Starting phenix.real_space_refine on Fri Jul 3 14:36:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud9_64065/07_2026/9ud9_64065.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud9_64065/07_2026/9ud9_64065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ud9_64065/07_2026/9ud9_64065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud9_64065/07_2026/9ud9_64065.map" model { file = "/net/cci-nas-00/data/ceres_data/9ud9_64065/07_2026/9ud9_64065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud9_64065/07_2026/9ud9_64065.cif" } resolution = 3.11 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= 0.033 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 4 5.49 5 S 92 5.16 5 C 9478 2.51 5 N 2407 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14665 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2964 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3157 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9088 SG CYS D 112 42.283 74.439 65.946 1.00125.00 S ATOM 10054 SG CYS E 26 43.610 71.456 66.547 1.00131.33 S ATOM 8449 SG CYS D 29 43.025 69.417 63.025 1.00126.37 S ATOM 10776 SG CYS E 120 39.891 69.511 61.720 1.00112.31 S ATOM 11898 SG CYS F 79 35.347 82.562 80.222 1.00282.06 S Time building chain proxies: 2.76, per 1000 atoms: 0.19 Number of scatterers: 14665 At special positions: 0 Unit cell: (91.52, 124.08, 153.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 4 15.00 O 2679 8.00 N 2407 7.00 C 9478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 644.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 79 " Number of angles added : 7 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 12 sheets defined 52.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.621A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.616A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.520A pdb=" N MET A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.644A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.776A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.821A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 444 removed outlier: 4.055A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.871A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.636A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.526A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.602A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 removed outlier: 4.018A pdb=" N GLN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 removed outlier: 3.501A pdb=" N LEU B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.990A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 removed outlier: 3.711A pdb=" N ILE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.534A pdb=" N PHE B 323 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 325' Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.089A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 374 removed outlier: 3.870A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.900A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.565A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.714A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.988A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 224 through 240 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'D' and resid 8 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 37 through 62 removed outlier: 3.575A pdb=" N ILE D 62 " --> pdb=" O PHE D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 removed outlier: 3.892A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.357A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.740A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.619A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.709A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.301A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 4 through 14 removed outlier: 4.130A pdb=" N LEU E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 30 through 33 removed outlier: 3.730A pdb=" N LYS E 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 34 through 63 removed outlier: 3.526A pdb=" N SER E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.670A pdb=" N ILE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.507A pdb=" N ALA E 108 " --> pdb=" O PRO E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.729A pdb=" N ILE E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 132 removed outlier: 3.969A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'F' and resid 3 through 24 removed outlier: 3.631A pdb=" N MET F 10 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 63 removed outlier: 4.007A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 196 removed outlier: 5.429A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.685A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 removed outlier: 4.102A pdb=" N MET F 317 " --> pdb=" O LYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 removed outlier: 4.192A pdb=" N PHE F 323 " --> pdb=" O TYR F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 347 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 364 through 367 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 380 through 395 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.479A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 8.214A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.706A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 94 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY A 74 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.560A pdb=" N GLU A 59 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.505A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 42 through 49 removed outlier: 6.461A pdb=" N LYS F 45 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE F 39 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 207 through 212 removed outlier: 3.537A pdb=" N GLU F 171 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N LYS F 257 " --> pdb=" O PRO F 173 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN F 140 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU F 149 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN F 142 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE F 147 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 152 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 224 " --> pdb=" O LEU F 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 177 through 178 Processing sheet with id=AB3, first strand: chain 'F' and resid 335 through 339 removed outlier: 6.945A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N LEU F 402 " --> pdb=" O CYS F 373 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1992 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: 2.33 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6091 1.41 - 1.61: 8741 1.61 - 1.81: 140 1.81 - 2.01: 21 2.01 - 2.20: 8 Bond restraints: 15001 Sorted by residual: bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.405 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" O5' FMN C 301 " pdb=" P FMN C 301 " ideal model delta sigma weight residual 1.676 1.612 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O5' FMN B 501 " pdb=" P FMN B 501 " ideal model delta sigma weight residual 1.676 1.614 0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" C2 FMN C 301 " pdb=" N3 FMN C 301 " ideal model delta sigma weight residual 1.404 1.354 0.050 2.00e-02 2.50e+03 6.13e+00 ... (remaining 14996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 19457 1.38 - 2.76: 735 2.76 - 4.15: 155 4.15 - 5.53: 15 5.53 - 6.91: 4 Bond angle restraints: 20366 Sorted by residual: angle pdb=" C SER B 44 " pdb=" CA SER B 44 " pdb=" CB SER B 44 " ideal model delta sigma weight residual 116.54 110.69 5.85 1.15e+00 7.56e-01 2.59e+01 angle pdb=" C SER D 102 " pdb=" CA SER D 102 " pdb=" CB SER D 102 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 angle pdb=" N PHE A 136 " pdb=" CA PHE A 136 " pdb=" CB PHE A 136 " ideal model delta sigma weight residual 114.17 110.12 4.05 1.14e+00 7.69e-01 1.27e+01 angle pdb=" CA SER D 102 " pdb=" C SER D 102 " pdb=" N VAL D 103 " ideal model delta sigma weight residual 119.98 117.18 2.80 8.50e-01 1.38e+00 1.08e+01 angle pdb=" N ASN C 120 " pdb=" CA ASN C 120 " pdb=" CB ASN C 120 " ideal model delta sigma weight residual 114.17 110.42 3.75 1.14e+00 7.69e-01 1.08e+01 ... (remaining 20361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7987 17.66 - 35.32: 632 35.32 - 52.97: 157 52.97 - 70.63: 36 70.63 - 88.29: 12 Dihedral angle restraints: 8824 sinusoidal: 3462 harmonic: 5362 Sorted by residual: dihedral pdb=" CA LEU A 184 " pdb=" C LEU A 184 " pdb=" N THR A 185 " pdb=" CA THR A 185 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLU B 274 " pdb=" C GLU B 274 " pdb=" N VAL B 275 " pdb=" CA VAL B 275 " ideal model delta harmonic sigma weight residual 180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PHE F 24 " pdb=" C PHE F 24 " pdb=" N ALA F 25 " pdb=" CA ALA F 25 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1393 0.029 - 0.058: 492 0.058 - 0.087: 228 0.087 - 0.116: 145 0.116 - 0.145: 42 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA TRP B 103 " pdb=" N TRP B 103 " pdb=" C TRP B 103 " pdb=" CB TRP B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE D 66 " pdb=" N ILE D 66 " pdb=" C ILE D 66 " pdb=" CB ILE D 66 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CB THR B 127 " pdb=" CA THR B 127 " pdb=" OG1 THR B 127 " pdb=" CG2 THR B 127 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 2297 not shown) Planarity restraints: 2567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 91 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C VAL E 91 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL E 91 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN E 92 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 95 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C GLU E 95 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU E 95 " 0.011 2.00e-02 2.50e+03 pdb=" N MET E 96 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 70 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.23e+00 pdb=" N PRO A 71 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " -0.021 5.00e-02 4.00e+02 ... (remaining 2564 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 53 2.52 - 3.12: 11460 3.12 - 3.71: 22093 3.71 - 4.31: 31656 4.31 - 4.90: 53971 Nonbonded interactions: 119233 Sorted by model distance: nonbonded pdb=" O VAL E 118 " pdb=" O HOH E 401 " model vdw 1.925 3.040 nonbonded pdb=" OD2 ASP A 60 " pdb=" N ASN A 63 " model vdw 2.075 3.120 nonbonded pdb=" OD2 ASP F 191 " pdb=" NH2 ARG F 315 " model vdw 2.170 3.120 nonbonded pdb=" O SER C 19 " pdb=" OG SER C 23 " model vdw 2.215 3.040 nonbonded pdb=" NZ LYS F 203 " pdb=" OD1 ASP F 205 " model vdw 2.226 3.120 ... (remaining 119228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.080 15006 Z= 0.158 Angle : 0.649 14.905 20373 Z= 0.370 Chirality : 0.044 0.145 2300 Planarity : 0.004 0.037 2567 Dihedral : 14.288 88.291 5404 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.84 % Allowed : 12.83 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 1882 helix: 1.18 (0.18), residues: 835 sheet: 0.04 (0.42), residues: 152 loop : -0.43 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 189 TYR 0.018 0.001 TYR F 319 PHE 0.013 0.001 PHE D 188 TRP 0.015 0.001 TRP B 103 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (15001) covalent geometry : angle 0.63290 / 0.37 (20366) hydrogen bonds : bond 0.13595 / 9.18 ( 704) hydrogen bonds : angle 5.83699 / 4.11 ( 1992) metal coordination : bond 0.01131 / 0.56 ( 5) metal coordination : angle 7.87588 / 3.91 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 245 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5610 (tmm) cc_final: 0.5153 (ttm) REVERT: A 22 ASP cc_start: 0.8802 (m-30) cc_final: 0.8255 (t0) REVERT: A 52 LYS cc_start: 0.7608 (mttp) cc_final: 0.7304 (mtpt) REVERT: A 84 LYS cc_start: 0.8275 (mttp) cc_final: 0.7992 (mttt) REVERT: A 101 THR cc_start: 0.7920 (m) cc_final: 0.7661 (p) REVERT: A 200 ARG cc_start: 0.8086 (ttp80) cc_final: 0.6334 (tpt170) REVERT: A 318 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.4673 (tmt90) REVERT: A 342 LYS cc_start: 0.8449 (tttt) cc_final: 0.7804 (tmtt) REVERT: A 430 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8648 (mt-10) REVERT: B 149 MET cc_start: 0.7039 (mtm) cc_final: 0.6694 (mtm) REVERT: B 152 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7317 (mptt) REVERT: C 62 GLN cc_start: 0.7382 (tp40) cc_final: 0.7095 (tt0) REVERT: C 77 ASP cc_start: 0.6640 (t0) cc_final: 0.6089 (p0) REVERT: C 90 ASN cc_start: 0.8549 (m-40) cc_final: 0.8136 (m-40) REVERT: C 132 LYS cc_start: 0.7571 (pttm) cc_final: 0.7271 (tptt) REVERT: C 241 ASP cc_start: 0.7751 (p0) cc_final: 0.7204 (m-30) REVERT: D 14 PRO cc_start: 0.5129 (Cg_exo) cc_final: 0.4855 (Cg_endo) REVERT: D 194 MET cc_start: 0.7740 (ttm) cc_final: 0.7440 (ttm) REVERT: E 129 MET cc_start: 0.5745 (tmm) cc_final: 0.5535 (tmm) REVERT: E 131 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7758 (tm-30) REVERT: E 162 GLU cc_start: 0.7226 (tt0) cc_final: 0.6776 (mt-10) REVERT: F 189 ARG cc_start: 0.6110 (tpp-160) cc_final: 0.5804 (tpp-160) REVERT: F 210 ARG cc_start: 0.1785 (tpp80) cc_final: 0.1242 (tpm170) REVERT: F 285 MET cc_start: 0.3875 (tpp) cc_final: 0.3641 (tpp) REVERT: F 317 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4060 (pmm) outliers start: 13 outliers final: 6 residues processed: 252 average time/residue: 0.1292 time to fit residues: 46.6120 Evaluate side-chains 183 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN B 243 GLN C 198 ASN C 199 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.180883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138568 restraints weight = 16158.254| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.65 r_work: 0.3126 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15006 Z= 0.217 Angle : 0.675 15.532 20373 Z= 0.343 Chirality : 0.047 0.164 2300 Planarity : 0.005 0.041 2567 Dihedral : 7.192 58.916 2117 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 2.79 % Allowed : 14.19 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1882 helix: 0.98 (0.18), residues: 850 sheet: 0.17 (0.40), residues: 163 loop : -0.59 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 199 TYR 0.015 0.002 TYR D 141 PHE 0.023 0.002 PHE F 333 TRP 0.028 0.002 TRP B 103 HIS 0.007 0.002 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (15001) covalent geometry : angle 0.65870 / 0.34 (20366) hydrogen bonds : bond 0.05714 / 3.78 ( 704) hydrogen bonds : angle 5.03098 / 3.49 ( 1992) metal coordination : bond 0.01315 / 0.77 ( 5) metal coordination : angle 8.08026 / 3.71 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6504 (tmm) cc_final: 0.5966 (ttm) REVERT: A 101 THR cc_start: 0.8338 (m) cc_final: 0.8014 (p) REVERT: A 168 ASN cc_start: 0.8938 (m-40) cc_final: 0.8678 (m110) REVERT: A 200 ARG cc_start: 0.8629 (ttp80) cc_final: 0.7451 (tpt90) REVERT: A 318 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7794 (tmt90) REVERT: B 91 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: B 152 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8260 (mptt) REVERT: B 382 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8478 (tpt) REVERT: C 232 GLN cc_start: 0.8837 (tp40) cc_final: 0.8626 (tp-100) REVERT: C 253 ASP cc_start: 0.7573 (m-30) cc_final: 0.7345 (m-30) REVERT: E 131 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8261 (tm-30) REVERT: F 83 ILE cc_start: 0.2030 (OUTLIER) cc_final: 0.1595 (tp) REVERT: F 163 ARG cc_start: 0.5165 (mpp80) cc_final: 0.3967 (tpm170) REVERT: F 225 MET cc_start: 0.5560 (OUTLIER) cc_final: 0.4745 (ttt) REVERT: F 285 MET cc_start: 0.4681 (tpp) cc_final: 0.4443 (tpp) REVERT: F 293 PHE cc_start: 0.6117 (m-80) cc_final: 0.5407 (m-80) REVERT: F 316 GLU cc_start: 0.5343 (mp0) cc_final: 0.4399 (mt-10) REVERT: F 317 MET cc_start: 0.5428 (OUTLIER) cc_final: 0.4645 (pmm) outliers start: 43 outliers final: 26 residues processed: 216 average time/residue: 0.1179 time to fit residues: 37.9568 Evaluate side-chains 201 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 116 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.178890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128070 restraints weight = 16353.606| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.61 r_work: 0.2945 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15006 Z= 0.191 Angle : 0.627 15.091 20373 Z= 0.317 Chirality : 0.046 0.222 2300 Planarity : 0.005 0.046 2567 Dihedral : 6.859 57.096 2112 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 3.50 % Allowed : 14.52 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.19), residues: 1882 helix: 0.92 (0.18), residues: 850 sheet: 0.09 (0.41), residues: 163 loop : -0.68 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 43 TYR 0.015 0.001 TYR D 141 PHE 0.026 0.002 PHE F 11 TRP 0.024 0.002 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (15001) covalent geometry : angle 0.60956 / 0.32 (20366) hydrogen bonds : bond 0.05329 / 3.52 ( 704) hydrogen bonds : angle 4.85675 / 3.35 ( 1992) metal coordination : bond 0.01176 / 0.62 ( 5) metal coordination : angle 8.03640 / 3.71 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6359 (tmm) cc_final: 0.5880 (ttm) REVERT: A 101 THR cc_start: 0.8317 (m) cc_final: 0.8056 (p) REVERT: A 168 ASN cc_start: 0.8973 (m-40) cc_final: 0.8682 (m110) REVERT: A 200 ARG cc_start: 0.8485 (ttp80) cc_final: 0.7209 (tpt90) REVERT: A 318 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7661 (tmt90) REVERT: B 152 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8142 (mptt) REVERT: C 77 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6743 (p0) REVERT: C 170 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.6663 (pp30) REVERT: D 111 ASN cc_start: 0.8404 (t0) cc_final: 0.8041 (t0) REVERT: D 146 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8510 (mmm) REVERT: E 22 PHE cc_start: 0.7435 (m-10) cc_final: 0.7086 (m-80) REVERT: E 131 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8350 (tt0) REVERT: F 163 ARG cc_start: 0.5165 (mpp80) cc_final: 0.3959 (tpm170) REVERT: F 225 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4688 (ttt) REVERT: F 293 PHE cc_start: 0.6107 (m-80) cc_final: 0.5329 (m-80) REVERT: F 316 GLU cc_start: 0.5218 (mp0) cc_final: 0.4368 (mt-10) REVERT: F 317 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.4388 (pmm) outliers start: 54 outliers final: 30 residues processed: 208 average time/residue: 0.1180 time to fit residues: 37.3552 Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 chunk 141 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 GLN F 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.182203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131371 restraints weight = 16123.890| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.90 r_work: 0.2993 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15006 Z= 0.126 Angle : 0.564 16.535 20373 Z= 0.283 Chirality : 0.043 0.230 2300 Planarity : 0.004 0.048 2567 Dihedral : 6.620 57.073 2110 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 2.92 % Allowed : 15.94 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1882 helix: 1.11 (0.18), residues: 850 sheet: 0.21 (0.40), residues: 165 loop : -0.60 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 46 TYR 0.013 0.001 TYR D 141 PHE 0.027 0.001 PHE F 11 TRP 0.023 0.001 TRP B 103 HIS 0.005 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15001) covalent geometry : angle 0.54356 / 0.28 (20366) hydrogen bonds : bond 0.04364 / 2.88 ( 704) hydrogen bonds : angle 4.63901 / 3.20 ( 1992) metal coordination : bond 0.00870 / 0.47 ( 5) metal coordination : angle 8.12891 / 4.16 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6224 (tmm) cc_final: 0.5865 (ttm) REVERT: A 101 THR cc_start: 0.8248 (m) cc_final: 0.8012 (p) REVERT: A 168 ASN cc_start: 0.8872 (m-40) cc_final: 0.8575 (m110) REVERT: A 200 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7317 (tpt90) REVERT: A 318 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7518 (tmt90) REVERT: B 152 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8121 (mptt) REVERT: C 170 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.6712 (pp30) REVERT: D 63 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.4933 (ptt-90) REVERT: D 111 ASN cc_start: 0.8356 (t0) cc_final: 0.7968 (t0) REVERT: E 131 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8308 (tt0) REVERT: F 163 ARG cc_start: 0.5135 (mpp80) cc_final: 0.4024 (tpm170) REVERT: F 225 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.4865 (ttt) REVERT: F 285 MET cc_start: 0.4434 (tpp) cc_final: 0.3724 (tpp) REVERT: F 293 PHE cc_start: 0.6237 (m-80) cc_final: 0.5976 (m-80) REVERT: F 316 GLU cc_start: 0.5170 (mp0) cc_final: 0.4917 (mp0) REVERT: F 317 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.4237 (pmm) REVERT: F 318 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6245 (p90) outliers start: 45 outliers final: 26 residues processed: 210 average time/residue: 0.1191 time to fit residues: 37.3985 Evaluate side-chains 198 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 153 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 GLN C 232 GLN F 362 ASN F 367 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.182440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133583 restraints weight = 16069.461| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.75 r_work: 0.2969 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15006 Z= 0.124 Angle : 0.551 16.455 20373 Z= 0.277 Chirality : 0.043 0.186 2300 Planarity : 0.004 0.049 2567 Dihedral : 6.539 57.941 2110 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 3.43 % Allowed : 15.42 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1882 helix: 1.18 (0.18), residues: 852 sheet: 0.25 (0.40), residues: 165 loop : -0.57 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 46 TYR 0.013 0.001 TYR D 141 PHE 0.020 0.001 PHE F 11 TRP 0.023 0.001 TRP B 103 HIS 0.006 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15001) covalent geometry : angle 0.53066 / 0.28 (20366) hydrogen bonds : bond 0.04232 / 2.78 ( 704) hydrogen bonds : angle 4.57022 / 3.16 ( 1992) metal coordination : bond 0.01094 / 0.59 ( 5) metal coordination : angle 7.95277 / 4.09 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6218 (tmm) cc_final: 0.5918 (ttm) REVERT: A 101 THR cc_start: 0.8274 (m) cc_final: 0.8007 (p) REVERT: A 168 ASN cc_start: 0.8918 (m-40) cc_final: 0.8616 (m110) REVERT: A 200 ARG cc_start: 0.8527 (ttp80) cc_final: 0.7373 (tpt90) REVERT: A 318 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7528 (tmt90) REVERT: B 152 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8084 (mptt) REVERT: C 95 LYS cc_start: 0.8325 (tppp) cc_final: 0.7397 (ttpt) REVERT: C 170 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.6730 (pp30) REVERT: D 63 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.5132 (ptt-90) REVERT: D 146 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8511 (mmm) REVERT: E 1 MET cc_start: 0.7436 (tpt) cc_final: 0.7178 (tpt) REVERT: E 22 PHE cc_start: 0.8011 (m-10) cc_final: 0.7803 (m-80) REVERT: E 131 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8342 (tt0) REVERT: F 163 ARG cc_start: 0.5167 (mpp80) cc_final: 0.4088 (tpm170) REVERT: F 225 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.4915 (ttt) REVERT: F 285 MET cc_start: 0.4297 (tpp) cc_final: 0.3932 (tpp) REVERT: F 293 PHE cc_start: 0.6485 (m-80) cc_final: 0.5720 (m-80) REVERT: F 317 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.4356 (pmm) REVERT: F 318 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6315 (p90) REVERT: F 401 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7413 (mt) outliers start: 53 outliers final: 36 residues processed: 210 average time/residue: 0.1155 time to fit residues: 36.4353 Evaluate side-chains 208 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 138 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.177790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128716 restraints weight = 16082.571| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.66 r_work: 0.2889 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15006 Z= 0.245 Angle : 0.657 17.708 20373 Z= 0.328 Chirality : 0.047 0.177 2300 Planarity : 0.005 0.048 2567 Dihedral : 6.903 56.942 2110 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 3.89 % Allowed : 15.42 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1882 helix: 0.88 (0.18), residues: 849 sheet: 0.22 (0.39), residues: 165 loop : -0.74 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 46 TYR 0.018 0.002 TYR D 141 PHE 0.027 0.002 PHE D 50 TRP 0.026 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.24 (15001) covalent geometry : angle 0.63325 / 0.33 (20366) hydrogen bonds : bond 0.05740 / 3.78 ( 704) hydrogen bonds : angle 4.81945 / 3.32 ( 1992) metal coordination : bond 0.01462 / 0.79 ( 5) metal coordination : angle 9.37551 / 4.62 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6169 (tmm) cc_final: 0.5901 (ttm) REVERT: A 101 THR cc_start: 0.8250 (m) cc_final: 0.8042 (p) REVERT: A 200 ARG cc_start: 0.8527 (ttp80) cc_final: 0.7438 (tpt90) REVERT: B 152 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8056 (mptt) REVERT: B 156 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8129 (t0) REVERT: C 95 LYS cc_start: 0.8341 (tppp) cc_final: 0.7445 (ttpt) REVERT: C 143 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8381 (m-40) REVERT: C 170 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: D 63 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.4950 (ptt-90) REVERT: D 111 ASN cc_start: 0.8288 (t0) cc_final: 0.8001 (t0) REVERT: D 146 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8478 (mmm) REVERT: E 131 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8371 (tt0) REVERT: F 119 MET cc_start: 0.1974 (tpt) cc_final: 0.1742 (mmp) REVERT: F 163 ARG cc_start: 0.5118 (mpp80) cc_final: 0.4226 (mmm160) REVERT: F 225 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.4911 (ttt) REVERT: F 285 MET cc_start: 0.4269 (tpp) cc_final: 0.3585 (tpp) REVERT: F 293 PHE cc_start: 0.6503 (m-80) cc_final: 0.5694 (m-80) REVERT: F 316 GLU cc_start: 0.5407 (mp0) cc_final: 0.3531 (tt0) REVERT: F 317 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.4412 (pmm) REVERT: F 318 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6382 (p90) outliers start: 60 outliers final: 38 residues processed: 211 average time/residue: 0.1115 time to fit residues: 35.6325 Evaluate side-chains 204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 GLN D 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.177969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128014 restraints weight = 15985.974| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.81 r_work: 0.2904 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15006 Z= 0.221 Angle : 0.636 18.169 20373 Z= 0.317 Chirality : 0.046 0.198 2300 Planarity : 0.005 0.049 2567 Dihedral : 6.764 57.615 2103 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 3.95 % Allowed : 16.01 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.19), residues: 1882 helix: 0.79 (0.18), residues: 850 sheet: 0.31 (0.40), residues: 160 loop : -0.81 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 46 TYR 0.016 0.001 TYR D 141 PHE 0.027 0.002 PHE D 50 TRP 0.025 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.22 (15001) covalent geometry : angle 0.61236 / 0.32 (20366) hydrogen bonds : bond 0.05469 / 3.60 ( 704) hydrogen bonds : angle 4.81623 / 3.32 ( 1992) metal coordination : bond 0.01419 / 0.77 ( 5) metal coordination : angle 9.34128 / 4.68 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6274 (tmm) cc_final: 0.6019 (ttm) REVERT: A 200 ARG cc_start: 0.8534 (ttp80) cc_final: 0.7411 (tpt90) REVERT: B 152 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8044 (mptt) REVERT: B 156 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8100 (t0) REVERT: C 95 LYS cc_start: 0.8348 (tppp) cc_final: 0.7490 (ttpt) REVERT: C 143 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8375 (m-40) REVERT: C 170 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7046 (pt0) REVERT: D 24 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.6251 (pm20) REVERT: D 63 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.5069 (ptt-90) REVERT: D 111 ASN cc_start: 0.8268 (t0) cc_final: 0.8017 (t0) REVERT: D 146 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8520 (mmm) REVERT: F 119 MET cc_start: 0.1956 (tpt) cc_final: 0.1734 (mmp) REVERT: F 163 ARG cc_start: 0.5208 (mpp80) cc_final: 0.4203 (mmm160) REVERT: F 225 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.4870 (ttt) REVERT: F 285 MET cc_start: 0.4129 (tpp) cc_final: 0.3477 (tpp) REVERT: F 293 PHE cc_start: 0.6551 (m-80) cc_final: 0.5750 (m-80) REVERT: F 318 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6290 (p90) outliers start: 61 outliers final: 42 residues processed: 205 average time/residue: 0.1115 time to fit residues: 35.0816 Evaluate side-chains 203 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 152 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 102 optimal weight: 0.3980 chunk 166 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.180933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130752 restraints weight = 16021.976| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.99 r_work: 0.2943 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15006 Z= 0.126 Angle : 0.562 18.663 20373 Z= 0.282 Chirality : 0.043 0.203 2300 Planarity : 0.004 0.052 2567 Dihedral : 6.516 58.024 2103 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 3.37 % Allowed : 16.79 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1882 helix: 1.05 (0.18), residues: 844 sheet: 0.36 (0.39), residues: 170 loop : -0.71 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 46 TYR 0.014 0.001 TYR D 141 PHE 0.021 0.001 PHE D 50 TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15001) covalent geometry : angle 0.53902 / 0.28 (20366) hydrogen bonds : bond 0.04404 / 2.90 ( 704) hydrogen bonds : angle 4.65689 / 3.21 ( 1992) metal coordination : bond 0.01113 / 0.60 ( 5) metal coordination : angle 8.61635 / 4.55 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6218 (tmm) cc_final: 0.6012 (ttm) REVERT: A 200 ARG cc_start: 0.8554 (ttp80) cc_final: 0.7443 (tpt90) REVERT: B 152 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8042 (mptt) REVERT: C 95 LYS cc_start: 0.8352 (tppp) cc_final: 0.7489 (ttpt) REVERT: C 170 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.6810 (pp30) REVERT: D 63 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.5219 (ptt-90) REVERT: D 111 ASN cc_start: 0.8238 (t0) cc_final: 0.7962 (t0) REVERT: F 119 MET cc_start: 0.1883 (tpt) cc_final: 0.1677 (mmp) REVERT: F 122 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6302 (pt0) REVERT: F 163 ARG cc_start: 0.5242 (mpp80) cc_final: 0.4300 (mmm160) REVERT: F 208 ILE cc_start: 0.1788 (OUTLIER) cc_final: 0.1548 (mt) REVERT: F 225 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.4920 (ttt) REVERT: F 285 MET cc_start: 0.4324 (tpp) cc_final: 0.3667 (tpp) REVERT: F 293 PHE cc_start: 0.6491 (m-80) cc_final: 0.5766 (m-80) REVERT: F 318 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6316 (p90) outliers start: 52 outliers final: 37 residues processed: 205 average time/residue: 0.1131 time to fit residues: 35.3134 Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 GLN D 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.181337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144453 restraints weight = 16120.287| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.50 r_work: 0.3305 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.003 0.038 15006 Z= 0.127 Angle : 0.565 16.997 20373 Z= 0.282 Chirality : 0.043 0.235 2300 Planarity : 0.004 0.052 2567 Dihedral : 6.443 58.027 2103 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 3.24 % Allowed : 16.85 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1882 helix: 1.11 (0.18), residues: 845 sheet: 0.34 (0.39), residues: 170 loop : -0.68 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 46 TYR 0.014 0.001 TYR D 141 PHE 0.025 0.001 PHE D 50 TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (15001) covalent geometry : angle 0.54492 / 0.28 (20366) hydrogen bonds : bond 0.04312 / 2.84 ( 704) hydrogen bonds : angle 4.59035 / 3.16 ( 1992) metal coordination : bond 0.01015 / 0.55 ( 5) metal coordination : angle 7.97276 / 4.16 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7783 (tpt90) REVERT: B 152 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8111 (mptt) REVERT: C 95 LYS cc_start: 0.8611 (tppp) cc_final: 0.8081 (ttpt) REVERT: C 170 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6648 (pp30) REVERT: D 63 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.5625 (ptt-90) REVERT: D 111 ASN cc_start: 0.8132 (t0) cc_final: 0.7791 (t0) REVERT: F 108 ARG cc_start: 0.3675 (ttp80) cc_final: 0.1146 (mpp80) REVERT: F 119 MET cc_start: 0.3702 (tpt) cc_final: 0.3373 (mmp) REVERT: F 163 ARG cc_start: 0.4455 (mpp80) cc_final: 0.4145 (mmm160) REVERT: F 225 MET cc_start: 0.5585 (OUTLIER) cc_final: 0.4719 (ttt) REVERT: F 285 MET cc_start: 0.5538 (tpp) cc_final: 0.5287 (tpp) REVERT: F 309 TYR cc_start: 0.3468 (t80) cc_final: 0.3236 (t80) REVERT: F 318 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.6001 (p90) outliers start: 50 outliers final: 39 residues processed: 200 average time/residue: 0.1061 time to fit residues: 32.3531 Evaluate side-chains 202 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 GLN D 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.180236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.130169 restraints weight = 16072.881| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.73 r_work: 0.2923 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15006 Z= 0.159 Angle : 0.585 16.880 20373 Z= 0.294 Chirality : 0.044 0.210 2300 Planarity : 0.005 0.051 2567 Dihedral : 6.520 57.721 2103 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.35 % Favored : 96.60 % Rotamer: Outliers : 3.05 % Allowed : 17.04 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1882 helix: 1.04 (0.18), residues: 844 sheet: 0.50 (0.43), residues: 148 loop : -0.71 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 46 TYR 0.016 0.001 TYR D 141 PHE 0.026 0.002 PHE D 50 TRP 0.024 0.001 TRP B 103 HIS 0.006 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (15001) covalent geometry : angle 0.56488 / 0.29 (20366) hydrogen bonds : bond 0.04715 / 3.10 ( 704) hydrogen bonds : angle 4.64729 / 3.20 ( 1992) metal coordination : bond 0.01222 / 0.66 ( 5) metal coordination : angle 8.28971 / 4.23 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8560 (ttp80) cc_final: 0.7489 (tpt90) REVERT: B 152 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8025 (mptt) REVERT: B 156 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7986 (t0) REVERT: C 95 LYS cc_start: 0.8387 (tppp) cc_final: 0.7514 (ttpt) REVERT: C 170 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.6814 (pp30) REVERT: D 63 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.5304 (ptt-90) REVERT: D 111 ASN cc_start: 0.8252 (t0) cc_final: 0.7952 (t0) REVERT: F 119 MET cc_start: 0.2209 (tpt) cc_final: 0.1993 (mmp) REVERT: F 163 ARG cc_start: 0.5234 (mpp80) cc_final: 0.4340 (mmm160) REVERT: F 225 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.4900 (ttt) REVERT: F 318 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6207 (p90) outliers start: 47 outliers final: 38 residues processed: 198 average time/residue: 0.1020 time to fit residues: 30.8614 Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 383 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 138 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 154 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 GLN D 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.183497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133881 restraints weight = 15995.423| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.73 r_work: 0.2973 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15006 Z= 0.105 Angle : 0.536 16.754 20373 Z= 0.269 Chirality : 0.042 0.186 2300 Planarity : 0.004 0.053 2567 Dihedral : 6.313 58.301 2103 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 2.33 % Allowed : 17.89 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 1882 helix: 1.21 (0.18), residues: 846 sheet: 0.39 (0.40), residues: 167 loop : -0.64 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 46 TYR 0.013 0.001 TYR F 217 PHE 0.019 0.001 PHE D 50 TRP 0.020 0.001 TRP B 103 HIS 0.009 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (15001) covalent geometry : angle 0.51689 / 0.27 (20366) hydrogen bonds : bond 0.03805 / 2.52 ( 704) hydrogen bonds : angle 4.50989 / 3.10 ( 1992) metal coordination : bond 0.00907 / 0.49 ( 5) metal coordination : angle 7.59852 / 4.03 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3937.71 seconds wall clock time: 68 minutes 4.52 seconds (4084.52 seconds total)