03808 / 3.81 ( 217) hydrogen bonds : angle 4.05375 / 3.61 ( 600) Misc. bond : bond 0.00356 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.287 Fit side-chains REVERT: A 67 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5958 (mm-30) REVERT: A 241 GLU cc_start: 0.8757 (tt0) cc_final: 0.8536 (tt0) REVERT: B 41 LYS cc_start: 0.6694 (mttt) cc_final: 0.5870 (mttm) REVERT: B 186 ASP cc_start: 0.8568 (m-30) cc_final: 0.8085 (m-30) REVERT: B 197 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8372 (mp0) REVERT: B 273 ASP cc_start: 0.8709 (t0) cc_final: 0.8457 (t0) REVERT: B 325 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8610 (mt-10) REVERT: C 36 ASP cc_start: 0.7115 (m-30) cc_final: 0.6886 (m-30) REVERT: C 41 LYS cc_start: 0.6093 (mttt) cc_final: 0.5487 (tptt) REVERT: C 201 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7436 (tt0) outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 0.0979 time to fit residues: 14.1380 Evaluate side-chains 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [79, 85, 90, 81, 32, 36, 65, 62, 8, 2, 39] chunk 79 optimal weight: 0.0030 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.9770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 HIS C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.127436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.091183 restraints weight = 9217.410| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.04 r_work: 0.2710 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7586 Z= 0.125 Angle : 0.481 6.100 10250 Z= 0.256 Chirality : 0.042 0.128 1155 Planarity : 0.007 0.168 1278 Dihedral : 14.358 178.754 1089 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.71 % Allowed : 17.13 % Favored : 81.16 % 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: -1.91 (0.27), residues: 912 helix: -0.79 (0.26), residues: 393 sheet: -0.98 (0.38), residues: 189 loop : -1.83 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 169 TYR 0.009 0.001 TYR C 316 PHE 0.014 0.001 PHE A 128 HIS 0.002 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 7583) covalent geometry : angle 0.48081 / 0.26 (10250) hydrogen bonds : bond 0.02970 / 3.01 ( 217) hydrogen bonds : angle 3.81577 / 3.43 ( 600) Misc. bond : bond 0.00367 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.332 Fit side-chains REVERT: A 241 GLU cc_start: 0.8734 (tt0) cc_final: 0.8495 (tt0) REVERT: B 41 LYS cc_start: 0.6661 (mttt) cc_final: 0.5846 (mttm) REVERT: B 186 ASP cc_start: 0.8490 (m-30) cc_final: 0.8007 (m-30) REVERT: B 197 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8286 (mt-10) REVERT: B 273 ASP cc_start: 0.8662 (t0) cc_final: 0.8421 (t0) REVERT: B 325 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8586 (mt-10) REVERT: C 36 ASP cc_start: 0.7121 (m-30) cc_final: 0.6907 (m-30) REVERT: C 41 LYS cc_start: 0.6011 (mttt) cc_final: 0.5455 (tptt) REVERT: C 201 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7414 (tt0) outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 0.0878 time to fit residues: 12.6967 Evaluate side-chains 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [18, 41, 8, 43, 48, 86, 37, 53, 29, 42, 5] chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.126577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.092050 restraints weight = 9231.063| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.16 r_work: 0.2705 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7586 Z= 0.149 Angle : 0.494 5.408 10250 Z= 0.263 Chirality : 0.043 0.140 1155 Planarity : 0.007 0.157 1278 Dihedral : 14.326 179.169 1089 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.32 % Allowed : 17.39 % Favored : 81.29 % 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: -1.83 (0.28), residues: 912 helix: -0.82 (0.26), residues: 414 sheet: -0.78 (0.39), residues: 183 loop : -1.80 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 169 TYR 0.011 0.001 TYR C 316 PHE 0.014 0.001 PHE A 128 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 7583) covalent geometry : angle 0.49383 / 0.26 (10250) hydrogen bonds : bond 0.03161 / 3.18 ( 217) hydrogen bonds : angle 3.83902 / 3.46 ( 600) Misc. bond : bond 0.00351 / 0.19 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.264 Fit side-chains REVERT: A 241 GLU cc_start: 0.8707 (tt0) cc_final: 0.8458 (tt0) REVERT: B 41 LYS cc_start: 0.6648 (mttt) cc_final: 0.5840 (mttm) REVERT: B 186 ASP cc_start: 0.8500 (m-30) cc_final: 0.8007 (m-30) REVERT: B 273 ASP cc_start: 0.8672 (t0) cc_final: 0.8429 (t0) REVERT: B 325 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8607 (mt-10) REVERT: C 41 LYS cc_start: 0.6120 (mttt) cc_final: 0.5571 (tptt) REVERT: C 201 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7387 (tt0) outliers start: 10 outliers final: 10 residues processed: 101 average time/residue: 0.0921 time to fit residues: 12.3619 Evaluate side-chains 101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: [18, 56, 0, 76, 81, 24, 84, 79, 50, 73, 23] chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.134565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.101170 restraints weight = 9012.384| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.09 r_work: 0.2752 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7586 Z= 0.101 Angle : 0.451 6.160 10250 Z= 0.241 Chirality : 0.042 0.131 1155 Planarity : 0.006 0.137 1278 Dihedral : 14.146 177.133 1089 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.19 % Allowed : 17.52 % Favored : 81.29 % 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 (0.28), residues: 912 helix: -0.63 (0.27), residues: 408 sheet: -0.92 (0.38), residues: 189 loop : -1.48 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 169 TYR 0.006 0.001 TYR B 316 PHE 0.013 0.001 PHE A 128 HIS 0.002 0.000 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 7583) covalent geometry : angle 0.45063 / 0.24 (10250) hydrogen bonds : bond 0.02577 / 2.61 ( 217) hydrogen bonds : angle 3.68256 / 3.35 ( 600) Misc. bond : bond 0.00258 / 0.13 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.88 seconds wall clock time: 34 minutes 17.82 seconds (2057.82 seconds total)