Starting phenix.real_space_refine on Wed Feb 4 21:14:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx5_47281/02_2026/9dx5_47281.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx5_47281/02_2026/9dx5_47281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dx5_47281/02_2026/9dx5_47281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx5_47281/02_2026/9dx5_47281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dx5_47281/02_2026/9dx5_47281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx5_47281/02_2026/9dx5_47281.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 48 5.16 5 C 8187 2.51 5 N 2287 2.21 5 O 2387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12911 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2254 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 269} Chain breaks: 3 Chain: "B" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2195 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 16, 'TRANS': 262} Chain breaks: 4 Chain: "C" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2304 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 276} Chain breaks: 1 Chain: "D" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2107 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 254} Chain breaks: 1 Chain: "E" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1964 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 233} Chain breaks: 5 Chain: "F" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2060 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 247} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.16, per 1000 atoms: 0.24 Number of scatterers: 12911 At special positions: 0 Unit cell: (81.32, 132.68, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 2 15.00 O 2387 8.00 N 2287 7.00 C 8187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 572.0 milliseconds 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 8 sheets defined 63.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 27 through 31 Processing helix chain 'A' and resid 34 through 52 Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.712A pdb=" N LEU A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.699A pdb=" N GLU A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.797A pdb=" N ARG A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 220 through 238 removed outlier: 4.146A pdb=" N LEU A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 253 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.554A pdb=" N TRP A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 52 Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.832A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.668A pdb=" N LEU B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.616A pdb=" N VAL B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Proline residue: B 128 - end of helix Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.552A pdb=" N ARG B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 293 through 300 removed outlier: 4.462A pdb=" N ILE B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.704A pdb=" N TYR B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 329 removed outlier: 3.893A pdb=" N TRP B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 34 through 52 Processing helix chain 'C' and resid 67 through 80 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.827A pdb=" N LEU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 118 Processing helix chain 'C' and resid 119 through 131 removed outlier: 3.589A pdb=" N VAL C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.741A pdb=" N ARG C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 205 through 217 removed outlier: 4.070A pdb=" N ARG C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 238 Processing helix chain 'C' and resid 245 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 293 through 300 removed outlier: 4.288A pdb=" N ILE C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 Processing helix chain 'C' and resid 321 through 329 Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 34 through 52 Processing helix chain 'D' and resid 67 through 80 Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.690A pdb=" N LEU D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 118 Processing helix chain 'D' and resid 119 through 132 removed outlier: 3.597A pdb=" N VAL D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Proline residue: D 128 - end of helix Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 205 through 215 removed outlier: 3.505A pdb=" N ARG D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 238 Processing helix chain 'D' and resid 243 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 282 through 290 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.546A pdb=" N ILE D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 34 through 52 Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 115 through 118 Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.628A pdb=" N LEU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) Proline residue: E 128 - end of helix Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 168 through 174 removed outlier: 3.803A pdb=" N ARG E 174 " --> pdb=" O PRO E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 200 Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 219 through 238 Processing helix chain 'E' and resid 243 through 251 Processing helix chain 'E' and resid 262 through 268 Processing helix chain 'E' and resid 271 through 276 removed outlier: 3.506A pdb=" N PHE E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 291 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 301 through 307 Processing helix chain 'E' and resid 321 through 329 removed outlier: 3.650A pdb=" N PHE E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 24 removed outlier: 3.626A pdb=" N ARG F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 24' Processing helix chain 'F' and resid 27 through 31 Processing helix chain 'F' and resid 34 through 52 Processing helix chain 'F' and resid 67 through 80 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.820A pdb=" N LEU F 97 " --> pdb=" O LYS F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 118 Processing helix chain 'F' and resid 119 through 132 removed outlier: 3.563A pdb=" N VAL F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 163 through 167 removed outlier: 3.525A pdb=" N LEU F 167 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 173 removed outlier: 3.858A pdb=" N ARG F 172 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP F 173 " --> pdb=" O SER F 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 168 through 173' Processing helix chain 'F' and resid 185 through 200 Processing helix chain 'F' and resid 205 through 215 Processing helix chain 'F' and resid 221 through 238 Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 262 through 275 Processing helix chain 'F' and resid 282 through 291 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 301 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.321A pdb=" N ARG A 84 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASP A 113 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 86 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP A 108 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE A 158 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A 110 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA A 160 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 112 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 58 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR A 161 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE A 60 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 314 Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 87 removed outlier: 6.233A pdb=" N ARG B 84 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP B 113 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR B 86 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP B 108 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE B 158 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 110 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ALA B 160 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 112 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 161 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 61 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 87 removed outlier: 6.435A pdb=" N ARG C 84 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP C 113 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C 86 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP C 108 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE C 158 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU C 110 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ALA C 160 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 112 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 59 " --> pdb=" O GLN C 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 87 removed outlier: 6.158A pdb=" N ARG D 84 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP D 113 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR D 86 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP D 108 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE D 158 " --> pdb=" O ASP D 108 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU D 110 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA D 160 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE D 112 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU D 59 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 108 through 113 removed outlier: 6.286A pdb=" N ASP E 108 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE E 158 " --> pdb=" O ASP E 108 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU E 110 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA E 160 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE E 112 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 83 through 87 removed outlier: 6.349A pdb=" N ARG F 84 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP F 113 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR F 86 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP F 108 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE F 158 " --> pdb=" O ASP F 108 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU F 110 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA F 160 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 112 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 61 " --> pdb=" O GLN F 179 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4414 1.34 - 1.46: 2465 1.46 - 1.58: 6156 1.58 - 1.69: 4 1.69 - 1.81: 96 Bond restraints: 13135 Sorted by residual: bond pdb=" C2' ADP A 401 " pdb=" C3' ADP A 401 " ideal model delta sigma weight residual 1.524 1.291 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " ideal model delta sigma weight residual 1.426 1.308 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " ideal model delta sigma weight residual 1.524 1.635 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C6 ADP A 401 " pdb=" N6 ADP A 401 " ideal model delta sigma weight residual 1.355 1.459 -0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 13130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.08: 17728 5.08 - 10.16: 33 10.16 - 15.25: 3 15.25 - 20.33: 0 20.33 - 25.41: 2 Bond angle restraints: 17766 Sorted by residual: angle pdb=" N9 ADP A 401 " pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " ideal model delta sigma weight residual 109.47 84.06 25.41 3.00e+00 1.11e-01 7.17e+01 angle pdb=" C2' ADP A 401 " pdb=" C1' ADP A 401 " pdb=" N9 ADP A 401 " ideal model delta sigma weight residual 109.47 131.94 -22.47 3.00e+00 1.11e-01 5.61e+01 angle pdb=" C ILE B 306 " pdb=" N GLN B 307 " pdb=" CA GLN B 307 " ideal model delta sigma weight residual 121.54 130.46 -8.92 1.91e+00 2.74e-01 2.18e+01 angle pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " pdb=" C4' ADP A 401 " ideal model delta sigma weight residual 111.80 99.01 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C ASP B 299 " pdb=" N VAL B 300 " pdb=" CA VAL B 300 " ideal model delta sigma weight residual 122.97 118.81 4.16 9.80e-01 1.04e+00 1.80e+01 ... (remaining 17761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.25: 7685 20.25 - 40.50: 316 40.50 - 60.75: 20 60.75 - 81.00: 6 81.00 - 101.25: 2 Dihedral angle restraints: 8029 sinusoidal: 3330 harmonic: 4699 Sorted by residual: dihedral pdb=" CA GLN B 307 " pdb=" C GLN B 307 " pdb=" N GLN B 308 " pdb=" CA GLN B 308 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -161.25 101.25 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" C1' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O4' ADP A 401 " pdb=" C5' ADP A 401 " ideal model delta sinusoidal sigma weight residual -150.00 -62.82 -87.18 1 2.00e+01 2.50e-03 2.28e+01 ... (remaining 8026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.955: 2011 0.955 - 1.909: 0 1.909 - 2.864: 0 2.864 - 3.818: 0 3.818 - 4.773: 2 Chirality restraints: 2013 Sorted by residual: chirality pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" N9 ADP A 401 " pdb=" O4' ADP A 401 " both_signs ideal model delta sigma weight residual False 2.48 -2.29 4.77 2.00e-01 2.50e+01 5.69e+02 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 2.25 -4.76 2.00e-01 2.50e+01 5.66e+02 chirality pdb=" C4' ADP A 401 " pdb=" C3' ADP A 401 " pdb=" C5' ADP A 401 " pdb=" O4' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.50 -3.31 0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 2010 not shown) Planarity restraints: 2335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 301 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C LEU A 301 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 301 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU A 302 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 308 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C GLN B 308 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN B 308 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY B 309 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 263 " 0.006 2.00e-02 2.50e+03 1.35e-02 3.67e+00 pdb=" CG TYR F 263 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR F 263 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR F 263 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR F 263 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 263 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 263 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 263 " 0.002 2.00e-02 2.50e+03 ... (remaining 2332 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 134 2.62 - 3.19: 11704 3.19 - 3.76: 20298 3.76 - 4.33: 28433 4.33 - 4.90: 46282 Nonbonded interactions: 106851 Sorted by model distance: nonbonded pdb=" OD1 ASN C 255 " pdb=" NH2 ARG C 266 " model vdw 2.050 3.120 nonbonded pdb=" OD2 ASP B 56 " pdb=" NH2 ARG C 229 " model vdw 2.108 3.120 nonbonded pdb=" OE2 GLU F 123 " pdb=" OG1 THR F 168 " model vdw 2.166 3.040 nonbonded pdb=" OE2 GLU C 123 " pdb=" OG1 THR C 168 " model vdw 2.214 3.040 nonbonded pdb=" NH1 ARG C 229 " pdb=" OD2 ASP C 232 " model vdw 2.237 3.120 ... (remaining 106846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 78 or resid 100 or resid 106 through 250 or res \ id 261 through 269 or resid 271 through 275 or resid 286 through 305)) selection = (chain 'B' and (resid 24 through 78 or resid 100 or resid 106 through 250 or res \ id 261 through 269 or resid 271 through 305)) selection = (chain 'C' and (resid 24 through 78 or resid 100 or resid 106 through 250 or res \ id 261 through 269 or resid 271 through 275 or resid 286 through 305)) selection = (chain 'D' and (resid 24 through 78 or resid 100 or resid 106 through 250 or res \ id 261 through 269 or resid 271 through 275 or resid 286 through 305)) selection = (chain 'E' and (resid 24 through 250 or resid 261 through 275 or resid 286 throu \ gh 305)) selection = (chain 'F' and (resid 24 through 78 or resid 100 or resid 106 through 269 or res \ id 271 through 275 or resid 286 through 305)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.930 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3699 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 : 0.004 0.233 13135 Z= 0.206 Angle : 0.714 25.410 17766 Z= 0.337 Chirality : 0.157 4.773 2013 Planarity : 0.006 0.072 2335 Dihedral : 10.640 101.250 4991 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.77 (0.22), residues: 1597 helix: 1.46 (0.18), residues: 886 sheet: 1.59 (0.45), residues: 153 loop : 0.80 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 217 TYR 0.027 0.002 TYR C 304 PHE 0.015 0.001 PHE B 233 TRP 0.021 0.003 TRP B 325 HIS 0.012 0.001 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00427 (13135) covalent geometry : angle 0.71415 (17766) hydrogen bonds : bond 0.15172 ( 639) hydrogen bonds : angle 6.37901 ( 1818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.6249 (p90) cc_final: 0.5869 (p90) REVERT: A 75 VAL cc_start: 0.5060 (t) cc_final: 0.4321 (p) REVERT: A 131 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6676 (mm-30) REVERT: B 79 MET cc_start: 0.3912 (mmm) cc_final: 0.3659 (mmm) REVERT: B 246 ILE cc_start: 0.5999 (mt) cc_final: 0.5759 (mt) REVERT: C 174 ARG cc_start: 0.2964 (mtt90) cc_final: 0.1828 (tpp-160) REVERT: E 295 GLU cc_start: 0.4775 (mp0) cc_final: 0.4310 (pp20) REVERT: F 219 THR cc_start: 0.5398 (m) cc_final: 0.5036 (m) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1203 time to fit residues: 43.6048 Evaluate side-chains 207 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.272268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.251987 restraints weight = 24674.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.254481 restraints weight = 17801.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.257279 restraints weight = 14392.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.258000 restraints weight = 11552.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.261221 restraints weight = 8919.068| |-----------------------------------------------------------------------------| r_work (final): 0.5184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4048 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13135 Z= 0.181 Angle : 0.735 10.675 17766 Z= 0.361 Chirality : 0.044 0.192 2013 Planarity : 0.007 0.094 2335 Dihedral : 6.632 153.271 1817 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 1.03 % Allowed : 5.83 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.22 (0.22), residues: 1597 helix: 0.97 (0.17), residues: 894 sheet: 1.29 (0.44), residues: 153 loop : 0.64 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 24 TYR 0.019 0.002 TYR A 184 PHE 0.036 0.002 PHE D 199 TRP 0.018 0.003 TRP B 325 HIS 0.008 0.002 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00397 (13135) covalent geometry : angle 0.73482 (17766) hydrogen bonds : bond 0.04220 ( 639) hydrogen bonds : angle 5.44872 ( 1818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6059 (mp10) REVERT: A 61 PHE cc_start: 0.6592 (p90) cc_final: 0.6260 (p90) REVERT: A 131 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6748 (mm-30) REVERT: A 190 GLN cc_start: 0.6196 (tm-30) cc_final: 0.5880 (tm-30) REVERT: A 192 ILE cc_start: 0.5569 (mt) cc_final: 0.5055 (tp) REVERT: A 200 MET cc_start: 0.0091 (mmt) cc_final: -0.0310 (mmt) REVERT: B 174 ARG cc_start: 0.6343 (mpt180) cc_final: 0.5861 (mpt180) REVERT: C 174 ARG cc_start: 0.3907 (mtt90) cc_final: 0.1943 (tpp-160) REVERT: D 57 HIS cc_start: 0.3772 (m-70) cc_final: 0.2189 (m-70) REVERT: E 295 GLU cc_start: 0.4987 (mp0) cc_final: 0.4619 (pp20) REVERT: E 325 TRP cc_start: 0.4320 (m100) cc_final: 0.3937 (m100) outliers start: 14 outliers final: 10 residues processed: 219 average time/residue: 0.0995 time to fit residues: 31.4223 Evaluate side-chains 214 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain F residue 29 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 118 optimal weight: 0.0170 chunk 101 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 179 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5265 r_free = 0.5265 target = 0.269931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.249139 restraints weight = 24493.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.252089 restraints weight = 17052.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.255031 restraints weight = 13353.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.256332 restraints weight = 10210.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.258822 restraints weight = 7860.434| |-----------------------------------------------------------------------------| r_work (final): 0.5154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4120 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13135 Z= 0.154 Angle : 0.694 10.512 17766 Z= 0.338 Chirality : 0.042 0.180 2013 Planarity : 0.006 0.071 2335 Dihedral : 6.577 158.373 1817 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 1.62 % Allowed : 7.16 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.03 (0.21), residues: 1597 helix: 0.86 (0.17), residues: 900 sheet: 0.97 (0.44), residues: 145 loop : 0.57 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 217 TYR 0.024 0.002 TYR B 127 PHE 0.050 0.002 PHE D 199 TRP 0.009 0.002 TRP A 325 HIS 0.006 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00334 (13135) covalent geometry : angle 0.69426 (17766) hydrogen bonds : bond 0.03840 ( 639) hydrogen bonds : angle 5.26078 ( 1818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6218 (mp10) REVERT: A 163 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.4595 (mtt180) REVERT: B 173 ASP cc_start: 0.2395 (m-30) cc_final: 0.2169 (m-30) REVERT: B 174 ARG cc_start: 0.6285 (mpt180) cc_final: 0.5969 (mpt180) REVERT: B 330 ILE cc_start: 0.6254 (pt) cc_final: 0.5863 (pt) REVERT: C 174 ARG cc_start: 0.3959 (mtt90) cc_final: 0.3171 (mtt90) REVERT: E 130 MET cc_start: 0.3128 (ptp) cc_final: 0.2174 (ptt) REVERT: E 295 GLU cc_start: 0.4981 (mp0) cc_final: 0.4667 (pp20) outliers start: 22 outliers final: 15 residues processed: 210 average time/residue: 0.1053 time to fit residues: 32.2408 Evaluate side-chains 210 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 148 optimal weight: 0.5980 chunk 112 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 65 optimal weight: 0.0000 chunk 122 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.267448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.246570 restraints weight = 24314.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.249981 restraints weight = 16794.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.251462 restraints weight = 13107.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.252870 restraints weight = 10938.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.255296 restraints weight = 8362.841| |-----------------------------------------------------------------------------| r_work (final): 0.5120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4199 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13135 Z= 0.147 Angle : 0.660 11.275 17766 Z= 0.324 Chirality : 0.041 0.171 2013 Planarity : 0.006 0.073 2335 Dihedral : 6.530 161.173 1817 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 1.40 % Allowed : 9.16 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.05 (0.21), residues: 1597 helix: 0.94 (0.18), residues: 893 sheet: 0.89 (0.44), residues: 146 loop : 0.50 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 195 TYR 0.016 0.002 TYR B 263 PHE 0.034 0.001 PHE A 61 TRP 0.008 0.001 TRP A 325 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00321 (13135) covalent geometry : angle 0.66036 (17766) hydrogen bonds : bond 0.03548 ( 639) hydrogen bonds : angle 5.09272 ( 1818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6369 (mp10) REVERT: A 163 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.4685 (mtt180) REVERT: E 130 MET cc_start: 0.2860 (ptp) cc_final: 0.2385 (ptt) REVERT: E 295 GLU cc_start: 0.5041 (mp0) cc_final: 0.4748 (pp20) REVERT: F 41 MET cc_start: 0.5403 (ttp) cc_final: 0.4738 (mtp) outliers start: 19 outliers final: 13 residues processed: 216 average time/residue: 0.1114 time to fit residues: 35.0407 Evaluate side-chains 216 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 29 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 HIS F 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.264006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.243187 restraints weight = 24335.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.246323 restraints weight = 16792.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.248996 restraints weight = 12903.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.250091 restraints weight = 10100.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.251759 restraints weight = 7802.170| |-----------------------------------------------------------------------------| r_work (final): 0.5090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4292 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13135 Z= 0.167 Angle : 0.684 11.836 17766 Z= 0.337 Chirality : 0.042 0.181 2013 Planarity : 0.006 0.074 2335 Dihedral : 6.611 162.029 1817 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 2.07 % Allowed : 9.45 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1597 helix: 0.88 (0.18), residues: 889 sheet: 0.71 (0.44), residues: 143 loop : 0.33 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 174 TYR 0.021 0.002 TYR B 263 PHE 0.029 0.002 PHE D 199 TRP 0.009 0.001 TRP A 325 HIS 0.007 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00362 (13135) covalent geometry : angle 0.68438 (17766) hydrogen bonds : bond 0.03653 ( 639) hydrogen bonds : angle 5.09795 ( 1818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: A 86 THR cc_start: 0.5586 (OUTLIER) cc_final: 0.5356 (p) REVERT: A 163 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.4854 (mtt180) REVERT: A 196 SER cc_start: 0.7945 (m) cc_final: 0.7681 (t) REVERT: C 292 GLU cc_start: 0.5147 (pm20) cc_final: 0.4918 (pm20) REVERT: D 57 HIS cc_start: 0.4193 (m-70) cc_final: 0.2028 (m-70) REVERT: E 130 MET cc_start: 0.3088 (ptp) cc_final: 0.2587 (ptt) REVERT: E 172 ARG cc_start: 0.4243 (ttp-110) cc_final: 0.3152 (ttp-170) REVERT: E 295 GLU cc_start: 0.5183 (mp0) cc_final: 0.4916 (pp20) REVERT: F 41 MET cc_start: 0.5472 (ttp) cc_final: 0.4578 (ttm) outliers start: 28 outliers final: 17 residues processed: 215 average time/residue: 0.1192 time to fit residues: 36.7350 Evaluate side-chains 213 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 29 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.265155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.244514 restraints weight = 24037.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.247364 restraints weight = 16756.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.250001 restraints weight = 13238.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5097 r_free = 0.5097 target = 0.251471 restraints weight = 9874.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.254186 restraints weight = 7772.257| |-----------------------------------------------------------------------------| r_work (final): 0.5110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4228 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13135 Z= 0.130 Angle : 0.654 12.395 17766 Z= 0.316 Chirality : 0.041 0.267 2013 Planarity : 0.005 0.067 2335 Dihedral : 6.499 163.747 1817 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 2.29 % Allowed : 9.90 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.12 (0.22), residues: 1597 helix: 1.05 (0.18), residues: 891 sheet: 0.83 (0.45), residues: 141 loop : 0.45 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 163 TYR 0.015 0.001 TYR A 191 PHE 0.024 0.001 PHE D 199 TRP 0.007 0.001 TRP E 325 HIS 0.007 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00287 (13135) covalent geometry : angle 0.65391 (17766) hydrogen bonds : bond 0.03399 ( 639) hydrogen bonds : angle 4.93265 ( 1818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.6552 (mp10) REVERT: A 163 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.4788 (mtt180) REVERT: A 196 SER cc_start: 0.7946 (m) cc_final: 0.7661 (t) REVERT: B 41 MET cc_start: 0.2969 (mmt) cc_final: 0.2538 (mmt) REVERT: B 181 LEU cc_start: 0.0803 (OUTLIER) cc_final: -0.0738 (tp) REVERT: C 79 MET cc_start: 0.6304 (mmm) cc_final: 0.5990 (mmp) REVERT: C 86 THR cc_start: 0.7057 (p) cc_final: 0.6807 (t) REVERT: D 57 HIS cc_start: 0.3847 (m-70) cc_final: 0.1875 (m170) REVERT: E 130 MET cc_start: 0.3031 (ptp) cc_final: 0.2590 (ptt) REVERT: E 172 ARG cc_start: 0.4397 (ttp-110) cc_final: 0.3292 (ttp-170) REVERT: E 295 GLU cc_start: 0.5158 (mp0) cc_final: 0.4936 (pp20) outliers start: 31 outliers final: 21 residues processed: 211 average time/residue: 0.1025 time to fit residues: 31.2707 Evaluate side-chains 217 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 29 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 126 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 135 optimal weight: 0.0020 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.265037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.244652 restraints weight = 24221.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.247174 restraints weight = 16663.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.251006 restraints weight = 13134.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.251874 restraints weight = 9171.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.252261 restraints weight = 7544.914| |-----------------------------------------------------------------------------| r_work (final): 0.5097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4263 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13135 Z= 0.126 Angle : 0.652 12.151 17766 Z= 0.316 Chirality : 0.041 0.191 2013 Planarity : 0.005 0.064 2335 Dihedral : 6.416 163.268 1817 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.92 % Allowed : 10.56 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.23 (0.22), residues: 1597 helix: 1.13 (0.18), residues: 894 sheet: 0.93 (0.45), residues: 141 loop : 0.50 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 217 TYR 0.025 0.002 TYR B 263 PHE 0.022 0.001 PHE D 199 TRP 0.008 0.002 TRP B 325 HIS 0.006 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00277 (13135) covalent geometry : angle 0.65173 (17766) hydrogen bonds : bond 0.03374 ( 639) hydrogen bonds : angle 4.88724 ( 1818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: A 66 LEU cc_start: 0.4786 (mt) cc_final: 0.4386 (mp) REVERT: A 163 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.4896 (mtt180) REVERT: B 41 MET cc_start: 0.3144 (mmt) cc_final: 0.2686 (mmt) REVERT: B 174 ARG cc_start: 0.6161 (mpt180) cc_final: 0.5601 (mpt180) REVERT: B 181 LEU cc_start: 0.0744 (OUTLIER) cc_final: -0.0823 (tp) REVERT: C 174 ARG cc_start: 0.3630 (mtt90) cc_final: 0.1962 (ttt180) REVERT: D 57 HIS cc_start: 0.3896 (m-70) cc_final: 0.1940 (m170) REVERT: D 237 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6872 (mmtt) REVERT: E 130 MET cc_start: 0.3278 (ptp) cc_final: 0.2885 (ptt) REVERT: E 172 ARG cc_start: 0.4247 (ttp-110) cc_final: 0.3162 (ttp-170) REVERT: F 41 MET cc_start: 0.5424 (ttp) cc_final: 0.4361 (ttm) outliers start: 26 outliers final: 20 residues processed: 216 average time/residue: 0.1071 time to fit residues: 33.0185 Evaluate side-chains 224 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 29 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 101 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 158 optimal weight: 0.0670 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5201 r_free = 0.5201 target = 0.262596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.241921 restraints weight = 23878.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.244440 restraints weight = 17031.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.248273 restraints weight = 12666.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.249036 restraints weight = 9107.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.249350 restraints weight = 7486.707| |-----------------------------------------------------------------------------| r_work (final): 0.5068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4333 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13135 Z= 0.142 Angle : 0.677 12.547 17766 Z= 0.329 Chirality : 0.041 0.176 2013 Planarity : 0.006 0.125 2335 Dihedral : 6.670 174.486 1817 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 2.29 % Allowed : 11.00 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.07 (0.22), residues: 1597 helix: 0.98 (0.18), residues: 898 sheet: 0.90 (0.45), residues: 141 loop : 0.43 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 294 TYR 0.029 0.002 TYR B 263 PHE 0.019 0.001 PHE D 199 TRP 0.010 0.002 TRP B 325 HIS 0.008 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00315 (13135) covalent geometry : angle 0.67687 (17766) hydrogen bonds : bond 0.03488 ( 639) hydrogen bonds : angle 4.96890 ( 1818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.6637 (mp10) REVERT: A 163 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.4956 (mtt180) REVERT: B 41 MET cc_start: 0.3567 (mmt) cc_final: 0.3049 (mmt) REVERT: B 174 ARG cc_start: 0.6092 (mpt180) cc_final: 0.5839 (mpt180) REVERT: B 181 LEU cc_start: 0.0841 (OUTLIER) cc_final: -0.0769 (tp) REVERT: B 275 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6152 (pttp) REVERT: C 86 THR cc_start: 0.7109 (p) cc_final: 0.6904 (t) REVERT: C 130 MET cc_start: 0.4812 (OUTLIER) cc_final: 0.4500 (ttp) REVERT: D 57 HIS cc_start: 0.4242 (m-70) cc_final: 0.2446 (m-70) REVERT: D 264 MET cc_start: 0.3460 (mmm) cc_final: 0.2590 (mmm) REVERT: F 41 MET cc_start: 0.5509 (ttp) cc_final: 0.4586 (ttm) REVERT: F 264 MET cc_start: 0.4877 (mpp) cc_final: 0.2969 (mmp) outliers start: 31 outliers final: 23 residues processed: 212 average time/residue: 0.1152 time to fit residues: 35.0842 Evaluate side-chains 224 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 66 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 79 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.0000 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.263577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.243479 restraints weight = 24073.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.246136 restraints weight = 17128.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.249173 restraints weight = 13151.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.250380 restraints weight = 9390.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.250969 restraints weight = 7502.209| |-----------------------------------------------------------------------------| r_work (final): 0.5084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4284 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13135 Z= 0.125 Angle : 0.675 13.139 17766 Z= 0.327 Chirality : 0.041 0.162 2013 Planarity : 0.005 0.066 2335 Dihedral : 6.545 171.644 1817 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.99 % Allowed : 12.26 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.24 (0.22), residues: 1597 helix: 1.09 (0.18), residues: 898 sheet: 0.68 (0.47), residues: 131 loop : 0.65 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 217 TYR 0.036 0.002 TYR F 304 PHE 0.027 0.001 PHE D 199 TRP 0.013 0.003 TRP C 325 HIS 0.007 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00277 (13135) covalent geometry : angle 0.67472 (17766) hydrogen bonds : bond 0.03346 ( 639) hydrogen bonds : angle 4.88970 ( 1818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6689 (mp10) REVERT: A 163 ARG cc_start: 0.5802 (OUTLIER) cc_final: 0.4953 (mtt180) REVERT: B 41 MET cc_start: 0.3320 (mmt) cc_final: 0.2874 (mmt) REVERT: B 181 LEU cc_start: 0.0809 (OUTLIER) cc_final: -0.0836 (tp) REVERT: C 86 THR cc_start: 0.7308 (p) cc_final: 0.7065 (t) REVERT: C 130 MET cc_start: 0.4901 (OUTLIER) cc_final: 0.4675 (ttp) REVERT: D 57 HIS cc_start: 0.3950 (m-70) cc_final: 0.1998 (m-70) REVERT: D 198 ARG cc_start: 0.6528 (tmm160) cc_final: 0.6203 (tmm160) REVERT: D 227 LEU cc_start: 0.5829 (tp) cc_final: 0.5489 (tp) REVERT: D 264 MET cc_start: 0.3556 (mmm) cc_final: 0.2608 (mmm) REVERT: F 41 MET cc_start: 0.5508 (ttp) cc_final: 0.4602 (ttm) REVERT: F 264 MET cc_start: 0.4763 (mpp) cc_final: 0.2924 (mmp) outliers start: 27 outliers final: 17 residues processed: 208 average time/residue: 0.1183 time to fit residues: 35.2874 Evaluate side-chains 214 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 135 optimal weight: 0.0020 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5196 r_free = 0.5196 target = 0.262362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.240884 restraints weight = 24117.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.244425 restraints weight = 16318.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.246960 restraints weight = 11847.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.248858 restraints weight = 9110.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.250141 restraints weight = 7398.720| |-----------------------------------------------------------------------------| r_work (final): 0.5073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4327 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13135 Z= 0.139 Angle : 0.703 13.208 17766 Z= 0.341 Chirality : 0.041 0.170 2013 Planarity : 0.005 0.062 2335 Dihedral : 6.647 174.043 1817 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.77 % Allowed : 12.41 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.04 (0.22), residues: 1597 helix: 0.94 (0.18), residues: 900 sheet: 0.62 (0.47), residues: 132 loop : 0.55 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 266 TYR 0.029 0.002 TYR F 304 PHE 0.020 0.001 PHE D 199 TRP 0.016 0.003 TRP C 325 HIS 0.007 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00309 (13135) covalent geometry : angle 0.70350 (17766) hydrogen bonds : bond 0.03430 ( 639) hydrogen bonds : angle 4.95088 ( 1818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3194 Ramachandran restraints generated. 1597 Oldfield, 0 Emsley, 1597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: A 163 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.4824 (mtt180) REVERT: A 195 ARG cc_start: 0.6747 (ptt90) cc_final: 0.6237 (ttp-110) REVERT: A 319 MET cc_start: 0.3362 (ttm) cc_final: 0.2440 (tpp) REVERT: B 41 MET cc_start: 0.3415 (mmt) cc_final: 0.2964 (mmt) REVERT: B 181 LEU cc_start: 0.0983 (OUTLIER) cc_final: 0.0287 (mt) REVERT: C 86 THR cc_start: 0.7379 (p) cc_final: 0.7155 (t) REVERT: C 130 MET cc_start: 0.4858 (OUTLIER) cc_final: 0.4630 (ttp) REVERT: D 198 ARG cc_start: 0.6645 (tmm160) cc_final: 0.6290 (tmm160) REVERT: D 227 LEU cc_start: 0.5704 (tp) cc_final: 0.5381 (tp) REVERT: D 264 MET cc_start: 0.3575 (mmm) cc_final: 0.2611 (mmm) REVERT: E 295 GLU cc_start: 0.1212 (pm20) cc_final: 0.0905 (pm20) REVERT: F 41 MET cc_start: 0.5515 (ttp) cc_final: 0.4602 (ttm) REVERT: F 100 MET cc_start: -0.3099 (ttt) cc_final: -0.3301 (ttt) REVERT: F 264 MET cc_start: 0.4854 (mpp) cc_final: 0.3011 (mmp) outliers start: 24 outliers final: 19 residues processed: 204 average time/residue: 0.1166 time to fit residues: 34.2717 Evaluate side-chains 215 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 206 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5198 r_free = 0.5198 target = 0.262609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.241340 restraints weight = 24126.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.244936 restraints weight = 16302.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.247518 restraints weight = 11824.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.249440 restraints weight = 9082.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.250695 restraints weight = 7327.050| |-----------------------------------------------------------------------------| r_work (final): 0.5079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4310 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13135 Z= 0.130 Angle : 0.690 13.361 17766 Z= 0.336 Chirality : 0.041 0.165 2013 Planarity : 0.005 0.059 2335 Dihedral : 6.557 171.538 1817 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 1.92 % Allowed : 12.56 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 1.12 (0.22), residues: 1597 helix: 0.99 (0.18), residues: 900 sheet: 0.58 (0.46), residues: 138 loop : 0.64 (0.29), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 266 TYR 0.016 0.001 TYR F 304 PHE 0.054 0.001 PHE A 61 TRP 0.014 0.002 TRP C 325 HIS 0.006 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00290 (13135) covalent geometry : angle 0.68977 (17766) hydrogen bonds : bond 0.03341 ( 639) hydrogen bonds : angle 4.90886 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2052.07 seconds wall clock time: 36 minutes 8.45 seconds (2168.45 seconds total)