Starting phenix.real_space_refine on Fri Jun 5 09:58:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p0m_71081/06_2026/9p0m_71081.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p0m_71081/06_2026/9p0m_71081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p0m_71081/06_2026/9p0m_71081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p0m_71081/06_2026/9p0m_71081.map" model { file = "/net/cci-nas-00/data/ceres_data/9p0m_71081/06_2026/9p0m_71081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p0m_71081/06_2026/9p0m_71081.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 71 5.16 5 C 6118 2.51 5 N 1664 2.21 5 O 1792 1.98 5 H 9595 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19240 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5168 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1128 Classifications: {'peptide': 69} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "D" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5092 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 876 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "C" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3462 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "F" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3514 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 3.48, per 1000 atoms: 0.18 Number of scatterers: 19240 At special positions: 0 Unit cell: (94.275, 157.125, 148.745, 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 71 16.00 O 1792 8.00 N 1664 7.00 C 6118 6.00 H 9595 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 36 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 53 " distance=2.04 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.04 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 230 " distance=2.04 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: 1.47 Conformation dependent library (CDL) restraints added in 594.5 milliseconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 17 sheets defined 39.7% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 12 through 18 Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.997A pdb=" N ASN A 22 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N SER A 24 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 25 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.192A pdb=" N GLU A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN A 32 " --> pdb=" O TYR A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 45 through 80 removed outlier: 4.403A pdb=" N PHE A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 86 through 105 removed outlier: 3.899A pdb=" N PHE A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.912A pdb=" N TRP A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 155 removed outlier: 3.563A pdb=" N ALA A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 3.693A pdb=" N ARG A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.592A pdb=" N PHE A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 224 removed outlier: 4.384A pdb=" N ALA A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 243 removed outlier: 3.617A pdb=" N ILE A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 283 removed outlier: 4.000A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 289 through 319 removed outlier: 3.964A pdb=" N ARG A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 322 through 336 removed outlier: 3.512A pdb=" N ARG A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.911A pdb=" N LEU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 25 removed outlier: 3.599A pdb=" N ILE D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'E' and resid 9 through 24 removed outlier: 4.015A pdb=" N LEU E 15 " --> pdb=" O GLN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 54 removed outlier: 3.887A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.466A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.146A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.696A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.621A pdb=" N VAL C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 56 through 59 removed outlier: 4.182A pdb=" N GLY F 59 " --> pdb=" O SER F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 59' Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 221 through 225 removed outlier: 3.608A pdb=" N VAL F 225 " --> pdb=" O ALA F 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.734A pdb=" N ALA B 27 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 26 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 40 " --> pdb=" O MET B 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.636A pdb=" N ALA A 200 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.574A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.590A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.903A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 134 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.581A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.902A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.688A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 259 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.738A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS D 294 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL D 307 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL D 296 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 185 through 189 removed outlier: 5.863A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AB4, first strand: chain 'F' and resid 13 through 15 removed outlier: 5.979A pdb=" N GLY F 13 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET F 37 " --> pdb=" O TYR F 53 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR F 53 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 13 through 15 removed outlier: 5.979A pdb=" N GLY F 13 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG F 101 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE F 113 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 141 through 143 Processing sheet with id=AB7, first strand: chain 'F' and resid 195 through 196 removed outlier: 6.673A pdb=" N TRP F 177 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR F 191 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU F 175 " --> pdb=" O TYR F 191 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR F 239 " --> pdb=" O GLN F 232 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 195 through 196 removed outlier: 6.673A pdb=" N TRP F 177 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR F 191 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU F 175 " --> pdb=" O TYR F 191 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1326 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: 4.40 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9564 1.04 - 1.24: 1347 1.24 - 1.44: 2920 1.44 - 1.64: 5502 1.64 - 1.84: 99 Bond restraints: 19432 Sorted by residual: bond pdb=" N PHE B 1 " pdb=" H3 PHE B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N PHE B 1 " pdb=" H2 PHE B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N THR C 4 " pdb=" CA THR C 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N PHE B 1 " pdb=" CA PHE B 1 " ideal model delta sigma weight residual 1.491 1.456 0.035 2.10e-02 2.27e+03 2.75e+00 bond pdb=" N ASP F 138 " pdb=" CA ASP F 138 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 19427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 34981 3.54 - 7.07: 39 7.07 - 10.61: 0 10.61 - 14.14: 1 14.14 - 17.68: 1 Bond angle restraints: 35022 Sorted by residual: angle pdb=" H1 PHE B 1 " pdb=" N PHE B 1 " pdb=" H2 PHE B 1 " ideal model delta sigma weight residual 109.47 91.79 17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" H1 PHE B 1 " pdb=" N PHE B 1 " pdb=" H3 PHE B 1 " ideal model delta sigma weight residual 109.47 120.77 -11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CG ARG F 101 " pdb=" CD ARG F 101 " pdb=" NE ARG F 101 " ideal model delta sigma weight residual 112.00 118.78 -6.78 2.20e+00 2.07e-01 9.49e+00 angle pdb=" CA ALA D 309 " pdb=" C ALA D 309 " pdb=" N GLY D 310 " ideal model delta sigma weight residual 114.76 118.22 -3.46 1.14e+00 7.69e-01 9.20e+00 angle pdb=" CA CYS A 124 " pdb=" CB CYS A 124 " pdb=" SG CYS A 124 " ideal model delta sigma weight residual 114.40 120.48 -6.08 2.30e+00 1.89e-01 7.00e+00 ... (remaining 35017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8483 17.86 - 35.71: 511 35.71 - 53.57: 120 53.57 - 71.42: 40 71.42 - 89.28: 6 Dihedral angle restraints: 9160 sinusoidal: 4929 harmonic: 4231 Sorted by residual: dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG F 192 " pdb=" C ARG F 192 " pdb=" N MET F 193 " pdb=" CA MET F 193 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS D 78 " pdb=" C LYS D 78 " pdb=" N LEU D 79 " pdb=" CA LEU D 79 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 898 0.028 - 0.056: 414 0.056 - 0.084: 109 0.084 - 0.112: 64 0.112 - 0.141: 28 Chirality restraints: 1513 Sorted by residual: chirality pdb=" CA ILE F 158 " pdb=" N ILE F 158 " pdb=" C ILE F 158 " pdb=" CB ILE F 158 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE D 81 " pdb=" N ILE D 81 " pdb=" C ILE D 81 " pdb=" CB ILE D 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA VAL E 54 " pdb=" N VAL E 54 " pdb=" C VAL E 54 " pdb=" CB VAL E 54 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1510 not shown) Planarity restraints: 2887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 101 " -0.163 9.50e-02 1.11e+02 5.52e-02 4.89e+00 pdb=" NE ARG F 101 " 0.000 2.00e-02 2.50e+03 pdb=" CZ ARG F 101 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG F 101 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 101 " -0.010 2.00e-02 2.50e+03 pdb="HH11 ARG F 101 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 101 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG F 101 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 151 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO F 152 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 152 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 152 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 109 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO F 110 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO F 110 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 110 " -0.021 5.00e-02 4.00e+02 ... (remaining 2884 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1646 2.24 - 2.83: 42434 2.83 - 3.42: 47869 3.42 - 4.01: 66266 4.01 - 4.60: 101584 Nonbonded interactions: 259799 Sorted by model distance: nonbonded pdb=" O LEU A 130 " pdb="HD21 ASN A 134 " model vdw 1.645 2.450 nonbonded pdb="HE22 GLN E 18 " pdb=" OE2 GLU E 22 " model vdw 1.685 2.450 nonbonded pdb=" O ALA A 265 " pdb=" HG1 THR A 269 " model vdw 1.699 2.450 nonbonded pdb=" OD1 ASP D 254 " pdb=" H ALA D 257 " model vdw 1.702 2.450 nonbonded pdb=" HG1 THR D 274 " pdb=" O VAL D 315 " model vdw 1.709 2.450 ... (remaining 259794 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 0.039 9843 Z= 0.165 Angle : 0.577 6.779 13329 Z= 0.320 Chirality : 0.040 0.141 1513 Planarity : 0.004 0.073 1695 Dihedral : 12.016 89.280 3553 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.36 (0.24), residues: 1220 helix: 0.54 (0.25), residues: 423 sheet: 0.98 (0.29), residues: 281 loop : -0.33 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 101 TYR 0.012 0.001 TYR C 320 PHE 0.020 0.001 PHE F 35 TRP 0.010 0.001 TRP C 211 HIS 0.007 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 9837) covalent geometry : angle 0.57310 / 0.32 (13317) SS BOND : bond 0.00530 / 0.38 ( 6) SS BOND : angle 2.17543 / 1.96 ( 12) hydrogen bonds : bond 0.24118 / 16.22 ( 462) hydrogen bonds : angle 8.00355 / 5.72 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.555 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: B 40 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8027 (mt-10) REVERT: D 219 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7745 (mmm-85) REVERT: E 27 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: E 52 THR cc_start: 0.7191 (p) cc_final: 0.6956 (t) REVERT: C 28 GLU cc_start: 0.7670 (tt0) cc_final: 0.7318 (mt-10) REVERT: C 198 MET cc_start: 0.7799 (ttm) cc_final: 0.7543 (ttp) REVERT: C 256 ASN cc_start: 0.8748 (t0) cc_final: 0.8516 (t0) REVERT: F 221 GLU cc_start: 0.7039 (mp0) cc_final: 0.6447 (mp0) REVERT: F 224 ASP cc_start: 0.8285 (m-30) cc_final: 0.8013 (m-30) outliers start: 0 outliers final: 1 residues processed: 218 average time/residue: 1.3533 time to fit residues: 314.5858 Evaluate side-chains 178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN C 269 ASN C 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095546 restraints weight = 38391.476| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.03 r_work: 0.2873 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9843 Z= 0.185 Angle : 0.602 5.267 13329 Z= 0.325 Chirality : 0.041 0.155 1513 Planarity : 0.005 0.069 1695 Dihedral : 4.742 35.116 1344 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.72 % Allowed : 9.45 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.66 (0.23), residues: 1220 helix: 1.38 (0.25), residues: 420 sheet: 0.77 (0.29), residues: 288 loop : -0.49 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 46 TYR 0.016 0.001 TYR A 136 PHE 0.010 0.001 PHE A 64 TRP 0.012 0.001 TRP D 339 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 9837) covalent geometry : angle 0.59920 / 0.32 (13317) SS BOND : bond 0.00786 / 0.51 ( 6) SS BOND : angle 2.13505 / 1.74 ( 12) hydrogen bonds : bond 0.06228 / 4.05 ( 462) hydrogen bonds : angle 5.29488 / 3.84 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.516 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 329 MET cc_start: 0.7682 (ttp) cc_final: 0.7350 (ttt) REVERT: B 17 LYS cc_start: 0.7463 (tppp) cc_final: 0.7235 (tppp) REVERT: B 62 ARG cc_start: 0.9046 (ttm110) cc_final: 0.8836 (ttm110) REVERT: D 46 ARG cc_start: 0.7758 (mmm160) cc_final: 0.7247 (mpp80) REVERT: D 130 GLU cc_start: 0.8518 (mp0) cc_final: 0.8259 (mp0) REVERT: E 52 THR cc_start: 0.7191 (p) cc_final: 0.6945 (t) REVERT: C 28 GLU cc_start: 0.7866 (tt0) cc_final: 0.7538 (mt-10) REVERT: C 198 MET cc_start: 0.8080 (ttm) cc_final: 0.7749 (ttp) REVERT: C 256 ASN cc_start: 0.8723 (t0) cc_final: 0.8367 (t0) REVERT: F 16 GLN cc_start: 0.8718 (mt0) cc_final: 0.8445 (mt0) REVERT: F 203 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8491 (mtm-85) REVERT: F 220 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8909 (tp) REVERT: F 224 ASP cc_start: 0.8522 (m-30) cc_final: 0.7840 (m-30) outliers start: 18 outliers final: 4 residues processed: 195 average time/residue: 1.3237 time to fit residues: 275.1172 Evaluate side-chains 182 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 134 ASN B 34 ASN D 75 GLN C 304 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.094403 restraints weight = 38426.562| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.05 r_work: 0.2851 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9843 Z= 0.196 Angle : 0.579 8.814 13329 Z= 0.311 Chirality : 0.041 0.151 1513 Planarity : 0.004 0.055 1695 Dihedral : 4.605 40.839 1342 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.53 % Allowed : 12.02 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.64 (0.23), residues: 1220 helix: 1.52 (0.25), residues: 416 sheet: 0.76 (0.29), residues: 278 loop : -0.63 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 219 TYR 0.011 0.001 TYR F 191 PHE 0.010 0.001 PHE D 199 TRP 0.011 0.001 TRP D 82 HIS 0.005 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 9837) covalent geometry : angle 0.57737 / 0.31 (13317) SS BOND : bond 0.01140 / 0.65 ( 6) SS BOND : angle 1.67137 / 1.44 ( 12) hydrogen bonds : bond 0.05624 / 3.66 ( 462) hydrogen bonds : angle 4.99734 / 3.61 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.560 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: A 329 MET cc_start: 0.7753 (ttp) cc_final: 0.7470 (ttt) REVERT: B 17 LYS cc_start: 0.7627 (tppp) cc_final: 0.7335 (tppp) REVERT: B 38 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8207 (mmtp) REVERT: D 46 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7290 (mpp80) REVERT: D 130 GLU cc_start: 0.8600 (mp0) cc_final: 0.8263 (mp0) REVERT: E 27 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7196 (mtt90) REVERT: C 28 GLU cc_start: 0.7843 (tt0) cc_final: 0.7508 (mt-10) REVERT: C 198 MET cc_start: 0.8088 (ttm) cc_final: 0.7758 (ttp) REVERT: C 243 MET cc_start: 0.7182 (tmm) cc_final: 0.6809 (tmm) REVERT: C 256 ASN cc_start: 0.8771 (t0) cc_final: 0.8376 (t0) REVERT: F 16 GLN cc_start: 0.8749 (mt0) cc_final: 0.8479 (mt0) REVERT: F 79 LYS cc_start: 0.8952 (mmtp) cc_final: 0.8689 (mmmm) REVERT: F 203 ARG cc_start: 0.8820 (mtm-85) cc_final: 0.8264 (mtm-85) REVERT: F 221 GLU cc_start: 0.7110 (mp0) cc_final: 0.6234 (mp0) REVERT: F 224 ASP cc_start: 0.8527 (m-30) cc_final: 0.7887 (m-30) outliers start: 16 outliers final: 8 residues processed: 190 average time/residue: 1.3981 time to fit residues: 283.1599 Evaluate side-chains 180 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.0010 chunk 102 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN D 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095727 restraints weight = 38190.199| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.04 r_work: 0.2876 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9843 Z= 0.143 Angle : 0.539 7.033 13329 Z= 0.288 Chirality : 0.039 0.154 1513 Planarity : 0.004 0.047 1695 Dihedral : 4.438 39.341 1342 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.10 % Allowed : 12.79 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.76 (0.24), residues: 1220 helix: 1.73 (0.25), residues: 417 sheet: 0.70 (0.30), residues: 278 loop : -0.58 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 219 TYR 0.012 0.001 TYR C 302 PHE 0.010 0.001 PHE A 207 TRP 0.009 0.001 TRP F 50 HIS 0.003 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9837) covalent geometry : angle 0.53736 / 0.29 (13317) SS BOND : bond 0.00824 / 0.49 ( 6) SS BOND : angle 1.66127 / 1.33 ( 12) hydrogen bonds : bond 0.04833 / 3.13 ( 462) hydrogen bonds : angle 4.77229 / 3.43 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.335 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 329 MET cc_start: 0.7749 (ttp) cc_final: 0.7273 (ptt) REVERT: B 17 LYS cc_start: 0.7586 (tppp) cc_final: 0.7277 (tppp) REVERT: D 46 ARG cc_start: 0.7781 (mmm160) cc_final: 0.7324 (mpp80) REVERT: D 76 ASP cc_start: 0.8346 (p0) cc_final: 0.8100 (p0) REVERT: D 130 GLU cc_start: 0.8606 (mp0) cc_final: 0.8222 (mp0) REVERT: D 266 HIS cc_start: 0.7482 (t-170) cc_final: 0.6768 (t70) REVERT: E 27 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7204 (mtt90) REVERT: C 28 GLU cc_start: 0.7805 (tt0) cc_final: 0.7492 (mt-10) REVERT: C 198 MET cc_start: 0.7989 (ttm) cc_final: 0.7666 (ttp) REVERT: C 243 MET cc_start: 0.7166 (tmm) cc_final: 0.6738 (tmm) REVERT: C 256 ASN cc_start: 0.8773 (t0) cc_final: 0.8358 (t0) REVERT: F 16 GLN cc_start: 0.8748 (mt0) cc_final: 0.8479 (mt0) REVERT: F 79 LYS cc_start: 0.8972 (mmtp) cc_final: 0.8701 (mmmm) REVERT: F 203 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8110 (mtm-85) REVERT: F 221 GLU cc_start: 0.7148 (mp0) cc_final: 0.6239 (mp0) REVERT: F 224 ASP cc_start: 0.8601 (m-30) cc_final: 0.8062 (m-30) outliers start: 22 outliers final: 9 residues processed: 192 average time/residue: 1.3372 time to fit residues: 273.4215 Evaluate side-chains 180 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain F residue 217 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN D 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096134 restraints weight = 38365.075| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.04 r_work: 0.2880 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9843 Z= 0.137 Angle : 0.534 6.268 13329 Z= 0.284 Chirality : 0.039 0.160 1513 Planarity : 0.004 0.037 1695 Dihedral : 4.329 38.138 1342 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.19 % Allowed : 14.22 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.82 (0.24), residues: 1220 helix: 1.86 (0.26), residues: 417 sheet: 0.60 (0.30), residues: 285 loop : -0.54 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 219 TYR 0.010 0.001 TYR F 191 PHE 0.010 0.001 PHE A 207 TRP 0.009 0.001 TRP F 50 HIS 0.003 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9837) covalent geometry : angle 0.53236 / 0.28 (13317) SS BOND : bond 0.00738 / 0.45 ( 6) SS BOND : angle 1.61719 / 1.28 ( 12) hydrogen bonds : bond 0.04572 / 2.96 ( 462) hydrogen bonds : angle 4.64544 / 3.33 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.7754 (ttp) cc_final: 0.7352 (ptt) REVERT: B 17 LYS cc_start: 0.7845 (tppp) cc_final: 0.7547 (tppp) REVERT: B 38 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8116 (mmtp) REVERT: D 46 ARG cc_start: 0.7810 (mmm160) cc_final: 0.7364 (mpp80) REVERT: D 76 ASP cc_start: 0.8336 (p0) cc_final: 0.8091 (p0) REVERT: D 130 GLU cc_start: 0.8553 (mp0) cc_final: 0.8166 (mp0) REVERT: E 27 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7222 (mtt90) REVERT: C 28 GLU cc_start: 0.7807 (tt0) cc_final: 0.7494 (mt-10) REVERT: C 243 MET cc_start: 0.7515 (tmm) cc_final: 0.7290 (tmm) REVERT: C 256 ASN cc_start: 0.8790 (t0) cc_final: 0.8383 (t0) REVERT: F 16 GLN cc_start: 0.8727 (mt0) cc_final: 0.8460 (mt0) REVERT: F 79 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8701 (mmmm) REVERT: F 221 GLU cc_start: 0.7369 (mp0) cc_final: 0.6857 (mp0) REVERT: F 224 ASP cc_start: 0.8515 (m-30) cc_final: 0.7953 (m-30) outliers start: 23 outliers final: 12 residues processed: 191 average time/residue: 1.3398 time to fit residues: 273.0832 Evaluate side-chains 181 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 11 CYS Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 304 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 107 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN D 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095693 restraints weight = 38139.120| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.03 r_work: 0.2869 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9843 Z= 0.152 Angle : 0.532 6.114 13329 Z= 0.284 Chirality : 0.040 0.159 1513 Planarity : 0.004 0.040 1695 Dihedral : 4.288 37.689 1342 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.48 % Allowed : 15.08 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.86 (0.24), residues: 1220 helix: 1.92 (0.26), residues: 417 sheet: 0.57 (0.29), residues: 290 loop : -0.53 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 219 TYR 0.012 0.001 TYR C 302 PHE 0.014 0.001 PHE B 4 TRP 0.009 0.001 TRP F 50 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9837) covalent geometry : angle 0.52965 / 0.28 (13317) SS BOND : bond 0.00751 / 0.46 ( 6) SS BOND : angle 1.59238 / 1.29 ( 12) hydrogen bonds : bond 0.04591 / 2.97 ( 462) hydrogen bonds : angle 4.59958 / 3.30 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.550 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 329 MET cc_start: 0.7776 (ttp) cc_final: 0.7380 (ptt) REVERT: B 17 LYS cc_start: 0.7955 (tppp) cc_final: 0.7608 (tppp) REVERT: B 38 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8126 (mmtp) REVERT: D 46 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7379 (mpp80) REVERT: D 76 ASP cc_start: 0.8342 (p0) cc_final: 0.8095 (p0) REVERT: D 130 GLU cc_start: 0.8565 (mp0) cc_final: 0.8171 (mp0) REVERT: E 27 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7166 (mtt90) REVERT: C 28 GLU cc_start: 0.7815 (tt0) cc_final: 0.7496 (mt-10) REVERT: C 243 MET cc_start: 0.7728 (tmm) cc_final: 0.7483 (tmm) REVERT: C 256 ASN cc_start: 0.8792 (t0) cc_final: 0.8381 (t0) REVERT: F 16 GLN cc_start: 0.8741 (mt0) cc_final: 0.8460 (mt0) REVERT: F 79 LYS cc_start: 0.8988 (mmtp) cc_final: 0.8739 (mmmm) REVERT: F 221 GLU cc_start: 0.7384 (mp0) cc_final: 0.6946 (mp0) REVERT: F 224 ASP cc_start: 0.8584 (m-30) cc_final: 0.7975 (m-30) outliers start: 26 outliers final: 12 residues processed: 188 average time/residue: 1.2998 time to fit residues: 261.1350 Evaluate side-chains 180 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain F residue 49 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN D 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.095537 restraints weight = 38286.950| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.04 r_work: 0.2867 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9843 Z= 0.152 Angle : 0.535 7.204 13329 Z= 0.285 Chirality : 0.039 0.168 1513 Planarity : 0.004 0.040 1695 Dihedral : 4.227 36.927 1342 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.29 % Allowed : 15.94 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.88 (0.24), residues: 1220 helix: 1.97 (0.26), residues: 417 sheet: 0.55 (0.29), residues: 285 loop : -0.52 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 219 TYR 0.010 0.001 TYR C 320 PHE 0.009 0.001 PHE A 207 TRP 0.009 0.001 TRP D 82 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9837) covalent geometry : angle 0.53275 / 0.28 (13317) SS BOND : bond 0.00731 / 0.45 ( 6) SS BOND : angle 1.55727 / 1.29 ( 12) hydrogen bonds : bond 0.04518 / 2.93 ( 462) hydrogen bonds : angle 4.56334 / 3.27 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.552 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 329 MET cc_start: 0.7795 (ttp) cc_final: 0.7415 (ptt) REVERT: B 17 LYS cc_start: 0.8007 (tppp) cc_final: 0.7664 (tppp) REVERT: D 46 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7384 (mpp80) REVERT: D 76 ASP cc_start: 0.8400 (p0) cc_final: 0.8163 (p0) REVERT: D 130 GLU cc_start: 0.8585 (mp0) cc_final: 0.8176 (mp0) REVERT: D 266 HIS cc_start: 0.7429 (t-170) cc_final: 0.6722 (t70) REVERT: E 27 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7207 (mtt90) REVERT: E 46 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8760 (mmmm) REVERT: C 28 GLU cc_start: 0.7814 (tt0) cc_final: 0.7510 (mt-10) REVERT: C 243 MET cc_start: 0.7794 (tmm) cc_final: 0.7561 (tmm) REVERT: C 256 ASN cc_start: 0.8781 (t0) cc_final: 0.8364 (t0) REVERT: F 16 GLN cc_start: 0.8750 (mt0) cc_final: 0.8490 (mt0) REVERT: F 79 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8736 (mmmm) REVERT: F 221 GLU cc_start: 0.7442 (mp0) cc_final: 0.6910 (mp0) REVERT: F 224 ASP cc_start: 0.8583 (m-30) cc_final: 0.7810 (m-30) outliers start: 24 outliers final: 12 residues processed: 185 average time/residue: 1.3141 time to fit residues: 259.4657 Evaluate side-chains 180 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN C 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.096093 restraints weight = 38141.499| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.04 r_work: 0.2878 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9843 Z= 0.137 Angle : 0.542 9.262 13329 Z= 0.286 Chirality : 0.039 0.166 1513 Planarity : 0.004 0.046 1695 Dihedral : 4.149 36.506 1342 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.62 % Allowed : 17.37 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.94 (0.24), residues: 1220 helix: 1.99 (0.26), residues: 418 sheet: 0.58 (0.29), residues: 290 loop : -0.46 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 219 TYR 0.009 0.001 TYR F 191 PHE 0.008 0.001 PHE B 4 TRP 0.008 0.001 TRP D 63 HIS 0.003 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9837) covalent geometry : angle 0.54019 / 0.29 (13317) SS BOND : bond 0.00708 / 0.43 ( 6) SS BOND : angle 1.42503 / 1.19 ( 12) hydrogen bonds : bond 0.04304 / 2.79 ( 462) hydrogen bonds : angle 4.47780 / 3.20 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.425 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 313 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7551 (mp) REVERT: A 329 MET cc_start: 0.7799 (ttp) cc_final: 0.7471 (ptt) REVERT: B 17 LYS cc_start: 0.8010 (tppp) cc_final: 0.7664 (tppp) REVERT: B 38 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8174 (mmtp) REVERT: D 46 ARG cc_start: 0.7803 (mmm160) cc_final: 0.7370 (mpp80) REVERT: D 76 ASP cc_start: 0.8445 (p0) cc_final: 0.8184 (p0) REVERT: D 130 GLU cc_start: 0.8572 (mp0) cc_final: 0.8155 (mp0) REVERT: D 266 HIS cc_start: 0.7431 (t-170) cc_final: 0.6718 (t70) REVERT: E 27 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7214 (mtt90) REVERT: E 46 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8787 (mmmm) REVERT: C 28 GLU cc_start: 0.7812 (tt0) cc_final: 0.7537 (mt-10) REVERT: C 243 MET cc_start: 0.7818 (tmm) cc_final: 0.7563 (tmm) REVERT: C 256 ASN cc_start: 0.8777 (t0) cc_final: 0.8362 (t0) REVERT: F 16 GLN cc_start: 0.8748 (mt0) cc_final: 0.8477 (mt0) REVERT: F 79 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8746 (mmmm) REVERT: F 220 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8855 (mm) REVERT: F 221 GLU cc_start: 0.7402 (mp0) cc_final: 0.6995 (mp0) REVERT: F 224 ASP cc_start: 0.8523 (m-30) cc_final: 0.7941 (m-30) outliers start: 17 outliers final: 11 residues processed: 181 average time/residue: 1.3767 time to fit residues: 265.7369 Evaluate side-chains 178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN D 75 GLN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095979 restraints weight = 38034.221| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.04 r_work: 0.2878 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9843 Z= 0.142 Angle : 0.548 10.050 13329 Z= 0.289 Chirality : 0.039 0.172 1513 Planarity : 0.004 0.051 1695 Dihedral : 4.130 36.231 1342 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.81 % Allowed : 17.75 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.94 (0.24), residues: 1220 helix: 2.01 (0.26), residues: 418 sheet: 0.54 (0.29), residues: 285 loop : -0.45 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 219 TYR 0.009 0.001 TYR F 191 PHE 0.008 0.001 PHE A 207 TRP 0.008 0.001 TRP D 82 HIS 0.007 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9837) covalent geometry : angle 0.54652 / 0.29 (13317) SS BOND : bond 0.00715 / 0.44 ( 6) SS BOND : angle 1.42202 / 1.19 ( 12) hydrogen bonds : bond 0.04306 / 2.80 ( 462) hydrogen bonds : angle 4.46601 / 3.20 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.512 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 313 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7550 (mp) REVERT: A 329 MET cc_start: 0.7828 (ttp) cc_final: 0.7511 (ptt) REVERT: B 17 LYS cc_start: 0.8011 (tppp) cc_final: 0.7636 (tppp) REVERT: B 38 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8222 (mttt) REVERT: B 64 ILE cc_start: 0.8938 (mp) cc_final: 0.8617 (tp) REVERT: D 46 ARG cc_start: 0.7814 (mmm160) cc_final: 0.7373 (mpp80) REVERT: D 76 ASP cc_start: 0.8442 (p0) cc_final: 0.8185 (p0) REVERT: D 130 GLU cc_start: 0.8571 (mp0) cc_final: 0.8146 (mp0) REVERT: D 266 HIS cc_start: 0.7434 (t-170) cc_final: 0.6721 (t70) REVERT: E 27 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7216 (mtt90) REVERT: E 46 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8780 (mmmm) REVERT: C 28 GLU cc_start: 0.7842 (tt0) cc_final: 0.7522 (mt-10) REVERT: C 243 MET cc_start: 0.7852 (tmm) cc_final: 0.7604 (tmm) REVERT: C 256 ASN cc_start: 0.8766 (t0) cc_final: 0.8370 (t0) REVERT: C 261 ASP cc_start: 0.9097 (p0) cc_final: 0.8823 (p0) REVERT: F 16 GLN cc_start: 0.8747 (mt0) cc_final: 0.8488 (mt0) REVERT: F 79 LYS cc_start: 0.9010 (mmtp) cc_final: 0.8750 (mmmm) REVERT: F 220 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8870 (mm) REVERT: F 221 GLU cc_start: 0.7395 (mp0) cc_final: 0.7046 (mp0) REVERT: F 224 ASP cc_start: 0.8517 (m-30) cc_final: 0.7955 (m-30) outliers start: 19 outliers final: 12 residues processed: 181 average time/residue: 1.3784 time to fit residues: 265.3595 Evaluate side-chains 177 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 105 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.150531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096227 restraints weight = 38231.289| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.05 r_work: 0.2883 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9843 Z= 0.135 Angle : 0.557 11.395 13329 Z= 0.291 Chirality : 0.039 0.165 1513 Planarity : 0.004 0.068 1695 Dihedral : 4.131 35.575 1342 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.43 % Allowed : 18.03 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.99 (0.24), residues: 1220 helix: 2.03 (0.26), residues: 418 sheet: 0.56 (0.29), residues: 290 loop : -0.40 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 219 TYR 0.009 0.001 TYR F 191 PHE 0.009 0.001 PHE A 207 TRP 0.008 0.001 TRP D 63 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 9837) covalent geometry : angle 0.55560 / 0.29 (13317) SS BOND : bond 0.00681 / 0.42 ( 6) SS BOND : angle 1.35889 / 1.14 ( 12) hydrogen bonds : bond 0.04206 / 2.73 ( 462) hydrogen bonds : angle 4.44066 / 3.18 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.584 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 313 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7661 (mp) REVERT: A 329 MET cc_start: 0.7824 (ttp) cc_final: 0.7517 (ptt) REVERT: B 17 LYS cc_start: 0.8004 (tppp) cc_final: 0.7613 (tppp) REVERT: B 38 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8212 (mmtp) REVERT: B 64 ILE cc_start: 0.8913 (mp) cc_final: 0.8617 (tp) REVERT: D 46 ARG cc_start: 0.7816 (mmm160) cc_final: 0.7361 (mpp80) REVERT: D 76 ASP cc_start: 0.8437 (p0) cc_final: 0.8185 (p0) REVERT: D 130 GLU cc_start: 0.8568 (mp0) cc_final: 0.8144 (mp0) REVERT: E 46 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8802 (mmmm) REVERT: E 59 ASN cc_start: 0.8293 (t0) cc_final: 0.8080 (t0) REVERT: C 28 GLU cc_start: 0.7836 (tt0) cc_final: 0.7508 (mt-10) REVERT: C 243 MET cc_start: 0.7866 (tmm) cc_final: 0.7621 (tmm) REVERT: C 256 ASN cc_start: 0.8743 (t0) cc_final: 0.8345 (t0) REVERT: C 261 ASP cc_start: 0.9103 (p0) cc_final: 0.8827 (p0) REVERT: F 16 GLN cc_start: 0.8757 (mt0) cc_final: 0.8498 (mt0) REVERT: F 79 LYS cc_start: 0.9011 (mmtp) cc_final: 0.8752 (mmmm) REVERT: F 221 GLU cc_start: 0.7347 (mp0) cc_final: 0.6998 (mp0) REVERT: F 224 ASP cc_start: 0.8515 (m-30) cc_final: 0.7969 (m-30) outliers start: 15 outliers final: 11 residues processed: 186 average time/residue: 1.3307 time to fit residues: 264.1982 Evaluate side-chains 175 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 107 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN D 75 GLN F 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.150985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096720 restraints weight = 38121.607| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.04 r_work: 0.2892 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9843 Z= 0.122 Angle : 0.552 9.356 13329 Z= 0.289 Chirality : 0.039 0.167 1513 Planarity : 0.004 0.060 1695 Dihedral : 4.075 35.166 1342 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.53 % Allowed : 18.23 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.00 (0.24), residues: 1220 helix: 2.07 (0.26), residues: 418 sheet: 0.62 (0.30), residues: 278 loop : -0.43 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 219 TYR 0.009 0.001 TYR F 191 PHE 0.009 0.001 PHE A 207 TRP 0.008 0.001 TRP F 50 HIS 0.012 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9837) covalent geometry : angle 0.55045 / 0.29 (13317) SS BOND : bond 0.00662 / 0.41 ( 6) SS BOND : angle 1.29477 / 1.10 ( 12) hydrogen bonds : bond 0.04027 / 2.61 ( 462) hydrogen bonds : angle 4.38339 / 3.14 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.96 seconds wall clock time: 131 minutes 18.76 seconds (7878.76 seconds total)