Starting phenix.real_space_refine on Fri Jun 5 08:18:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p0l_71080/06_2026/9p0l_71080.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p0l_71080/06_2026/9p0l_71080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p0l_71080/06_2026/9p0l_71080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p0l_71080/06_2026/9p0l_71080.map" model { file = "/net/cci-nas-00/data/ceres_data/9p0l_71080/06_2026/9p0l_71080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p0l_71080/06_2026/9p0l_71080.cif" } resolution = 3.1 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= 1.124 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 68 5.16 5 C 5957 2.51 5 N 1624 2.21 5 O 1735 1.98 5 H 9372 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 18756 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4732 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "B" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1117 Classifications: {'peptide': 69} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "C" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3440 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 2 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: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 861 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: 3.82, per 1000 atoms: 0.20 Number of scatterers: 18756 At special positions: 0 Unit cell: (149.628, 117.647, 86.8072, 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 68 16.00 O 1735 8.00 N 1624 7.00 C 5957 6.00 H 9372 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 230 " distance=2.03 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: 1.42 Conformation dependent library (CDL) restraints added in 771.2 milliseconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 39.6% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 45 through 80 Proline residue: A 57 - end of helix removed outlier: 3.641A pdb=" N SER A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 removed outlier: 3.610A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.655A pdb=" N ASP A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 154 removed outlier: 3.812A pdb=" N CYS A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 3.561A pdb=" N ARG A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 189 removed outlier: 3.705A pdb=" N LEU A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 208 through 224 removed outlier: 3.757A pdb=" N ARG A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 245 removed outlier: 4.067A pdb=" N VAL A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 283 removed outlier: 3.988A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 289 through 319 removed outlier: 3.582A pdb=" N HIS A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 207 through 218 removed outlier: 4.284A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY C 217 " --> pdb=" O CYS C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.268A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.897A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 25 Processing helix chain 'D' and resid 29 through 35 removed outlier: 4.002A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 25 removed outlier: 4.013A pdb=" N VAL E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 48 through 52 Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 56 through 59 removed outlier: 4.096A 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 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 221 through 225 removed outlier: 3.626A pdb=" N VAL F 225 " --> pdb=" O ALA F 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.651A pdb=" N HIS A 193 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 202 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 30 removed outlier: 6.837A pdb=" N THR B 44 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU B 27 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 42 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE B 29 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU B 40 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 41 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 185 through 191 removed outlier: 8.740A pdb=" N ALA C 220 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 47 through 51 Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.825A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.280A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 5.901A 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: 3.540A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.604A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 273 through 278 removed outlier: 6.388A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE D 278 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU D 284 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.711A pdb=" N THR F 81 " --> pdb=" O ASP F 76 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 74 " --> pdb=" O PHE F 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 13 through 15 removed outlier: 6.127A pdb=" N GLY F 13 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET F 37 " --> pdb=" O TYR F 53 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR F 53 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 13 through 15 removed outlier: 6.127A pdb=" N GLY F 13 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE F 113 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 141 through 143 Processing sheet with id=AB6, first strand: chain 'F' and resid 195 through 196 removed outlier: 6.697A pdb=" N TRP F 177 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR F 191 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 175 " --> pdb=" O TYR F 191 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR F 239 " --> pdb=" O GLN F 232 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 195 through 196 removed outlier: 6.697A pdb=" N TRP F 177 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR F 191 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 175 " --> pdb=" O TYR F 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 226 " --> pdb=" O LEU F 246 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1365 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: 4.36 Time building geometry restraints manager: 2.05 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: 9343 1.04 - 1.24: 1304 1.24 - 1.44: 2835 1.44 - 1.64: 5367 1.64 - 1.84: 95 Bond restraints: 18944 Sorted by residual: bond pdb=" N VAL B 1 " pdb=" H3 VAL B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N VAL B 1 " pdb=" H2 VAL B 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N ARG B 22 " pdb=" H ARG B 22 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" N ARG B 22 " pdb=" CA ARG B 22 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.27e-02 6.20e+03 5.13e+00 bond pdb=" N THR C 4 " pdb=" CA THR C 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 ... (remaining 18939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 33873 2.56 - 5.12: 260 5.12 - 7.67: 19 7.67 - 10.23: 4 10.23 - 12.79: 1 Bond angle restraints: 34157 Sorted by residual: angle pdb=" CA CYS C 325 " pdb=" C CYS C 325 " pdb=" N ALA C 326 " ideal model delta sigma weight residual 118.14 127.91 -9.77 1.31e+00 5.83e-01 5.56e+01 angle pdb=" CA CYS C 325 " pdb=" C CYS C 325 " pdb=" O CYS C 325 " ideal model delta sigma weight residual 119.38 113.65 5.73 1.23e+00 6.61e-01 2.17e+01 angle pdb=" H1 VAL B 1 " pdb=" N VAL B 1 " pdb=" H2 VAL B 1 " ideal model delta sigma weight residual 109.47 96.68 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" CB LYS E 46 " pdb=" CG LYS E 46 " pdb=" CD LYS E 46 " ideal model delta sigma weight residual 111.30 120.81 -9.51 2.30e+00 1.89e-01 1.71e+01 angle pdb=" CA ASP D 258 " pdb=" CB ASP D 258 " pdb=" CG ASP D 258 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 ... (remaining 34152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 8095 16.75 - 33.50: 616 33.50 - 50.26: 154 50.26 - 67.01: 56 67.01 - 83.76: 9 Dihedral angle restraints: 8930 sinusoidal: 4818 harmonic: 4112 Sorted by residual: dihedral pdb=" CB CYS A 43 " pdb=" SG CYS A 43 " pdb=" SG CYS A 290 " pdb=" CB CYS A 290 " ideal model delta sinusoidal sigma weight residual -86.00 -25.68 -60.32 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA CYS A 203 " pdb=" C CYS A 203 " pdb=" N GLN A 204 " pdb=" CA GLN A 204 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 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 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1104 0.044 - 0.087: 290 0.087 - 0.131: 78 0.131 - 0.175: 9 0.175 - 0.218: 1 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CB THR F 173 " pdb=" CA THR F 173 " pdb=" OG1 THR F 173 " pdb=" CG2 THR F 173 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CG LEU A 243 " pdb=" CB LEU A 243 " pdb=" CD1 LEU A 243 " pdb=" CD2 LEU A 243 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CG LEU A 313 " pdb=" CB LEU A 313 " pdb=" CD1 LEU A 313 " pdb=" CD2 LEU A 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 1479 not shown) Planarity restraints: 2803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 22 " 0.351 9.50e-02 1.11e+02 1.69e-01 3.47e+02 pdb=" NE ARG B 22 " 0.099 2.00e-02 2.50e+03 pdb=" CZ ARG B 22 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG B 22 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 22 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG B 22 " 0.235 2.00e-02 2.50e+03 pdb="HH12 ARG B 22 " -0.247 2.00e-02 2.50e+03 pdb="HH21 ARG B 22 " -0.036 2.00e-02 2.50e+03 pdb="HH22 ARG B 22 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 258 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.19e+01 pdb=" CG ASP D 258 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASP D 258 " -0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP D 258 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 182 " 0.025 2.00e-02 2.50e+03 1.81e-02 9.83e+00 pdb=" CG PHE A 182 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 182 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 182 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 182 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 182 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 182 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 182 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 182 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 182 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 182 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 182 " 0.000 2.00e-02 2.50e+03 ... (remaining 2800 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1598 2.23 - 2.82: 41859 2.82 - 3.42: 50907 3.42 - 4.01: 69482 4.01 - 4.60: 105708 Nonbonded interactions: 269554 Sorted by model distance: nonbonded pdb="HH21 ARG A 216 " pdb=" O LEU B 3 " model vdw 1.639 2.450 nonbonded pdb="HD22 ASN D 230 " pdb=" OD1 ASP D 246 " model vdw 1.655 2.450 nonbonded pdb=" O ASP D 298 " pdb=" H ALA D 302 " model vdw 1.683 2.450 nonbonded pdb=" O ASN A 152 " pdb="HD21 ASN C 347 " model vdw 1.695 2.450 nonbonded pdb=" HG SER D 147 " pdb=" O VAL D 187 " model vdw 1.696 2.450 ... (remaining 269549 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: 2.010 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: 0.040 Set scattering table: 0.030 Process input model: 19.040 Find NCS groups from input model: 0.070 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 0.040 9578 Z= 0.164 Angle : 0.732 9.767 12977 Z= 0.396 Chirality : 0.043 0.218 1482 Planarity : 0.006 0.090 1646 Dihedral : 12.621 80.363 3459 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.02 (0.25), residues: 1187 helix: 0.32 (0.27), residues: 390 sheet: -0.21 (0.30), residues: 302 loop : 0.13 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 313 TYR 0.016 0.002 TYR C 296 PHE 0.054 0.002 PHE A 182 TRP 0.011 0.001 TRP D 99 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 9572) covalent geometry : angle 0.73213 / 0.40 (12965) SS BOND : bond 0.00479 / 0.27 ( 6) SS BOND : angle 1.03181 / 0.88 ( 12) hydrogen bonds : bond 0.23597 / 16.08 ( 476) hydrogen bonds : angle 8.85843 / 6.35 ( 1365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.515 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 206 ASN cc_start: 0.7776 (m-40) cc_final: 0.7426 (m-40) REVERT: A 273 LEU cc_start: 0.7704 (tp) cc_final: 0.7466 (tp) REVERT: A 292 ARG cc_start: 0.7812 (ttm110) cc_final: 0.6707 (ttm110) REVERT: C 256 ASN cc_start: 0.8345 (t0) cc_final: 0.7705 (t0) REVERT: C 302 TYR cc_start: 0.8842 (t80) cc_final: 0.8639 (t80) REVERT: C 333 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7441 (tp-100) REVERT: E 21 MET cc_start: 0.8678 (mmp) cc_final: 0.8452 (mmm) REVERT: F 21 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7954 (tpp80) REVERT: F 167 LEU cc_start: 0.8516 (tt) cc_final: 0.8222 (tp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2843 time to fit residues: 81.2253 Evaluate side-chains 193 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.161888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119913 restraints weight = 39305.392| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.95 r_work: 0.3287 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9578 Z= 0.275 Angle : 0.659 7.670 12977 Z= 0.360 Chirality : 0.044 0.152 1482 Planarity : 0.005 0.062 1646 Dihedral : 5.503 25.816 1307 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.88 % Allowed : 8.02 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.07 (0.24), residues: 1187 helix: 0.53 (0.25), residues: 398 sheet: -0.29 (0.30), residues: 296 loop : -0.17 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 314 TYR 0.016 0.002 TYR F 191 PHE 0.033 0.002 PHE A 207 TRP 0.013 0.002 TRP D 169 HIS 0.007 0.002 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 ( 9572) covalent geometry : angle 0.65782 / 0.36 (12965) SS BOND : bond 0.00321 / 0.20 ( 6) SS BOND : angle 1.26301 / 0.91 ( 12) hydrogen bonds : bond 0.06275 / 4.16 ( 476) hydrogen bonds : angle 6.23381 / 4.52 ( 1365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 0.534 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 206 ASN cc_start: 0.8328 (m-40) cc_final: 0.8000 (m-40) REVERT: A 278 ASP cc_start: 0.7800 (t0) cc_final: 0.7428 (t0) REVERT: A 281 MET cc_start: 0.8645 (mpp) cc_final: 0.8367 (mpp) REVERT: C 256 ASN cc_start: 0.8768 (t0) cc_final: 0.8082 (t0) REVERT: C 302 TYR cc_start: 0.9112 (t80) cc_final: 0.7787 (t80) REVERT: C 309 ASP cc_start: 0.8325 (m-30) cc_final: 0.7772 (m-30) REVERT: D 258 ASP cc_start: 0.8246 (t0) cc_final: 0.7850 (t0) REVERT: D 262 MET cc_start: 0.7498 (tpp) cc_final: 0.7079 (tpp) REVERT: E 21 MET cc_start: 0.9166 (mmp) cc_final: 0.8789 (mmm) REVERT: E 27 ARG cc_start: 0.8609 (mtt90) cc_final: 0.8358 (mtt-85) REVERT: F 154 GLU cc_start: 0.7797 (pt0) cc_final: 0.7565 (pt0) outliers start: 9 outliers final: 7 residues processed: 204 average time/residue: 0.2714 time to fit residues: 72.7252 Evaluate side-chains 198 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain F residue 165 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 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 = 0.4017 r_free = 0.4017 target = 0.164077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123030 restraints weight = 39409.259| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.95 r_work: 0.3335 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9578 Z= 0.138 Angle : 0.561 5.789 12977 Z= 0.303 Chirality : 0.041 0.152 1482 Planarity : 0.004 0.041 1646 Dihedral : 5.107 23.916 1307 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.78 % Allowed : 9.78 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.03 (0.24), residues: 1187 helix: 0.78 (0.25), residues: 394 sheet: -0.30 (0.30), residues: 293 loop : -0.23 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 314 TYR 0.015 0.001 TYR F 191 PHE 0.018 0.001 PHE A 207 TRP 0.009 0.001 TRP D 169 HIS 0.007 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9572) covalent geometry : angle 0.56012 / 0.30 (12965) SS BOND : bond 0.00352 / 0.18 ( 6) SS BOND : angle 1.00397 / 0.66 ( 12) hydrogen bonds : bond 0.05105 / 3.42 ( 476) hydrogen bonds : angle 5.66935 / 4.10 ( 1365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.507 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 104 LEU cc_start: 0.7830 (tt) cc_final: 0.7583 (mp) REVERT: A 206 ASN cc_start: 0.8324 (m-40) cc_final: 0.8055 (m-40) REVERT: A 255 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7137 (mtt90) REVERT: B 14 ILE cc_start: 0.8468 (mp) cc_final: 0.8199 (mt) REVERT: C 256 ASN cc_start: 0.8648 (t0) cc_final: 0.7966 (t0) REVERT: D 258 ASP cc_start: 0.8184 (t0) cc_final: 0.7785 (t0) REVERT: D 259 GLN cc_start: 0.7589 (tp40) cc_final: 0.7005 (tm-30) REVERT: D 262 MET cc_start: 0.7395 (tpp) cc_final: 0.6960 (tpp) REVERT: E 21 MET cc_start: 0.9171 (mmp) cc_final: 0.8806 (mmm) REVERT: E 27 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8272 (mtt-85) REVERT: F 187 GLN cc_start: 0.8524 (mt0) cc_final: 0.8286 (mt0) outliers start: 8 outliers final: 6 residues processed: 202 average time/residue: 0.2806 time to fit residues: 74.5145 Evaluate side-chains 188 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 231 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** D 17 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 = 0.3996 r_free = 0.3996 target = 0.162410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120774 restraints weight = 39573.196| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.95 r_work: 0.3307 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 9578 Z= 0.204 Angle : 0.589 12.306 12977 Z= 0.317 Chirality : 0.041 0.151 1482 Planarity : 0.004 0.054 1646 Dihedral : 5.071 23.420 1307 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.08 % Allowed : 11.74 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.01 (0.24), residues: 1187 helix: 0.89 (0.25), residues: 396 sheet: -0.49 (0.30), residues: 293 loop : -0.24 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.013 0.002 TYR F 191 PHE 0.014 0.001 PHE A 207 TRP 0.010 0.001 TRP D 169 HIS 0.007 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 9572) covalent geometry : angle 0.57497 / 0.31 (12965) SS BOND : bond 0.00528 / 0.29 ( 6) SS BOND : angle 4.18485 / 2.34 ( 12) hydrogen bonds : bond 0.04835 / 3.23 ( 476) hydrogen bonds : angle 5.56187 / 4.02 ( 1365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.459 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 104 LEU cc_start: 0.7763 (tt) cc_final: 0.7536 (mp) REVERT: A 206 ASN cc_start: 0.8397 (m-40) cc_final: 0.8167 (m-40) REVERT: A 255 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7186 (mtt90) REVERT: A 278 ASP cc_start: 0.7810 (t0) cc_final: 0.7299 (t0) REVERT: A 281 MET cc_start: 0.8643 (mpp) cc_final: 0.8247 (mpp) REVERT: C 256 ASN cc_start: 0.8667 (t0) cc_final: 0.7992 (t0) REVERT: D 258 ASP cc_start: 0.8328 (t0) cc_final: 0.7840 (t0) REVERT: D 259 GLN cc_start: 0.7582 (tp40) cc_final: 0.7097 (tm-30) REVERT: E 21 MET cc_start: 0.9183 (mmp) cc_final: 0.8777 (mmm) REVERT: E 27 ARG cc_start: 0.8599 (mtt90) cc_final: 0.8313 (mtt-85) REVERT: F 187 GLN cc_start: 0.8543 (mt0) cc_final: 0.8332 (mt0) outliers start: 11 outliers final: 9 residues processed: 195 average time/residue: 0.2636 time to fit residues: 68.5077 Evaluate side-chains 191 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 231 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 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 = 0.3988 r_free = 0.3988 target = 0.161706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120003 restraints weight = 39398.382| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.96 r_work: 0.3295 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9578 Z= 0.202 Angle : 0.567 6.560 12977 Z= 0.308 Chirality : 0.041 0.147 1482 Planarity : 0.004 0.064 1646 Dihedral : 5.006 23.107 1307 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.88 % Allowed : 12.43 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.04 (0.25), residues: 1187 helix: 0.92 (0.25), residues: 396 sheet: -0.63 (0.30), residues: 293 loop : -0.26 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 62 TYR 0.013 0.001 TYR F 228 PHE 0.014 0.001 PHE A 207 TRP 0.010 0.001 TRP D 169 HIS 0.007 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 9572) covalent geometry : angle 0.56344 / 0.31 (12965) SS BOND : bond 0.00523 / 0.27 ( 6) SS BOND : angle 2.11621 / 1.27 ( 12) hydrogen bonds : bond 0.04677 / 3.16 ( 476) hydrogen bonds : angle 5.44720 / 3.95 ( 1365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.529 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 104 LEU cc_start: 0.7706 (tt) cc_final: 0.7505 (mp) REVERT: A 255 ARG cc_start: 0.7739 (mtt90) cc_final: 0.7215 (mtt90) REVERT: A 267 CYS cc_start: 0.7073 (m) cc_final: 0.6841 (m) REVERT: A 281 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8320 (mpp) REVERT: C 256 ASN cc_start: 0.8723 (t0) cc_final: 0.8036 (t0) REVERT: D 217 MET cc_start: 0.7256 (pmm) cc_final: 0.7033 (pmm) REVERT: D 258 ASP cc_start: 0.8359 (t0) cc_final: 0.7933 (t0) REVERT: D 259 GLN cc_start: 0.7614 (tp40) cc_final: 0.7187 (tm-30) REVERT: E 21 MET cc_start: 0.9174 (mmp) cc_final: 0.8751 (mmm) REVERT: E 27 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8367 (mtt-85) outliers start: 9 outliers final: 8 residues processed: 201 average time/residue: 0.2827 time to fit residues: 74.9813 Evaluate side-chains 198 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 231 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119387 restraints weight = 39270.478| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.94 r_work: 0.3286 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9578 Z= 0.213 Angle : 0.567 5.260 12977 Z= 0.307 Chirality : 0.041 0.147 1482 Planarity : 0.005 0.069 1646 Dihedral : 4.962 23.101 1307 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.47 % Allowed : 12.62 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.03 (0.25), residues: 1187 helix: 1.04 (0.25), residues: 397 sheet: -0.71 (0.30), residues: 293 loop : -0.30 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 292 TYR 0.020 0.002 TYR C 302 PHE 0.013 0.001 PHE A 207 TRP 0.010 0.001 TRP D 169 HIS 0.007 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 ( 9572) covalent geometry : angle 0.56548 / 0.31 (12965) SS BOND : bond 0.00301 / 0.18 ( 6) SS BOND : angle 1.44549 / 0.92 ( 12) hydrogen bonds : bond 0.04484 / 3.01 ( 476) hydrogen bonds : angle 5.36991 / 3.90 ( 1365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.483 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: symmetry clash REVERT: A 255 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7178 (mtt90) REVERT: A 267 CYS cc_start: 0.7076 (m) cc_final: 0.6836 (m) REVERT: A 273 LEU cc_start: 0.8036 (tp) cc_final: 0.7752 (tp) REVERT: A 281 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8407 (mpp) REVERT: C 302 TYR cc_start: 0.8418 (t80) cc_final: 0.8165 (t80) REVERT: D 258 ASP cc_start: 0.8409 (t0) cc_final: 0.7942 (t0) REVERT: D 259 GLN cc_start: 0.7630 (tp40) cc_final: 0.7209 (tm-30) REVERT: E 21 MET cc_start: 0.9195 (mmp) cc_final: 0.8765 (mmm) REVERT: E 27 ARG cc_start: 0.8563 (mtt90) cc_final: 0.8344 (mtt-85) outliers start: 15 outliers final: 10 residues processed: 204 average time/residue: 0.2745 time to fit residues: 74.0771 Evaluate side-chains 205 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 231 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 110 optimal weight: 0.9980 chunk 49 optimal weight: 0.0170 chunk 17 optimal weight: 0.9980 chunk 109 optimal weight: 0.2980 chunk 99 optimal weight: 0.1980 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.164074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123773 restraints weight = 39190.032| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.89 r_work: 0.3348 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9578 Z= 0.111 Angle : 0.526 6.224 12977 Z= 0.280 Chirality : 0.040 0.149 1482 Planarity : 0.004 0.054 1646 Dihedral : 4.670 22.509 1307 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.68 % Allowed : 13.99 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.24 (0.25), residues: 1187 helix: 1.36 (0.26), residues: 398 sheet: -0.58 (0.30), residues: 293 loop : -0.23 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 292 TYR 0.018 0.001 TYR C 302 PHE 0.015 0.001 PHE A 207 TRP 0.010 0.001 TRP D 169 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9572) covalent geometry : angle 0.52540 / 0.28 (12965) SS BOND : bond 0.00317 / 0.18 ( 6) SS BOND : angle 0.85020 / 0.54 ( 12) hydrogen bonds : bond 0.03940 / 2.66 ( 476) hydrogen bonds : angle 5.01695 / 3.63 ( 1365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 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: symmetry clash revert: symmetry clash REVERT: A 267 CYS cc_start: 0.6984 (m) cc_final: 0.6755 (m) REVERT: A 281 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8346 (mpp) REVERT: B 14 ILE cc_start: 0.8476 (mt) cc_final: 0.8257 (mm) REVERT: D 217 MET cc_start: 0.7170 (pmm) cc_final: 0.6914 (pmm) REVERT: D 258 ASP cc_start: 0.8342 (t0) cc_final: 0.7804 (t0) REVERT: D 259 GLN cc_start: 0.7593 (tp40) cc_final: 0.7222 (tm-30) REVERT: D 303 ASP cc_start: 0.7880 (m-30) cc_final: 0.7631 (m-30) REVERT: E 21 MET cc_start: 0.9159 (mmp) cc_final: 0.8736 (mmm) REVERT: E 27 ARG cc_start: 0.8431 (mtt90) cc_final: 0.8205 (mtt-85) outliers start: 7 outliers final: 5 residues processed: 205 average time/residue: 0.2758 time to fit residues: 74.5728 Evaluate side-chains 200 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 231 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 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 = 0.4014 r_free = 0.4014 target = 0.163601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122316 restraints weight = 39319.917| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.94 r_work: 0.3327 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9578 Z= 0.148 Angle : 0.528 5.952 12977 Z= 0.282 Chirality : 0.040 0.144 1482 Planarity : 0.004 0.060 1646 Dihedral : 4.622 22.149 1307 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.98 % Allowed : 14.38 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.29 (0.25), residues: 1187 helix: 1.48 (0.26), residues: 398 sheet: -0.61 (0.30), residues: 292 loop : -0.22 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 292 TYR 0.018 0.001 TYR C 302 PHE 0.013 0.001 PHE A 47 TRP 0.009 0.001 TRP D 169 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 9572) covalent geometry : angle 0.52768 / 0.28 (12965) SS BOND : bond 0.00270 / 0.16 ( 6) SS BOND : angle 1.09304 / 0.72 ( 12) hydrogen bonds : bond 0.03982 / 2.69 ( 476) hydrogen bonds : angle 5.01029 / 3.63 ( 1365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.530 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 255 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7086 (mtt90) REVERT: A 267 CYS cc_start: 0.7031 (m) cc_final: 0.6811 (m) REVERT: A 281 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8377 (mpp) REVERT: B 14 ILE cc_start: 0.8488 (mt) cc_final: 0.8264 (mm) REVERT: D 258 ASP cc_start: 0.8310 (t0) cc_final: 0.7813 (t0) REVERT: D 259 GLN cc_start: 0.7596 (tp40) cc_final: 0.7242 (tm-30) REVERT: D 262 MET cc_start: 0.7525 (tpp) cc_final: 0.6925 (tpp) REVERT: D 303 ASP cc_start: 0.7942 (m-30) cc_final: 0.7699 (m-30) REVERT: E 21 MET cc_start: 0.9177 (mmp) cc_final: 0.8745 (mmm) REVERT: E 27 ARG cc_start: 0.8464 (mtt90) cc_final: 0.8246 (mtt-85) REVERT: E 46 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8372 (tppt) outliers start: 10 outliers final: 7 residues processed: 197 average time/residue: 0.2860 time to fit residues: 74.3263 Evaluate side-chains 200 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 231 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121629 restraints weight = 39313.854| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.95 r_work: 0.3319 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9578 Z= 0.162 Angle : 0.538 6.841 12977 Z= 0.288 Chirality : 0.040 0.148 1482 Planarity : 0.004 0.063 1646 Dihedral : 4.627 22.000 1307 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.88 % Allowed : 14.77 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.30 (0.25), residues: 1187 helix: 1.55 (0.26), residues: 395 sheet: -0.65 (0.30), residues: 293 loop : -0.24 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 292 TYR 0.012 0.001 TYR C 302 PHE 0.013 0.001 PHE A 207 TRP 0.010 0.001 TRP D 169 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9572) covalent geometry : angle 0.53717 / 0.29 (12965) SS BOND : bond 0.00222 / 0.14 ( 6) SS BOND : angle 1.23047 / 0.80 ( 12) hydrogen bonds : bond 0.03987 / 2.70 ( 476) hydrogen bonds : angle 4.99598 / 3.63 ( 1365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.538 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 267 CYS cc_start: 0.7099 (m) cc_final: 0.6849 (m) REVERT: A 273 LEU cc_start: 0.8055 (tp) cc_final: 0.7801 (tp) REVERT: A 281 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8314 (mpp) REVERT: B 14 ILE cc_start: 0.8505 (mt) cc_final: 0.8275 (mm) REVERT: B 45 MET cc_start: 0.7720 (mmm) cc_final: 0.6950 (mmm) REVERT: D 217 MET cc_start: 0.7076 (pmm) cc_final: 0.6819 (pmm) REVERT: D 258 ASP cc_start: 0.8311 (t0) cc_final: 0.7802 (t0) REVERT: D 259 GLN cc_start: 0.7588 (tp40) cc_final: 0.7256 (tm-30) REVERT: D 262 MET cc_start: 0.7557 (tpp) cc_final: 0.6958 (tpp) REVERT: D 303 ASP cc_start: 0.7954 (m-30) cc_final: 0.7717 (m-30) REVERT: E 21 MET cc_start: 0.9173 (mmp) cc_final: 0.8739 (mmm) REVERT: E 27 ARG cc_start: 0.8458 (mtt90) cc_final: 0.8253 (mtt-85) REVERT: E 46 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8396 (tppt) REVERT: F 21 ARG cc_start: 0.8389 (tpp80) cc_final: 0.8158 (tpp80) outliers start: 9 outliers final: 5 residues processed: 197 average time/residue: 0.2848 time to fit residues: 73.7961 Evaluate side-chains 196 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain F residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 111 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 101 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 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 = 0.4023 r_free = 0.4023 target = 0.164332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123330 restraints weight = 39266.931| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.94 r_work: 0.3340 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9578 Z= 0.121 Angle : 0.527 5.751 12977 Z= 0.279 Chirality : 0.040 0.144 1482 Planarity : 0.004 0.057 1646 Dihedral : 4.533 21.905 1307 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.68 % Allowed : 15.17 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.38 (0.25), residues: 1187 helix: 1.64 (0.26), residues: 398 sheet: -0.62 (0.30), residues: 294 loop : -0.21 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 292 TYR 0.013 0.001 TYR F 191 PHE 0.013 0.001 PHE A 207 TRP 0.009 0.001 TRP D 169 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9572) covalent geometry : angle 0.52577 / 0.28 (12965) SS BOND : bond 0.00261 / 0.16 ( 6) SS BOND : angle 1.07684 / 0.68 ( 12) hydrogen bonds : bond 0.03798 / 2.57 ( 476) hydrogen bonds : angle 4.87427 / 3.53 ( 1365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 0.471 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 267 CYS cc_start: 0.7016 (m) cc_final: 0.6792 (m) REVERT: A 273 LEU cc_start: 0.8061 (tp) cc_final: 0.7806 (tp) REVERT: A 281 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8319 (mpp) REVERT: B 14 ILE cc_start: 0.8485 (mt) cc_final: 0.8262 (mm) REVERT: D 217 MET cc_start: 0.7257 (pmm) cc_final: 0.6960 (pmm) REVERT: D 258 ASP cc_start: 0.8293 (t0) cc_final: 0.7788 (t0) REVERT: D 259 GLN cc_start: 0.7543 (tp40) cc_final: 0.7243 (tm-30) REVERT: D 262 MET cc_start: 0.7536 (tpp) cc_final: 0.6945 (tpp) REVERT: D 303 ASP cc_start: 0.7927 (m-30) cc_final: 0.7691 (m-30) REVERT: E 21 MET cc_start: 0.9174 (mmp) cc_final: 0.8732 (mmm) REVERT: E 27 ARG cc_start: 0.8442 (mtt90) cc_final: 0.8242 (mtt-85) REVERT: E 46 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8405 (tppt) REVERT: F 79 LYS cc_start: 0.8247 (ptpp) cc_final: 0.8031 (ptmm) outliers start: 7 outliers final: 6 residues processed: 195 average time/residue: 0.2681 time to fit residues: 68.8422 Evaluate side-chains 198 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 11 optimal weight: 0.0770 chunk 109 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 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 = 0.4024 r_free = 0.4024 target = 0.164353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123327 restraints weight = 39397.886| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.92 r_work: 0.3343 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9578 Z= 0.128 Angle : 0.526 8.187 12977 Z= 0.279 Chirality : 0.040 0.143 1482 Planarity : 0.004 0.052 1646 Dihedral : 4.480 21.579 1307 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.88 % Allowed : 15.07 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.43 (0.25), residues: 1187 helix: 1.73 (0.26), residues: 398 sheet: -0.64 (0.30), residues: 294 loop : -0.20 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 292 TYR 0.012 0.001 TYR F 191 PHE 0.013 0.001 PHE A 207 TRP 0.009 0.001 TRP D 169 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9572) covalent geometry : angle 0.52488 / 0.28 (12965) SS BOND : bond 0.00234 / 0.14 ( 6) SS BOND : angle 0.99503 / 0.65 ( 12) hydrogen bonds : bond 0.03766 / 2.56 ( 476) hydrogen bonds : angle 4.82767 / 3.50 ( 1365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5017.74 seconds wall clock time: 85 minutes 51.83 seconds (5151.83 seconds total)