Starting phenix.real_space_refine on Sat Aug 8 18:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q2c_72156/08_2026/9q2c_72156_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q2c_72156/08_2026/9q2c_72156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q2c_72156/08_2026/9q2c_72156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q2c_72156/08_2026/9q2c_72156.map" model { file = "/net/cci-nas-00/data/ceres_data/9q2c_72156/08_2026/9q2c_72156_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q2c_72156/08_2026/9q2c_72156_trim.cif" } resolution = 3.06 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= 0.011 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 14 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 9119 2.51 5 N 2397 2.21 5 O 2715 1.98 5 H 14309 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28625 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4901 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 308} Chain: "A" Number of atoms: 4423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4423 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 6, 'TRANS': 265} Chain breaks: 3 Chain: "B" Number of atoms: 6217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 6217 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "E" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2387 Classifications: {'peptide': 147} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 137} Chain breaks: 1 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3368 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 3 Chain: "D" Number of atoms: 3839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3839 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3140 Classifications: {'peptide': 188} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Classifications: {'DNA': 9} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 8} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19504 SG CYS F 114 26.816 36.143 190.261 1.00289.67 S ATOM 19526 SG CYS F 116 24.429 37.695 192.729 1.00291.69 S ATOM 20512 SG CYS F 176 26.919 35.054 193.751 1.00296.59 S Time building chain proxies: 5.02, per 1000 atoms: 0.18 Number of scatterers: 28625 At special positions: 0 Unit cell: (99.6875, 97.875, 219.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 68 16.00 P 14 15.00 Mg 2 11.99 O 2715 8.00 N 2397 7.00 C 9119 6.00 H 14309 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 146 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 933.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 178 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 176 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 114 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 116 " Number of angles added : 3 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 14 sheets defined 50.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 92 through 102 removed outlier: 3.503A pdb=" N VAL G 96 " --> pdb=" O THR G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 114 through 121 Processing helix chain 'G' and resid 125 through 140 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 164 through 172 Processing helix chain 'G' and resid 190 through 202 Processing helix chain 'G' and resid 203 through 204 No H-bonds generated for 'chain 'G' and resid 203 through 204' Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 225 through 237 removed outlier: 3.739A pdb=" N LEU G 229 " --> pdb=" O ARG G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 246 Processing helix chain 'G' and resid 254 through 272 Processing helix chain 'G' and resid 281 through 290 removed outlier: 4.511A pdb=" N LEU G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR G 286 " --> pdb=" O VAL G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 318 Processing helix chain 'G' and resid 346 through 354 removed outlier: 3.604A pdb=" N MET G 350 " --> pdb=" O GLY G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 400 Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.528A pdb=" N VAL A 12 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 48 through 67 Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 123 Processing helix chain 'A' and resid 136 through 153 removed outlier: 3.522A pdb=" N LEU A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS A 150 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.609A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 24 through 30 removed outlier: 6.151A pdb=" N GLU B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU B 30 " --> pdb=" O TYR B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 52 through 61 Processing helix chain 'B' and resid 63 through 88 removed outlier: 3.897A pdb=" N LYS B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.834A pdb=" N ILE B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 removed outlier: 4.324A pdb=" N LEU B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 265 Processing helix chain 'B' and resid 292 through 302 removed outlier: 4.613A pdb=" N GLY B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TRP B 299 " --> pdb=" O TYR B 295 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 318 Processing helix chain 'B' and resid 322 through 328 removed outlier: 4.316A pdb=" N GLU B 325 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.692A pdb=" N MET B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 removed outlier: 3.601A pdb=" N TRP B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 30 through 38 removed outlier: 3.527A pdb=" N GLU E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 82 Processing helix chain 'E' and resid 95 through 100 removed outlier: 4.007A pdb=" N LEU E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 121 Processing helix chain 'E' and resid 136 through 149 Processing helix chain 'F' and resid 7 through 15 removed outlier: 3.745A pdb=" N LEU F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 36 removed outlier: 3.709A pdb=" N ALA F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N MET F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 49 Processing helix chain 'F' and resid 71 through 80 removed outlier: 4.126A pdb=" N ASP F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE F 80 " --> pdb=" O LEU F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 129 Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.663A pdb=" N VAL F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 187 Processing helix chain 'F' and resid 189 through 198 removed outlier: 3.697A pdb=" N LEU F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 217 removed outlier: 4.268A pdb=" N LEU F 217 " --> pdb=" O GLU F 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 15 No H-bonds generated for 'chain 'D' and resid 13 through 15' Processing helix chain 'D' and resid 35 through 41 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 113 through 121 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 156 through 172 removed outlier: 3.559A pdb=" N LEU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 7.186A pdb=" N ILE D 188 " --> pdb=" O TYR D 185 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU D 189 " --> pdb=" O ASN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 218 removed outlier: 3.993A pdb=" N GLY D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 76 through 96 removed outlier: 3.659A pdb=" N ILE C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.519A pdb=" N MET C 122 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 152 Processing helix chain 'C' and resid 166 through 169 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 198 through 207 Processing sheet with id=AA1, first strand: chain 'G' and resid 145 through 146 removed outlier: 7.188A pdb=" N LYS B 154 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE B 223 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 156 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 267 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 271 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 145 through 146 removed outlier: 7.188A pdb=" N LYS B 154 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE B 223 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 156 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 267 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 271 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 125 " --> pdb=" O ASN B 272 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 274 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 120 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N SER B 397 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER B 440 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG B 399 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL B 431 " --> pdb=" O ILE B 452 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE B 452 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 433 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 446 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 159 through 160 Processing sheet with id=AA4, first strand: chain 'G' and resid 247 through 251 removed outlier: 6.721A pdb=" N CYS G 215 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA G 250 " --> pdb=" O CYS G 215 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR G 217 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS G 214 " --> pdb=" O SER G 275 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE G 277 " --> pdb=" O LYS G 214 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU G 216 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL G 279 " --> pdb=" O LEU G 216 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE G 218 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER G 275 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL G 322 " --> pdb=" O SER G 275 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE G 277 " --> pdb=" O VAL G 322 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR G 324 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL G 279 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLN G 326 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS G 343 " --> pdb=" O VAL G 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 247 through 251 removed outlier: 6.721A pdb=" N CYS G 215 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ALA G 250 " --> pdb=" O CYS G 215 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR G 217 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS G 214 " --> pdb=" O SER G 275 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE G 277 " --> pdb=" O LYS G 214 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU G 216 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL G 279 " --> pdb=" O LEU G 216 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE G 218 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER G 275 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL G 322 " --> pdb=" O SER G 275 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE G 277 " --> pdb=" O VAL G 322 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR G 324 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL G 279 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLN G 326 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL G 327 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE G 180 " --> pdb=" O THR G 356 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU G 358 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU G 182 " --> pdb=" O LEU G 358 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE G 360 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE G 184 " --> pdb=" O PHE G 360 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LYS G 362 " --> pdb=" O PHE G 184 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG G 357 " --> pdb=" O VAL G 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 106 removed outlier: 6.097A pdb=" N ILE A 74 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 105 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TRP A 76 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG A 258 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU A 305 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 102 through 106 removed outlier: 6.097A pdb=" N ILE A 74 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 105 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TRP A 76 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG A 258 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N ASN A 306 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE A 344 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 192 through 195 Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AB1, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.565A pdb=" N VAL E 91 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR E 129 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL E 93 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 25 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR E 94 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE E 27 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL E 24 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL E 64 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL E 26 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR D 10 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 113 through 114 removed outlier: 3.835A pdb=" N ILE F 105 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET F 53 " --> pdb=" O PHE F 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 57 through 58 removed outlier: 5.751A pdb=" N ILE F 57 " --> pdb=" O ILE F 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 90 through 92 removed outlier: 5.840A pdb=" N ILE D 70 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET D 92 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 72 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS D 69 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY D 132 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG D 131 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE D 176 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D 133 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS D 178 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE D 135 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 71 through 73 removed outlier: 7.290A pdb=" N ASN C 72 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE C 39 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN C 36 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TYR C 115 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE C 38 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C 117 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 40 " --> pdb=" O ASN C 117 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 158 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C 10 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE C 165 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP C 12 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER C 210 " --> pdb=" O ILE C 9 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1902 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: 7.10 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14279 1.03 - 1.24: 1259 1.24 - 1.44: 4911 1.44 - 1.64: 8341 1.64 - 1.84: 110 Bond restraints: 28900 Sorted by residual: bond pdb=" C1' DT H 6 " pdb=" N1 DT H 6 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.03e+00 bond pdb=" C1' DT H 2 " pdb=" N1 DT H 2 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.92e+00 bond pdb=" C3' DT H 6 " pdb=" C2' DT H 6 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.50e+00 bond pdb=" C1' DT H 7 " pdb=" N1 DT H 7 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.68e+00 bond pdb=" C1' DT H 4 " pdb=" N1 DT H 4 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.58e+00 ... (remaining 28895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.42: 52268 5.42 - 10.84: 10 10.84 - 16.26: 1 16.26 - 21.68: 0 21.68 - 27.10: 3 Bond angle restraints: 52282 Sorted by residual: angle pdb=" CG2 THR A 159 " pdb=" CB THR A 159 " pdb=" HB THR A 159 " ideal model delta sigma weight residual 108.00 80.90 27.10 3.00e+00 1.11e-01 8.16e+01 angle pdb=" OG1 THR A 159 " pdb=" CB THR A 159 " pdb=" HB THR A 159 " ideal model delta sigma weight residual 109.00 82.58 26.42 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CA THR A 159 " pdb=" CB THR A 159 " pdb=" HB THR A 159 " ideal model delta sigma weight residual 109.00 83.37 25.63 3.00e+00 1.11e-01 7.30e+01 angle pdb=" OG1 THR A 159 " pdb=" CB THR A 159 " pdb=" CG2 THR A 159 " ideal model delta sigma weight residual 109.30 120.43 -11.13 2.00e+00 2.50e-01 3.10e+01 angle pdb=" CA THR A 159 " pdb=" CB THR A 159 " pdb=" CG2 THR A 159 " ideal model delta sigma weight residual 110.50 118.59 -8.09 1.70e+00 3.46e-01 2.26e+01 ... (remaining 52277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 12936 34.19 - 68.38: 501 68.38 - 102.56: 31 102.56 - 136.75: 1 136.75 - 170.94: 1 Dihedral angle restraints: 13470 sinusoidal: 7460 harmonic: 6010 Sorted by residual: dihedral pdb=" CA VAL G 331 " pdb=" C VAL G 331 " pdb=" N ASP G 332 " pdb=" CA ASP G 332 " ideal model delta harmonic sigma weight residual -180.00 -126.04 -53.96 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA ASP B 225 " pdb=" C ASP B 225 " pdb=" N SER B 226 " pdb=" CA SER B 226 " ideal model delta harmonic sigma weight residual 180.00 137.30 42.70 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 146 " pdb=" CB CYS A 146 " ideal model delta sinusoidal sigma weight residual 93.00 50.15 42.85 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 13467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 2255 0.274 - 0.548: 0 0.548 - 0.822: 0 0.822 - 1.097: 0 1.097 - 1.371: 1 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CB THR A 159 " pdb=" CA THR A 159 " pdb=" OG1 THR A 159 " pdb=" CG2 THR A 159 " both_signs ideal model delta sigma weight residual False 2.55 1.18 1.37 2.00e-01 2.50e+01 4.70e+01 chirality pdb=" C3' DT H 3 " pdb=" C4' DT H 3 " pdb=" O3' DT H 3 " pdb=" C2' DT H 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" C3' DT H 6 " pdb=" C4' DT H 6 " pdb=" O3' DT H 6 " pdb=" C2' DT H 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 2253 not shown) Planarity restraints: 4152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 164 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 165 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 231 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO D 232 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 232 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 232 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 105 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO E 106 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 106 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 106 " 0.022 5.00e-02 4.00e+02 ... (remaining 4149 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 167 2.03 - 2.67: 44384 2.67 - 3.31: 87262 3.31 - 3.96: 112161 3.96 - 4.60: 174431 Nonbonded interactions: 418405 Sorted by model distance: nonbonded pdb=" HD2 HIS F 178 " pdb="ZN ZN F 301 " model vdw 1.387 1.408 nonbonded pdb=" HB THR A 159 " pdb="HG23 THR A 159 " model vdw 1.748 1.952 nonbonded pdb=" HD2 TYR F 122 " pdb=" H CYS F 175 " model vdw 1.756 2.100 nonbonded pdb="HE22 GLN G 330 " pdb="HD22 ASN G 338 " model vdw 1.763 2.100 nonbonded pdb=" HE ARG D 119 " pdb=" HZ PHE D 126 " model vdw 1.776 2.100 ... (remaining 418400 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 35.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 0.003 0.208 14597 Z= 0.160 Angle : 0.581 11.134 19766 Z= 0.339 Chirality : 0.050 1.371 2256 Planarity : 0.004 0.050 2477 Dihedral : 14.060 170.939 5486 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.13 % Favored : 94.58 % Rotamer: Outliers : 1.90 % Allowed : 11.46 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.32 (0.21), residues: 1715 helix: 1.49 (0.19), residues: 742 sheet: -0.60 (0.32), residues: 272 loop : -0.80 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 188 TYR 0.009 0.001 TYR C 202 PHE 0.023 0.001 PHE E 144 TRP 0.008 0.001 TRP D 174 HIS 0.006 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (14591) covalent geometry : angle 0.57377 / 0.34 (19761) SS BOND : bond 0.01630 / 0.86 ( 1) SS BOND : angle 4.24170 / 2.29 ( 2) hydrogen bonds : bond 0.13403 / 9.38 ( 644) hydrogen bonds : angle 6.38847 / 4.59 ( 1902) metal coordination : bond 0.10626 / 5.31 ( 4) metal coordination : angle 6.70182 / 4.48 ( 3) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.841 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 131 LYS cc_start: 0.7892 (mttt) cc_final: 0.7594 (mmmm) REVERT: G 245 ASN cc_start: 0.8920 (m-40) cc_final: 0.8629 (m110) REVERT: G 281 SER cc_start: 0.8429 (m) cc_final: 0.8093 (m) REVERT: A 1 MET cc_start: 0.2794 (OUTLIER) cc_final: 0.2587 (ptt) REVERT: A 5 ILE cc_start: 0.8924 (mp) cc_final: 0.8351 (tp) REVERT: A 155 MET cc_start: 0.8526 (ptp) cc_final: 0.8292 (ptt) REVERT: A 198 GLN cc_start: 0.8442 (tt0) cc_final: 0.8239 (mm-40) REVERT: A 200 ASN cc_start: 0.5804 (p0) cc_final: 0.5049 (t0) REVERT: B 289 TYR cc_start: 0.6930 (t80) cc_final: 0.6692 (t80) REVERT: B 292 ASP cc_start: 0.8619 (m-30) cc_final: 0.8115 (m-30) REVERT: E 2 GLN cc_start: 0.7401 (tp40) cc_final: 0.6528 (mt0) REVERT: E 14 ASP cc_start: 0.8386 (m-30) cc_final: 0.7615 (t0) REVERT: E 48 THR cc_start: 0.8237 (p) cc_final: 0.8002 (t) REVERT: E 119 CYS cc_start: 0.7794 (m) cc_final: 0.7554 (m) REVERT: F 204 PHE cc_start: 0.7072 (m-10) cc_final: 0.6798 (m-80) REVERT: D 17 THR cc_start: 0.7186 (p) cc_final: 0.6929 (p) REVERT: D 148 ASN cc_start: 0.8610 (m110) cc_final: 0.8279 (m-40) REVERT: C 93 MET cc_start: 0.7398 (ttp) cc_final: 0.6480 (mmp) outliers start: 30 outliers final: 19 residues processed: 205 average time/residue: 0.3067 time to fit residues: 91.1778 Evaluate side-chains 150 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 178 HIS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 168 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 325 ASN ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN E 87 GLN ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN C 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.133021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088428 restraints weight = 78930.914| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.94 r_work: 0.3231 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 14597 Z= 0.193 Angle : 0.594 11.231 19766 Z= 0.313 Chirality : 0.052 1.395 2256 Planarity : 0.004 0.065 2477 Dihedral : 10.176 174.040 2055 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.06 % Favored : 93.70 % Rotamer: Outliers : 1.90 % Allowed : 12.98 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.25 (0.21), residues: 1715 helix: 1.38 (0.19), residues: 755 sheet: -0.76 (0.31), residues: 288 loop : -0.72 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 117 TYR 0.011 0.001 TYR E 75 PHE 0.024 0.001 PHE E 144 TRP 0.009 0.001 TRP D 174 HIS 0.006 0.001 HIS E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (14591) covalent geometry : angle 0.58584 / 0.31 (19761) SS BOND : bond 0.02248 / 1.18 ( 1) SS BOND : angle 2.89775 / 1.69 ( 2) hydrogen bonds : bond 0.04185 / 2.90 ( 644) hydrogen bonds : angle 5.27724 / 3.81 ( 1902) metal coordination : bond 0.08977 / 4.49 ( 4) metal coordination : angle 7.62568 / 4.47 ( 3) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.739 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 131 LYS cc_start: 0.8029 (mttt) cc_final: 0.7700 (mmmt) REVERT: G 245 ASN cc_start: 0.8960 (m-40) cc_final: 0.8683 (m110) REVERT: G 281 SER cc_start: 0.8502 (m) cc_final: 0.8041 (p) REVERT: A 5 ILE cc_start: 0.9074 (mp) cc_final: 0.8698 (mm) REVERT: A 9 GLN cc_start: 0.8129 (tt0) cc_final: 0.7835 (tm-30) REVERT: B 431 VAL cc_start: 0.8420 (t) cc_final: 0.8147 (p) REVERT: E 14 ASP cc_start: 0.8493 (m-30) cc_final: 0.7677 (t0) REVERT: E 119 CYS cc_start: 0.7698 (m) cc_final: 0.7494 (m) REVERT: D 6 ASN cc_start: 0.8748 (m-40) cc_final: 0.8288 (p0) REVERT: C 89 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7503 (tp40) REVERT: C 93 MET cc_start: 0.7723 (ttp) cc_final: 0.6747 (mmp) outliers start: 30 outliers final: 19 residues processed: 156 average time/residue: 0.2589 time to fit residues: 60.3590 Evaluate side-chains 145 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 168 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 158 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 163 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 HIS ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.132030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087370 restraints weight = 79221.395| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.93 r_work: 0.3215 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14597 Z= 0.168 Angle : 0.569 11.137 19766 Z= 0.300 Chirality : 0.051 1.392 2256 Planarity : 0.004 0.066 2477 Dihedral : 10.060 174.685 2049 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.76 % Rotamer: Outliers : 1.96 % Allowed : 14.12 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.21 (0.21), residues: 1715 helix: 1.38 (0.19), residues: 757 sheet: -0.88 (0.31), residues: 288 loop : -0.75 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 188 TYR 0.018 0.001 TYR E 88 PHE 0.020 0.001 PHE E 144 TRP 0.009 0.001 TRP D 174 HIS 0.028 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (14591) covalent geometry : angle 0.55902 / 0.30 (19761) SS BOND : bond 0.02190 / 1.15 ( 1) SS BOND : angle 5.75852 / 3.28 ( 2) hydrogen bonds : bond 0.03825 / 2.65 ( 644) hydrogen bonds : angle 5.03890 / 3.64 ( 1902) metal coordination : bond 0.03256 / 1.65 ( 4) metal coordination : angle 7.04519 / 6.20 ( 3) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.586 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 131 LYS cc_start: 0.8027 (mttt) cc_final: 0.7695 (mmmt) REVERT: G 245 ASN cc_start: 0.8959 (m-40) cc_final: 0.8686 (m110) REVERT: G 281 SER cc_start: 0.8367 (m) cc_final: 0.7718 (p) REVERT: A 5 ILE cc_start: 0.9083 (mp) cc_final: 0.8707 (mm) REVERT: A 9 GLN cc_start: 0.8198 (tt0) cc_final: 0.7870 (tm-30) REVERT: A 155 MET cc_start: 0.8625 (ptp) cc_final: 0.8284 (ptt) REVERT: B 431 VAL cc_start: 0.8476 (t) cc_final: 0.8195 (p) REVERT: E 14 ASP cc_start: 0.8553 (m-30) cc_final: 0.7742 (t0) REVERT: E 119 CYS cc_start: 0.7712 (m) cc_final: 0.7493 (m) REVERT: D 6 ASN cc_start: 0.8766 (m-40) cc_final: 0.8351 (p0) REVERT: C 93 MET cc_start: 0.7715 (ttp) cc_final: 0.7051 (tpp) outliers start: 31 outliers final: 22 residues processed: 153 average time/residue: 0.2590 time to fit residues: 59.5014 Evaluate side-chains 141 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.132350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.087824 restraints weight = 78438.005| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.91 r_work: 0.3224 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 14597 Z= 0.133 Angle : 0.547 11.202 19766 Z= 0.287 Chirality : 0.051 1.384 2256 Planarity : 0.004 0.066 2477 Dihedral : 9.842 176.780 2040 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 1.52 % Allowed : 14.82 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.21), residues: 1715 helix: 1.38 (0.19), residues: 766 sheet: -0.89 (0.31), residues: 278 loop : -0.73 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 188 TYR 0.013 0.001 TYR F 91 PHE 0.020 0.001 PHE E 144 TRP 0.008 0.001 TRP D 174 HIS 0.017 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (14591) covalent geometry : angle 0.53945 / 0.29 (19761) SS BOND : bond 0.03183 / 1.68 ( 1) SS BOND : angle 3.44805 / 2.02 ( 2) hydrogen bonds : bond 0.03420 / 2.37 ( 644) hydrogen bonds : angle 4.84351 / 3.51 ( 1902) metal coordination : bond 0.06981 / 3.49 ( 4) metal coordination : angle 6.86049 / 3.74 ( 3) Misc. bond : bond 0.00104 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.875 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 131 LYS cc_start: 0.8019 (mttt) cc_final: 0.7636 (mmmt) REVERT: G 245 ASN cc_start: 0.8966 (m-40) cc_final: 0.8665 (m110) REVERT: G 281 SER cc_start: 0.8382 (m) cc_final: 0.7908 (p) REVERT: A 5 ILE cc_start: 0.9088 (mp) cc_final: 0.8716 (mm) REVERT: A 9 GLN cc_start: 0.8189 (tt0) cc_final: 0.7872 (tm-30) REVERT: A 155 MET cc_start: 0.8639 (ptp) cc_final: 0.8333 (ptt) REVERT: B 431 VAL cc_start: 0.8486 (t) cc_final: 0.8203 (p) REVERT: E 14 ASP cc_start: 0.8582 (m-30) cc_final: 0.7733 (t0) REVERT: E 119 CYS cc_start: 0.7721 (m) cc_final: 0.7502 (m) REVERT: D 6 ASN cc_start: 0.8768 (m-40) cc_final: 0.8364 (p0) REVERT: D 83 LYS cc_start: 0.9250 (mmmm) cc_final: 0.9017 (mttt) REVERT: C 93 MET cc_start: 0.7749 (ttp) cc_final: 0.7068 (tpp) outliers start: 24 outliers final: 21 residues processed: 145 average time/residue: 0.2814 time to fit residues: 61.8659 Evaluate side-chains 139 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.131302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086817 restraints weight = 78849.164| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.91 r_work: 0.3204 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 14597 Z= 0.158 Angle : 0.549 11.184 19766 Z= 0.288 Chirality : 0.050 1.389 2256 Planarity : 0.004 0.066 2477 Dihedral : 9.715 176.740 2037 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 1.77 % Allowed : 14.76 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.20 (0.21), residues: 1715 helix: 1.38 (0.19), residues: 764 sheet: -0.97 (0.31), residues: 272 loop : -0.76 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 188 TYR 0.010 0.001 TYR B 439 PHE 0.019 0.001 PHE E 144 TRP 0.010 0.001 TRP D 174 HIS 0.011 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14591) covalent geometry : angle 0.54047 / 0.29 (19761) SS BOND : bond 0.02344 / 1.23 ( 1) SS BOND : angle 5.63987 / 3.27 ( 2) hydrogen bonds : bond 0.03401 / 2.35 ( 644) hydrogen bonds : angle 4.74858 / 3.43 ( 1902) metal coordination : bond 0.07462 / 3.73 ( 4) metal coordination : angle 6.12889 / 3.67 ( 3) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.894 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: symmetry clash revert: symmetry clash REVERT: G 131 LYS cc_start: 0.7944 (mttt) cc_final: 0.7564 (mmmt) REVERT: G 152 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7428 (mpm) REVERT: G 245 ASN cc_start: 0.8974 (m-40) cc_final: 0.8680 (m110) REVERT: G 281 SER cc_start: 0.8272 (m) cc_final: 0.7871 (p) REVERT: A 5 ILE cc_start: 0.9069 (mp) cc_final: 0.8698 (mm) REVERT: A 9 GLN cc_start: 0.8242 (tt0) cc_final: 0.7928 (tm-30) REVERT: B 431 VAL cc_start: 0.8513 (t) cc_final: 0.8235 (p) REVERT: E 14 ASP cc_start: 0.8586 (m-30) cc_final: 0.7684 (t0) REVERT: E 119 CYS cc_start: 0.7762 (m) cc_final: 0.7530 (m) REVERT: D 6 ASN cc_start: 0.8758 (m-40) cc_final: 0.8362 (p0) REVERT: D 15 PHE cc_start: 0.8906 (m-80) cc_final: 0.8644 (m-80) REVERT: D 83 LYS cc_start: 0.9250 (mmmm) cc_final: 0.9036 (mttt) REVERT: C 93 MET cc_start: 0.7746 (ttp) cc_final: 0.7074 (tpp) outliers start: 28 outliers final: 21 residues processed: 144 average time/residue: 0.2672 time to fit residues: 59.3996 Evaluate side-chains 143 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 105 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 158 optimal weight: 0.0270 chunk 111 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** 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 = 0.4042 r_free = 0.4042 target = 0.130068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.085512 restraints weight = 78964.365| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.88 r_work: 0.3179 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 14597 Z= 0.179 Angle : 0.563 11.195 19766 Z= 0.295 Chirality : 0.051 1.401 2256 Planarity : 0.004 0.066 2477 Dihedral : 9.531 176.057 2031 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.60 % Favored : 94.17 % Rotamer: Outliers : 2.28 % Allowed : 14.69 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.10 (0.21), residues: 1715 helix: 1.31 (0.19), residues: 764 sheet: -1.09 (0.32), residues: 258 loop : -0.82 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 188 TYR 0.011 0.001 TYR B 439 PHE 0.017 0.001 PHE E 144 TRP 0.010 0.001 TRP D 174 HIS 0.011 0.001 HIS E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (14591) covalent geometry : angle 0.55479 / 0.29 (19761) SS BOND : bond 0.02480 / 1.31 ( 1) SS BOND : angle 6.57181 / 3.77 ( 2) hydrogen bonds : bond 0.03403 / 2.36 ( 644) hydrogen bonds : angle 4.69670 / 3.39 ( 1902) metal coordination : bond 0.06448 / 3.23 ( 4) metal coordination : angle 5.72358 / 3.55 ( 3) Misc. bond : bond 0.00135 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.815 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: symmetry clash REVERT: G 131 LYS cc_start: 0.7972 (mttt) cc_final: 0.7578 (mmmt) REVERT: G 152 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7440 (mpm) REVERT: G 245 ASN cc_start: 0.8953 (m-40) cc_final: 0.8664 (m110) REVERT: G 281 SER cc_start: 0.8248 (m) cc_final: 0.7785 (p) REVERT: A 5 ILE cc_start: 0.9054 (mp) cc_final: 0.8681 (mm) REVERT: A 9 GLN cc_start: 0.8265 (tt0) cc_final: 0.7984 (tm-30) REVERT: A 155 MET cc_start: 0.8883 (ptp) cc_final: 0.8457 (ptt) REVERT: B 431 VAL cc_start: 0.8490 (t) cc_final: 0.8251 (p) REVERT: E 14 ASP cc_start: 0.8597 (m-30) cc_final: 0.7663 (t0) REVERT: E 119 CYS cc_start: 0.7803 (m) cc_final: 0.7586 (m) REVERT: D 6 ASN cc_start: 0.8759 (m-40) cc_final: 0.8363 (p0) REVERT: D 15 PHE cc_start: 0.8905 (m-80) cc_final: 0.8608 (m-80) REVERT: D 83 LYS cc_start: 0.9264 (mmmm) cc_final: 0.9048 (mttt) REVERT: C 93 MET cc_start: 0.7651 (ttp) cc_final: 0.7009 (tpp) outliers start: 36 outliers final: 28 residues processed: 150 average time/residue: 0.2786 time to fit residues: 63.7590 Evaluate side-chains 149 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 7 optimal weight: 0.0670 chunk 132 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 143 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 136 optimal weight: 0.3980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.131538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087203 restraints weight = 78882.259| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.89 r_work: 0.3217 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 14597 Z= 0.111 Angle : 0.539 11.196 19766 Z= 0.280 Chirality : 0.050 1.400 2256 Planarity : 0.004 0.063 2477 Dihedral : 9.463 177.910 2031 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 1.84 % Allowed : 15.33 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.26 (0.21), residues: 1715 helix: 1.41 (0.19), residues: 764 sheet: -0.95 (0.31), residues: 276 loop : -0.69 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 188 TYR 0.008 0.001 TYR B 439 PHE 0.019 0.001 PHE E 144 TRP 0.009 0.001 TRP D 174 HIS 0.018 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14591) covalent geometry : angle 0.52854 / 0.28 (19761) SS BOND : bond 0.02129 / 1.12 ( 1) SS BOND : angle 6.30627 / 3.58 ( 2) hydrogen bonds : bond 0.03187 / 2.20 ( 644) hydrogen bonds : angle 4.54752 / 3.29 ( 1902) metal coordination : bond 0.08732 / 4.37 ( 4) metal coordination : angle 6.84071 / 3.87 ( 3) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.812 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: G 131 LYS cc_start: 0.7948 (mttt) cc_final: 0.7567 (mmmt) REVERT: G 152 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7393 (mpm) REVERT: G 245 ASN cc_start: 0.8969 (m-40) cc_final: 0.8678 (m110) REVERT: G 281 SER cc_start: 0.8255 (m) cc_final: 0.7416 (p) REVERT: A 5 ILE cc_start: 0.9056 (mp) cc_final: 0.8685 (mm) REVERT: A 9 GLN cc_start: 0.8239 (tt0) cc_final: 0.7933 (tm-30) REVERT: A 155 MET cc_start: 0.8884 (ptp) cc_final: 0.8452 (ptt) REVERT: B 431 VAL cc_start: 0.8512 (t) cc_final: 0.8265 (p) REVERT: E 14 ASP cc_start: 0.8613 (m-30) cc_final: 0.7681 (t0) REVERT: E 72 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7884 (pp) REVERT: D 6 ASN cc_start: 0.8754 (m-40) cc_final: 0.8372 (p0) REVERT: D 15 PHE cc_start: 0.8941 (m-80) cc_final: 0.8597 (m-80) REVERT: D 83 LYS cc_start: 0.9275 (mmmm) cc_final: 0.9062 (mttt) REVERT: C 93 MET cc_start: 0.7617 (ttp) cc_final: 0.7013 (tpp) outliers start: 29 outliers final: 23 residues processed: 150 average time/residue: 0.2702 time to fit residues: 61.9213 Evaluate side-chains 147 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 178 HIS ** 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 = 0.4044 r_free = 0.4044 target = 0.130223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085761 restraints weight = 79009.366| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.89 r_work: 0.3184 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 14597 Z= 0.155 Angle : 0.548 11.188 19766 Z= 0.286 Chirality : 0.051 1.397 2256 Planarity : 0.004 0.065 2477 Dihedral : 9.456 177.814 2031 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.76 % Rotamer: Outliers : 1.77 % Allowed : 15.64 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.22 (0.21), residues: 1715 helix: 1.39 (0.19), residues: 764 sheet: -1.00 (0.31), residues: 276 loop : -0.71 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 131 TYR 0.010 0.001 TYR G 286 PHE 0.017 0.001 PHE E 144 TRP 0.009 0.001 TRP D 174 HIS 0.011 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (14591) covalent geometry : angle 0.54040 / 0.28 (19761) SS BOND : bond 0.02354 / 1.24 ( 1) SS BOND : angle 5.67391 / 3.23 ( 2) hydrogen bonds : bond 0.03236 / 2.24 ( 644) hydrogen bonds : angle 4.54028 / 3.28 ( 1902) metal coordination : bond 0.09457 / 4.73 ( 4) metal coordination : angle 5.83177 / 3.66 ( 3) Misc. bond : bond 0.00127 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.861 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: symmetry clash REVERT: G 131 LYS cc_start: 0.7956 (mttt) cc_final: 0.7573 (mmmt) REVERT: G 152 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7455 (mpm) REVERT: G 245 ASN cc_start: 0.8953 (m-40) cc_final: 0.8696 (m110) REVERT: G 281 SER cc_start: 0.8281 (m) cc_final: 0.7844 (p) REVERT: A 5 ILE cc_start: 0.9049 (mp) cc_final: 0.8688 (mm) REVERT: A 9 GLN cc_start: 0.8268 (tt0) cc_final: 0.7994 (tm-30) REVERT: A 155 MET cc_start: 0.8918 (ptp) cc_final: 0.8483 (ptt) REVERT: B 431 VAL cc_start: 0.8562 (t) cc_final: 0.8336 (p) REVERT: E 72 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7917 (pp) REVERT: D 6 ASN cc_start: 0.8737 (m-40) cc_final: 0.8354 (p0) REVERT: D 15 PHE cc_start: 0.8940 (m-80) cc_final: 0.8601 (m-80) REVERT: D 83 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9070 (mttt) REVERT: C 93 MET cc_start: 0.7631 (ttp) cc_final: 0.6987 (tpp) outliers start: 28 outliers final: 21 residues processed: 143 average time/residue: 0.2866 time to fit residues: 61.6673 Evaluate side-chains 140 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 159 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 178 HIS ** 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 = 0.4045 r_free = 0.4045 target = 0.130282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085878 restraints weight = 78443.058| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.89 r_work: 0.3191 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 14597 Z= 0.153 Angle : 0.565 11.887 19766 Z= 0.296 Chirality : 0.051 1.397 2256 Planarity : 0.004 0.063 2477 Dihedral : 9.458 177.874 2031 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.12 % Favored : 93.64 % Rotamer: Outliers : 1.65 % Allowed : 15.83 % Favored : 82.52 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1715 helix: 1.39 (0.19), residues: 764 sheet: -0.98 (0.31), residues: 276 loop : -0.68 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 188 TYR 0.017 0.001 TYR F 91 PHE 0.017 0.001 PHE E 144 TRP 0.009 0.001 TRP D 174 HIS 0.011 0.001 HIS E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (14591) covalent geometry : angle 0.55240 / 0.29 (19761) SS BOND : bond 0.05536 / 2.91 ( 1) SS BOND : angle 9.78562 / 5.32 ( 2) hydrogen bonds : bond 0.03200 / 2.20 ( 644) hydrogen bonds : angle 4.55362 / 3.29 ( 1902) metal coordination : bond 0.07317 / 3.66 ( 4) metal coordination : angle 5.55020 / 3.73 ( 3) Misc. bond : bond 0.00106 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.884 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: G 131 LYS cc_start: 0.7970 (mttt) cc_final: 0.7582 (mmmt) REVERT: G 152 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7451 (mpm) REVERT: G 245 ASN cc_start: 0.8953 (m-40) cc_final: 0.8665 (m110) REVERT: G 281 SER cc_start: 0.8254 (m) cc_final: 0.7783 (p) REVERT: A 5 ILE cc_start: 0.9057 (mp) cc_final: 0.8696 (mm) REVERT: A 9 GLN cc_start: 0.8273 (tt0) cc_final: 0.7994 (tm-30) REVERT: A 155 MET cc_start: 0.8927 (ptp) cc_final: 0.8502 (ptt) REVERT: B 431 VAL cc_start: 0.8583 (t) cc_final: 0.8377 (p) REVERT: E 72 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7902 (pp) REVERT: D 6 ASN cc_start: 0.8730 (m-40) cc_final: 0.8353 (p0) REVERT: D 15 PHE cc_start: 0.8947 (m-80) cc_final: 0.8624 (m-80) REVERT: D 83 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9071 (mttt) REVERT: C 93 MET cc_start: 0.7655 (ttp) cc_final: 0.6976 (tpp) outliers start: 26 outliers final: 21 residues processed: 141 average time/residue: 0.2854 time to fit residues: 60.4069 Evaluate side-chains 142 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 164 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** 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 = 0.4046 r_free = 0.4046 target = 0.130411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086070 restraints weight = 78150.538| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.88 r_work: 0.3191 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 14597 Z= 0.142 Angle : 0.555 11.176 19766 Z= 0.290 Chirality : 0.051 1.398 2256 Planarity : 0.004 0.064 2477 Dihedral : 9.447 178.418 2031 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.18 % Favored : 93.59 % Rotamer: Outliers : 1.46 % Allowed : 15.83 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.28 (0.21), residues: 1715 helix: 1.41 (0.19), residues: 765 sheet: -0.97 (0.31), residues: 276 loop : -0.65 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 188 TYR 0.012 0.001 TYR F 91 PHE 0.017 0.001 PHE E 144 TRP 0.009 0.001 TRP D 174 HIS 0.011 0.001 HIS E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14591) covalent geometry : angle 0.54442 / 0.29 (19761) SS BOND : bond 0.05092 / 2.68 ( 1) SS BOND : angle 8.59876 / 4.69 ( 2) hydrogen bonds : bond 0.03131 / 2.15 ( 644) hydrogen bonds : angle 4.51001 / 3.26 ( 1902) metal coordination : bond 0.07208 / 3.61 ( 4) metal coordination : angle 5.39515 / 3.73 ( 3) Misc. bond : bond 0.00107 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.857 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: G 131 LYS cc_start: 0.7964 (mttt) cc_final: 0.7576 (mmmt) REVERT: G 152 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7447 (mpm) REVERT: G 245 ASN cc_start: 0.8973 (m-40) cc_final: 0.8721 (m110) REVERT: G 281 SER cc_start: 0.8219 (m) cc_final: 0.7708 (p) REVERT: A 5 ILE cc_start: 0.9060 (mp) cc_final: 0.8703 (mm) REVERT: A 9 GLN cc_start: 0.8277 (tt0) cc_final: 0.7994 (tm-30) REVERT: A 155 MET cc_start: 0.8935 (ptp) cc_final: 0.8500 (ptt) REVERT: B 431 VAL cc_start: 0.8622 (t) cc_final: 0.8411 (p) REVERT: E 72 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7918 (pp) REVERT: D 6 ASN cc_start: 0.8717 (m-40) cc_final: 0.8353 (p0) REVERT: D 15 PHE cc_start: 0.8958 (m-80) cc_final: 0.8655 (m-80) REVERT: D 83 LYS cc_start: 0.9302 (mmmm) cc_final: 0.9081 (mttt) REVERT: C 93 MET cc_start: 0.7572 (ttp) cc_final: 0.6849 (tpp) outliers start: 23 outliers final: 18 residues processed: 145 average time/residue: 0.2858 time to fit residues: 61.7769 Evaluate side-chains 139 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 155 optimal weight: 0.0070 chunk 157 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 149 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** 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 = 0.4056 r_free = 0.4056 target = 0.131164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086921 restraints weight = 78512.364| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.90 r_work: 0.3208 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 14597 Z= 0.117 Angle : 0.545 11.160 19766 Z= 0.283 Chirality : 0.051 1.395 2256 Planarity : 0.004 0.062 2477 Dihedral : 9.362 179.381 2027 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 1.33 % Allowed : 16.02 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1715 helix: 1.47 (0.19), residues: 764 sheet: -0.90 (0.32), residues: 276 loop : -0.57 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 188 TYR 0.012 0.001 TYR F 91 PHE 0.017 0.001 PHE E 144 TRP 0.009 0.001 TRP D 196 HIS 0.012 0.001 HIS E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (14591) covalent geometry : angle 0.53719 / 0.28 (19761) SS BOND : bond 0.03900 / 2.05 ( 1) SS BOND : angle 6.73704 / 3.74 ( 2) hydrogen bonds : bond 0.03017 / 2.08 ( 644) hydrogen bonds : angle 4.43065 / 3.21 ( 1902) metal coordination : bond 0.06901 / 3.45 ( 4) metal coordination : angle 5.09572 / 3.63 ( 3) Misc. bond : bond 0.00084 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8962.49 seconds wall clock time: 152 minutes 26.58 seconds (9146.58 seconds total)