Starting phenix.real_space_refine on Fri Jul 3 17:06:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrr_63340/07_2026/9lrr_63340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrr_63340/07_2026/9lrr_63340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lrr_63340/07_2026/9lrr_63340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrr_63340/07_2026/9lrr_63340.map" model { file = "/net/cci-nas-00/data/ceres_data/9lrr_63340/07_2026/9lrr_63340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrr_63340/07_2026/9lrr_63340.cif" } resolution = 2.68 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= 0.175 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 6 5.49 5 S 92 5.16 5 C 9787 2.51 5 N 2449 2.21 5 O 2795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s 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: 15134 Number of models: 1 Model: "" Number of chains: 15 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': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3178 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} 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: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1580 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} 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: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'FMN': 1, 'IQT': 1, 'LMT': 1, 'PEE': 1, 'RBF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'FAD': 1, 'FES': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9320 SG CYS D 112 45.429 75.575 87.644 1.00130.90 S ATOM 10286 SG CYS E 26 43.833 72.660 86.389 1.00135.05 S ATOM 8681 SG CYS D 29 45.380 69.714 90.781 1.00128.23 S ATOM 11008 SG CYS E 120 46.919 72.962 92.106 1.00135.48 S ATOM 12111 SG CYS F 76 45.390 92.243 58.545 1.00276.23 S ATOM 12130 SG CYS F 79 48.930 93.417 59.622 1.00272.04 S ATOM 12369 SG CYS F 111 49.395 92.052 62.704 1.00262.59 S Time building chain proxies: 2.82, per 1000 atoms: 0.19 Number of scatterers: 15134 At special positions: 0 Unit cell: (90.64, 128.48, 154, 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 6 15.00 O 2795 8.00 N 2449 7.00 C 9787 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: 1.05 Conformation dependent library (CDL) restraints added in 640.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb=" FES F 502 " pdb="FE2 FES F 502 " - pdb=" SG CYS F 111 " pdb="FE1 FES F 502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F 502 " - pdb=" SG CYS F 76 " Number of angles added : 12 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 13 sheets defined 55.5% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 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 106 through 113 removed outlier: 3.652A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.629A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.698A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 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 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.772A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.973A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.645A 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 Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 445 removed outlier: 3.896A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 11 through 14 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.526A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.715A 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 98 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.655A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.218A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.562A pdb=" N ALA B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 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 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.837A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.521A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.060A 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 375 removed outlier: 3.799A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.804A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.792A 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: 3.601A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 3.643A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.152A pdb=" N GLN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 99 removed outlier: 3.853A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.765A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.729A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.600A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'D' and resid 6 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.761A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 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 Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.585A pdb=" N LEU D 107 " --> pdb=" O PHE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.808A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.528A 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: 3.617A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.502A 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 178 through 182 removed outlier: 3.598A pdb=" N MET D 181 " --> pdb=" O ASN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.299A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.707A 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 2 through 13 Processing helix chain 'E' and resid 16 through 22 removed outlier: 3.555A pdb=" N PHE E 21 " --> pdb=" O MET E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 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 102 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.707A pdb=" N ILE E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 135 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 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 Processing helix chain 'F' and resid 54 through 61 removed outlier: 3.522A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 97 removed outlier: 3.675A pdb=" N LEU F 95 " --> pdb=" O PRO F 92 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP F 96 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.653A pdb=" N ARG F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 130 removed outlier: 4.042A pdb=" N GLU F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 129 " --> pdb=" O GLU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 158 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 193 removed outlier: 5.940A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 199 removed outlier: 3.536A pdb=" N ARG F 199 " --> pdb=" O ASN F 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 196 through 199' Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.544A pdb=" N SER F 251 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.608A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.505A pdb=" N MET F 317 " --> pdb=" O LYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 343 through 347 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'F' and resid 380 through 393 removed outlier: 4.138A pdb=" N ALA F 386 " --> pdb=" O MET F 382 " (cutoff:3.500A) 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: 6.429A 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: 3.840A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.693A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.062A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.695A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.646A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.676A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 47 through 49 removed outlier: 6.704A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 213 removed outlier: 6.618A pdb=" N TYR F 167 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU F 171 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR F 136 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN F 140 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLU F 149 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN F 142 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE F 147 " --> pdb=" O ASN F 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB4, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.903A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL F 277 " --> pdb=" O TYR F 376 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N CYS F 378 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE F 279 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ASP F 404 " --> pdb=" O TYR F 375 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET F 377 " --> pdb=" O ASP F 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 744 hydrogen bonds defined for protein. 2097 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: 2.00 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 6107 1.40 - 1.60: 9166 1.60 - 1.80: 79 1.80 - 2.00: 86 2.00 - 2.20: 8 Bond restraints: 15446 Sorted by residual: bond pdb=" C12 IQT B 505 " pdb=" C13 IQT B 505 " ideal model delta sigma weight residual 1.454 1.278 0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C1 IQT B 505 " pdb=" C7 IQT B 505 " ideal model delta sigma weight residual 1.479 1.376 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.57e+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 1.55e+01 bond pdb=" C6 IQT B 505 " pdb=" C7 IQT B 505 " ideal model delta sigma weight residual 1.333 1.398 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 15441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 20434 1.78 - 3.57: 456 3.57 - 5.35: 41 5.35 - 7.14: 2 7.14 - 8.92: 1 Bond angle restraints: 20934 Sorted by residual: angle pdb=" C SER D 102 " pdb=" CA SER D 102 " pdb=" CB SER D 102 " ideal model delta sigma weight residual 116.34 110.44 5.90 1.40e+00 5.10e-01 1.77e+01 angle pdb=" N VAL D 165 " pdb=" CA VAL D 165 " pdb=" C VAL D 165 " ideal model delta sigma weight residual 111.62 108.38 3.24 7.90e-01 1.60e+00 1.68e+01 angle pdb=" N PHE A 136 " pdb=" CA PHE A 136 " pdb=" CB PHE A 136 " ideal model delta sigma weight residual 114.17 110.07 4.10 1.14e+00 7.69e-01 1.29e+01 angle pdb=" CB MET F 382 " pdb=" CG MET F 382 " pdb=" SD MET F 382 " ideal model delta sigma weight residual 112.70 121.62 -8.92 3.00e+00 1.11e-01 8.85e+00 angle pdb=" C VAL A 424 " pdb=" CA VAL A 424 " pdb=" CB VAL A 424 " ideal model delta sigma weight residual 112.19 108.81 3.38 1.15e+00 7.56e-01 8.63e+00 ... (remaining 20929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 9009 34.66 - 69.33: 189 69.33 - 103.99: 16 103.99 - 138.65: 0 138.65 - 173.31: 3 Dihedral angle restraints: 9217 sinusoidal: 3778 harmonic: 5439 Sorted by residual: dihedral pdb=" C14 IQT B 505 " pdb=" C15 IQT B 505 " pdb=" C16 IQT B 505 " pdb=" C17 IQT B 505 " ideal model delta sinusoidal sigma weight residual 87.07 -99.62 -173.31 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C14 IQT B 505 " pdb=" C15 IQT B 505 " pdb=" C16 IQT B 505 " pdb=" O4 IQT B 505 " ideal model delta sinusoidal sigma weight residual 157.21 -29.56 -173.23 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C13 IQT B 505 " pdb=" C14 IQT B 505 " pdb=" C15 IQT B 505 " pdb=" C16 IQT B 505 " ideal model delta sinusoidal sigma weight residual 108.58 -52.23 160.81 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 9214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1509 0.031 - 0.062: 469 0.062 - 0.093: 236 0.093 - 0.124: 128 0.124 - 0.155: 13 Chirality restraints: 2355 Sorted by residual: chirality pdb=" CB THR C 249 " pdb=" CA THR C 249 " pdb=" OG1 THR C 249 " pdb=" CG2 THR C 249 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA PRO F 381 " pdb=" N PRO F 381 " pdb=" C PRO F 381 " pdb=" CB PRO F 381 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE F 154 " pdb=" N ILE F 154 " pdb=" C ILE F 154 " pdb=" CB ILE F 154 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2352 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 IQT B 505 " -0.205 2.00e-02 2.50e+03 1.88e-01 3.52e+02 pdb=" C13 IQT B 505 " 0.210 2.00e-02 2.50e+03 pdb=" C14 IQT B 505 " 0.163 2.00e-02 2.50e+03 pdb=" C15 IQT B 505 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IQT B 505 " 0.084 2.00e-02 2.50e+03 1.84e-01 3.39e+02 pdb=" C11 IQT B 505 " -0.234 2.00e-02 2.50e+03 pdb=" C12 IQT B 505 " 0.252 2.00e-02 2.50e+03 pdb=" C13 IQT B 505 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 IQT B 505 " -0.086 2.00e-02 2.50e+03 6.94e-02 6.02e+01 pdb=" C8 IQT B 505 " 0.039 2.00e-02 2.50e+03 pdb=" C9 IQT B 505 " -0.064 2.00e-02 2.50e+03 pdb=" N1 IQT B 505 " 0.105 2.00e-02 2.50e+03 pdb=" O5 IQT B 505 " 0.006 2.00e-02 2.50e+03 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 87 2.58 - 3.16: 12549 3.16 - 3.74: 22510 3.74 - 4.32: 33122 4.32 - 4.90: 55761 Nonbonded interactions: 124029 Sorted by model distance: nonbonded pdb=" OG1 THR C 225 " pdb=" O3P FMN C 301 " model vdw 1.995 3.040 nonbonded pdb=" O PRO F 31 " pdb=" OG1 THR F 32 " model vdw 2.022 3.040 nonbonded pdb=" N GLU F 206 " pdb=" OE1 GLU F 206 " model vdw 2.053 3.120 nonbonded pdb=" O HOH A 503 " pdb=" O HOH A 518 " model vdw 2.106 3.040 nonbonded pdb=" O HOH A 508 " pdb=" O HOH A 514 " model vdw 2.126 3.040 ... (remaining 124024 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: 2.750 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.370 Find NCS groups from input model: 0.070 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:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 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 0.176 15453 Z= 0.179 Angle : 0.821 68.519 20946 Z= 0.349 Chirality : 0.043 0.155 2355 Planarity : 0.006 0.188 2616 Dihedral : 14.414 173.314 5747 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.06 % Allowed : 10.03 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1909 helix: 1.75 (0.18), residues: 868 sheet: 0.38 (0.36), residues: 185 loop : -0.26 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 104 TYR 0.012 0.001 TYR D 141 PHE 0.014 0.001 PHE D 50 TRP 0.019 0.001 TRP B 103 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (15446) covalent geometry : angle 0.60267 / 0.34 (20934) hydrogen bonds : bond 0.12877 / 7.93 ( 744) hydrogen bonds : angle 5.35126 / 3.77 ( 2097) metal coordination : bond 0.00549 / 0.32 ( 7) metal coordination : angle 23.28663 / 15.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.6031 (ptp90) cc_final: 0.5226 (mtm-85) REVERT: A 50 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6915 (mt-10) REVERT: A 59 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7271 (mt-10) REVERT: A 98 ASP cc_start: 0.7019 (m-30) cc_final: 0.6675 (m-30) REVERT: A 116 ASP cc_start: 0.5688 (m-30) cc_final: 0.5388 (m-30) REVERT: A 147 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6340 (mt-10) REVERT: A 186 THR cc_start: 0.6623 (m) cc_final: 0.6353 (p) REVERT: A 202 GLN cc_start: 0.7027 (mm110) cc_final: 0.6598 (mm110) REVERT: A 212 ASP cc_start: 0.6368 (t0) cc_final: 0.5559 (m-30) REVERT: A 259 GLN cc_start: 0.5945 (mm110) cc_final: 0.5052 (mt0) REVERT: A 289 SER cc_start: 0.7317 (t) cc_final: 0.7078 (m) REVERT: A 333 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5474 (mt-10) REVERT: A 433 GLN cc_start: 0.4957 (mt0) cc_final: 0.4123 (mm110) REVERT: B 42 LYS cc_start: 0.6331 (mmtm) cc_final: 0.5358 (mtpt) REVERT: B 72 MET cc_start: 0.6426 (mtm) cc_final: 0.6213 (mtm) REVERT: B 154 GLU cc_start: 0.6383 (pm20) cc_final: 0.5594 (pm20) REVERT: B 256 GLN cc_start: 0.5293 (mm110) cc_final: 0.4796 (mt0) REVERT: B 262 ASP cc_start: 0.5568 (m-30) cc_final: 0.5213 (m-30) REVERT: B 281 MET cc_start: 0.5695 (mtm) cc_final: 0.5390 (mtt) REVERT: B 318 ASP cc_start: 0.7203 (m-30) cc_final: 0.5935 (p0) REVERT: B 406 LYS cc_start: 0.4876 (mtmt) cc_final: 0.4220 (mtmt) REVERT: C 48 LYS cc_start: 0.4642 (mmmt) cc_final: 0.4034 (mttt) REVERT: C 68 ASN cc_start: 0.5567 (m-40) cc_final: 0.5297 (m110) REVERT: C 84 VAL cc_start: 0.5739 (t) cc_final: 0.5328 (m) REVERT: C 116 GLN cc_start: 0.5869 (mt0) cc_final: 0.4868 (mm-40) REVERT: E 10 LYS cc_start: 0.3680 (ttpt) cc_final: 0.3385 (tttt) REVERT: E 27 THR cc_start: 0.5604 (m) cc_final: 0.5376 (p) REVERT: E 191 MET cc_start: 0.6186 (mtm) cc_final: 0.5979 (mtp) REVERT: E 197 GLN cc_start: 0.3067 (OUTLIER) cc_final: 0.2189 (mt0) REVERT: F 107 GLU cc_start: 0.5215 (mm-30) cc_final: 0.4597 (mm-30) REVERT: F 113 VAL cc_start: 0.5075 (t) cc_final: 0.3839 (t) REVERT: F 300 LYS cc_start: 0.5887 (mttm) cc_final: 0.5598 (mtmt) REVERT: F 302 LYS cc_start: 0.5851 (mmmt) cc_final: 0.5482 (mttp) REVERT: F 317 MET cc_start: 0.6929 (ptp) cc_final: 0.5652 (pp-130) REVERT: F 349 THR cc_start: 0.6093 (p) cc_final: 0.5807 (m) REVERT: F 382 MET cc_start: 0.5421 (pmm) cc_final: 0.4818 (ttp) REVERT: F 392 LYS cc_start: 0.5885 (mmmt) cc_final: 0.5653 (mtmm) REVERT: F 399 GLU cc_start: 0.6000 (mp0) cc_final: 0.5679 (mm-30) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.5829 time to fit residues: 166.2736 Evaluate side-chains 200 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 197 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 285 GLN A 362 ASN C 143 ASN C 160 ASN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.185234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.144613 restraints weight = 12963.231| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.49 r_work: 0.3024 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15453 Z= 0.163 Angle : 0.672 40.495 20946 Z= 0.314 Chirality : 0.045 0.158 2355 Planarity : 0.005 0.045 2616 Dihedral : 8.965 106.206 2377 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.72 % Allowed : 11.43 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.98 (0.19), residues: 1909 helix: 1.59 (0.18), residues: 880 sheet: 0.68 (0.38), residues: 165 loop : -0.30 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 55 TYR 0.020 0.002 TYR D 141 PHE 0.020 0.002 PHE D 50 TRP 0.023 0.002 TRP B 103 HIS 0.005 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (15446) covalent geometry : angle 0.58583 / 0.31 (20934) hydrogen bonds : bond 0.05630 / 3.63 ( 744) hydrogen bonds : angle 4.77094 / 3.36 ( 2097) metal coordination : bond 0.01297 / 0.67 ( 7) metal coordination : angle 13.77527 / 9.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7875 (ptp90) cc_final: 0.7328 (mtm-85) REVERT: A 50 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 59 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8779 (mt-10) REVERT: A 98 ASP cc_start: 0.8557 (m-30) cc_final: 0.8249 (m-30) REVERT: A 116 ASP cc_start: 0.7998 (m-30) cc_final: 0.7717 (m-30) REVERT: A 147 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 172 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: A 212 ASP cc_start: 0.8598 (t0) cc_final: 0.8336 (m-30) REVERT: A 259 GLN cc_start: 0.8095 (mm110) cc_final: 0.7678 (mt0) REVERT: A 333 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7811 (mt-10) REVERT: A 433 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7720 (pp30) REVERT: A 444 LYS cc_start: 0.7782 (tppp) cc_final: 0.7551 (tttt) REVERT: B 42 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7890 (mtpt) REVERT: B 154 GLU cc_start: 0.7916 (pm20) cc_final: 0.7530 (pm20) REVERT: B 262 ASP cc_start: 0.8747 (m-30) cc_final: 0.8546 (m-30) REVERT: B 281 MET cc_start: 0.8856 (mtm) cc_final: 0.8543 (mtt) REVERT: B 380 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: B 406 LYS cc_start: 0.8625 (mtmt) cc_final: 0.7989 (mtmt) REVERT: C 48 LYS cc_start: 0.7610 (mmmt) cc_final: 0.6826 (mttt) REVERT: C 58 LYS cc_start: 0.7163 (mmtt) cc_final: 0.6722 (tttm) REVERT: C 84 VAL cc_start: 0.6987 (t) cc_final: 0.6678 (m) REVERT: D 99 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7861 (mtmt) REVERT: E 10 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7084 (tttt) REVERT: F 49 THR cc_start: 0.6133 (m) cc_final: 0.5873 (p) REVERT: F 214 MET cc_start: 0.5906 (ttm) cc_final: 0.5526 (ttm) REVERT: F 293 PHE cc_start: 0.5881 (m-80) cc_final: 0.5277 (m-80) REVERT: F 300 LYS cc_start: 0.6617 (mttm) cc_final: 0.6276 (mtmt) REVERT: F 302 LYS cc_start: 0.6423 (mmmt) cc_final: 0.5977 (mtmm) REVERT: F 317 MET cc_start: 0.7096 (ptp) cc_final: 0.6055 (pp-130) REVERT: F 322 ASP cc_start: 0.6383 (m-30) cc_final: 0.5876 (m-30) REVERT: F 382 MET cc_start: 0.5751 (pmm) cc_final: 0.4972 (ttp) REVERT: F 399 GLU cc_start: 0.7098 (mp0) cc_final: 0.6784 (mm-30) outliers start: 27 outliers final: 8 residues processed: 218 average time/residue: 0.5415 time to fit residues: 129.3395 Evaluate side-chains 203 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 171 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 285 GLN B 13 HIS B 324 ASN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.186452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.127238 restraints weight = 13162.784| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.63 r_work: 0.2885 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15453 Z= 0.117 Angle : 0.561 30.632 20946 Z= 0.271 Chirality : 0.042 0.155 2355 Planarity : 0.004 0.044 2616 Dihedral : 8.653 98.549 2374 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.23 % Allowed : 11.24 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1909 helix: 1.61 (0.18), residues: 886 sheet: 0.76 (0.39), residues: 163 loop : -0.28 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100 TYR 0.019 0.001 TYR D 141 PHE 0.017 0.001 PHE D 50 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (15446) covalent geometry : angle 0.50725 / 0.27 (20934) hydrogen bonds : bond 0.04806 / 3.11 ( 744) hydrogen bonds : angle 4.54522 / 3.19 ( 2097) metal coordination : bond 0.00967 / 0.55 ( 7) metal coordination : angle 10.06872 / 6.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 46 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7247 (mtm-85) REVERT: A 50 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 59 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8685 (mt-10) REVERT: A 98 ASP cc_start: 0.8371 (m-30) cc_final: 0.8039 (m-30) REVERT: A 147 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8214 (mt-10) REVERT: A 172 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: A 212 ASP cc_start: 0.8522 (t0) cc_final: 0.8254 (m-30) REVERT: A 259 GLN cc_start: 0.7934 (mm110) cc_final: 0.7536 (mt0) REVERT: A 333 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7700 (mt-10) REVERT: A 433 GLN cc_start: 0.8308 (mt0) cc_final: 0.7535 (pp30) REVERT: A 444 LYS cc_start: 0.7663 (tppp) cc_final: 0.7439 (tttt) REVERT: B 42 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7793 (mtpt) REVERT: B 49 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8359 (t70) REVERT: B 154 GLU cc_start: 0.7839 (pm20) cc_final: 0.7363 (pm20) REVERT: B 406 LYS cc_start: 0.8486 (mtmt) cc_final: 0.7835 (mtmt) REVERT: C 48 LYS cc_start: 0.7446 (mmmt) cc_final: 0.6605 (mttt) REVERT: C 56 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7297 (mm-30) REVERT: C 84 VAL cc_start: 0.7092 (t) cc_final: 0.6885 (m) REVERT: D 99 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7644 (mtmt) REVERT: E 10 LYS cc_start: 0.7318 (ttpt) cc_final: 0.6890 (tttt) REVERT: E 191 MET cc_start: 0.8761 (mtm) cc_final: 0.8448 (mtp) REVERT: F 49 THR cc_start: 0.5796 (m) cc_final: 0.5467 (p) REVERT: F 118 ASP cc_start: 0.5414 (m-30) cc_final: 0.5212 (m-30) REVERT: F 214 MET cc_start: 0.5614 (ttm) cc_final: 0.5223 (ttm) REVERT: F 245 MET cc_start: 0.4444 (tpp) cc_final: 0.3748 (tpt) REVERT: F 293 PHE cc_start: 0.5732 (m-80) cc_final: 0.5139 (m-80) REVERT: F 300 LYS cc_start: 0.6512 (mttm) cc_final: 0.6148 (mtmt) REVERT: F 302 LYS cc_start: 0.6459 (mmmt) cc_final: 0.6012 (mttp) REVERT: F 317 MET cc_start: 0.7021 (ptp) cc_final: 0.5986 (pp-130) REVERT: F 322 ASP cc_start: 0.6265 (m-30) cc_final: 0.5842 (m-30) REVERT: F 382 MET cc_start: 0.5745 (pmm) cc_final: 0.5016 (ttp) REVERT: F 399 GLU cc_start: 0.7046 (mp0) cc_final: 0.6754 (mm-30) outliers start: 35 outliers final: 13 residues processed: 214 average time/residue: 0.5623 time to fit residues: 131.9778 Evaluate side-chains 204 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 22 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 183 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 285 GLN B 13 HIS ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.184725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141874 restraints weight = 13131.076| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.45 r_work: 0.3023 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15453 Z= 0.145 Angle : 0.574 23.945 20946 Z= 0.287 Chirality : 0.044 0.157 2355 Planarity : 0.005 0.043 2616 Dihedral : 8.792 91.808 2374 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.55 % Allowed : 11.24 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.88 (0.19), residues: 1909 helix: 1.42 (0.18), residues: 888 sheet: 0.80 (0.39), residues: 163 loop : -0.29 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.020 0.002 TYR D 141 PHE 0.017 0.002 PHE D 50 TRP 0.022 0.002 TRP B 103 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (15446) covalent geometry : angle 0.54267 / 0.29 (20934) hydrogen bonds : bond 0.05362 / 3.46 ( 744) hydrogen bonds : angle 4.60640 / 3.24 ( 2097) metal coordination : bond 0.00862 / 0.55 ( 7) metal coordination : angle 7.78550 / 5.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 46 ARG cc_start: 0.8035 (ptp90) cc_final: 0.7227 (mtm-85) REVERT: A 98 ASP cc_start: 0.8506 (m-30) cc_final: 0.8188 (m-30) REVERT: A 147 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8350 (mt-10) REVERT: A 172 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: A 212 ASP cc_start: 0.8637 (t0) cc_final: 0.8398 (m-30) REVERT: A 259 GLN cc_start: 0.8042 (mm110) cc_final: 0.7644 (mt0) REVERT: A 333 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7919 (mt-10) REVERT: A 433 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: A 444 LYS cc_start: 0.7802 (tppp) cc_final: 0.7542 (tttt) REVERT: B 42 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7940 (mtpt) REVERT: B 154 GLU cc_start: 0.7902 (pm20) cc_final: 0.7399 (pm20) REVERT: B 380 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: B 406 LYS cc_start: 0.8599 (mtmt) cc_final: 0.7916 (mtmt) REVERT: C 48 LYS cc_start: 0.7656 (mmmt) cc_final: 0.6770 (mttt) REVERT: C 56 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: D 145 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8118 (mp) REVERT: E 1 MET cc_start: 0.6471 (tpp) cc_final: 0.6078 (tpt) REVERT: E 10 LYS cc_start: 0.7523 (ttpt) cc_final: 0.7118 (tttt) REVERT: F 107 GLU cc_start: 0.6240 (tp30) cc_final: 0.5926 (mm-30) REVERT: F 118 ASP cc_start: 0.5552 (OUTLIER) cc_final: 0.5243 (m-30) REVERT: F 214 MET cc_start: 0.5855 (ttm) cc_final: 0.5541 (ttm) REVERT: F 245 MET cc_start: 0.4697 (tpp) cc_final: 0.4444 (mmt) REVERT: F 293 PHE cc_start: 0.5823 (m-80) cc_final: 0.5186 (m-80) REVERT: F 300 LYS cc_start: 0.6562 (mttm) cc_final: 0.6222 (mtmt) REVERT: F 302 LYS cc_start: 0.6553 (mmmt) cc_final: 0.6250 (mttm) REVERT: F 317 MET cc_start: 0.7094 (ptp) cc_final: 0.6093 (pp-130) REVERT: F 322 ASP cc_start: 0.6250 (m-30) cc_final: 0.5843 (m-30) REVERT: F 382 MET cc_start: 0.5853 (pmm) cc_final: 0.5096 (ttp) REVERT: F 399 GLU cc_start: 0.7162 (mp0) cc_final: 0.6860 (mm-30) outliers start: 40 outliers final: 14 residues processed: 213 average time/residue: 0.5549 time to fit residues: 129.1485 Evaluate side-chains 204 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 153 optimal weight: 0.0980 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 285 GLN B 13 HIS C 40 ASN F 142 ASN F 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.183666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.141341 restraints weight = 13202.410| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.47 r_work: 0.3010 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15453 Z= 0.165 Angle : 0.592 22.291 20946 Z= 0.298 Chirality : 0.044 0.163 2355 Planarity : 0.005 0.048 2616 Dihedral : 9.007 102.309 2374 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.00 % Allowed : 11.43 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.72 (0.19), residues: 1909 helix: 1.27 (0.18), residues: 886 sheet: 0.67 (0.39), residues: 169 loop : -0.34 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 55 TYR 0.021 0.002 TYR D 141 PHE 0.018 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15446) covalent geometry : angle 0.56643 / 0.30 (20934) hydrogen bonds : bond 0.05690 / 3.67 ( 744) hydrogen bonds : angle 4.67266 / 3.29 ( 2097) metal coordination : bond 0.00866 / 0.53 ( 7) metal coordination : angle 7.21920 / 5.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8550 (mp) REVERT: A 46 ARG cc_start: 0.8006 (ptp90) cc_final: 0.7297 (mtm-85) REVERT: A 98 ASP cc_start: 0.8434 (m-30) cc_final: 0.8190 (m-30) REVERT: A 172 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: A 433 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: A 444 LYS cc_start: 0.7919 (tppp) cc_final: 0.7668 (tttt) REVERT: B 49 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8420 (t70) REVERT: B 154 GLU cc_start: 0.7883 (pm20) cc_final: 0.7556 (pm20) REVERT: B 380 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: B 406 LYS cc_start: 0.8481 (mtmt) cc_final: 0.7877 (mtmt) REVERT: C 48 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7250 (mttt) REVERT: C 56 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: D 145 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8182 (mp) REVERT: E 10 LYS cc_start: 0.7582 (ttpt) cc_final: 0.7270 (tttt) REVERT: F 214 MET cc_start: 0.6485 (ttm) cc_final: 0.6262 (ttm) REVERT: F 293 PHE cc_start: 0.6667 (m-80) cc_final: 0.6445 (m-80) REVERT: F 317 MET cc_start: 0.6875 (ptp) cc_final: 0.6666 (pp-130) REVERT: F 382 MET cc_start: 0.5828 (pmm) cc_final: 0.5255 (ttp) REVERT: F 399 GLU cc_start: 0.7351 (mp0) cc_final: 0.7106 (mm-30) outliers start: 47 outliers final: 21 residues processed: 216 average time/residue: 0.5646 time to fit residues: 133.9097 Evaluate side-chains 207 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 187 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 259 GLN A 285 GLN B 13 HIS C 40 ASN F 142 ASN F 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.183848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124281 restraints weight = 13123.559| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.74 r_work: 0.2893 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15453 Z= 0.123 Angle : 0.534 19.035 20946 Z= 0.270 Chirality : 0.042 0.157 2355 Planarity : 0.005 0.045 2616 Dihedral : 8.807 94.089 2374 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.30 % Allowed : 12.26 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.78 (0.19), residues: 1909 helix: 1.35 (0.18), residues: 893 sheet: 0.68 (0.39), residues: 169 loop : -0.35 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.021 0.001 TYR D 141 PHE 0.016 0.001 PHE D 50 TRP 0.021 0.002 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15446) covalent geometry : angle 0.51196 / 0.27 (20934) hydrogen bonds : bond 0.04966 / 3.21 ( 744) hydrogen bonds : angle 4.54245 / 3.19 ( 2097) metal coordination : bond 0.00632 / 0.42 ( 7) metal coordination : angle 6.35693 / 4.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 46 ARG cc_start: 0.7929 (ptp90) cc_final: 0.7026 (mtm-85) REVERT: A 98 ASP cc_start: 0.8372 (m-30) cc_final: 0.8034 (m-30) REVERT: A 172 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: A 212 ASP cc_start: 0.8528 (t0) cc_final: 0.8308 (m-30) REVERT: A 433 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: A 444 LYS cc_start: 0.7596 (tppp) cc_final: 0.7379 (tttt) REVERT: B 49 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8415 (t70) REVERT: B 154 GLU cc_start: 0.7722 (pm20) cc_final: 0.7262 (pm20) REVERT: B 380 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: B 406 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7758 (mtmt) REVERT: C 48 LYS cc_start: 0.7550 (mmmt) cc_final: 0.6625 (mttt) REVERT: C 56 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: E 1 MET cc_start: 0.6359 (tpp) cc_final: 0.6132 (tpt) REVERT: E 10 LYS cc_start: 0.7320 (ttpt) cc_final: 0.6895 (tttt) REVERT: F 293 PHE cc_start: 0.5858 (m-80) cc_final: 0.5180 (m-80) REVERT: F 317 MET cc_start: 0.7081 (ptp) cc_final: 0.6074 (pp-130) REVERT: F 382 MET cc_start: 0.5817 (pmm) cc_final: 0.5333 (ptm) REVERT: F 399 GLU cc_start: 0.7100 (mp0) cc_final: 0.6783 (mm-30) outliers start: 36 outliers final: 20 residues processed: 207 average time/residue: 0.5929 time to fit residues: 134.8120 Evaluate side-chains 204 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 142 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 28 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 chunk 70 optimal weight: 0.2980 chunk 168 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 285 GLN B 13 HIS C 40 ASN F 142 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.187212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.144592 restraints weight = 13075.747| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.44 r_work: 0.3001 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15453 Z= 0.096 Angle : 0.489 16.624 20946 Z= 0.249 Chirality : 0.041 0.152 2355 Planarity : 0.004 0.041 2616 Dihedral : 8.511 87.208 2374 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.92 % Allowed : 12.45 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.95 (0.19), residues: 1909 helix: 1.53 (0.18), residues: 900 sheet: 0.73 (0.39), residues: 169 loop : -0.32 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.020 0.001 TYR D 141 PHE 0.015 0.001 PHE D 50 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.10 (15446) covalent geometry : angle 0.46946 / 0.25 (20934) hydrogen bonds : bond 0.04190 / 2.74 ( 744) hydrogen bonds : angle 4.39110 / 3.08 ( 2097) metal coordination : bond 0.00474 / 0.34 ( 7) metal coordination : angle 5.77682 / 3.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 46 ARG cc_start: 0.8077 (ptp90) cc_final: 0.7288 (mtm-85) REVERT: A 98 ASP cc_start: 0.8458 (m-30) cc_final: 0.8146 (m-30) REVERT: A 172 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: A 433 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: A 444 LYS cc_start: 0.7774 (tppp) cc_final: 0.7560 (tttt) REVERT: B 42 LYS cc_start: 0.8480 (mtpt) cc_final: 0.7926 (mtpp) REVERT: B 49 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8285 (t70) REVERT: B 154 GLU cc_start: 0.7895 (pm20) cc_final: 0.7511 (pm20) REVERT: B 406 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7917 (mtmt) REVERT: C 48 LYS cc_start: 0.7797 (mmmt) cc_final: 0.6958 (mttt) REVERT: C 56 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: D 145 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8137 (mp) REVERT: E 1 MET cc_start: 0.6290 (tpp) cc_final: 0.6004 (tpt) REVERT: E 10 LYS cc_start: 0.7622 (ttpt) cc_final: 0.7219 (tttt) REVERT: E 191 MET cc_start: 0.8773 (mtm) cc_final: 0.8492 (mtp) REVERT: F 293 PHE cc_start: 0.5948 (m-80) cc_final: 0.5289 (m-80) REVERT: F 317 MET cc_start: 0.7114 (ptp) cc_final: 0.6225 (pp-130) REVERT: F 382 MET cc_start: 0.5919 (pmm) cc_final: 0.5426 (ptm) REVERT: F 399 GLU cc_start: 0.7200 (mp0) cc_final: 0.6883 (mm-30) outliers start: 30 outliers final: 16 residues processed: 203 average time/residue: 0.6302 time to fit residues: 140.8623 Evaluate side-chains 199 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 259 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN B 13 HIS C 40 ASN F 142 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.192750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137395 restraints weight = 13895.585| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.43 r_work: 0.3246 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15453 Z= 0.195 Angle : 0.607 16.694 20946 Z= 0.309 Chirality : 0.046 0.161 2355 Planarity : 0.005 0.049 2616 Dihedral : 9.099 106.174 2374 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.30 % Allowed : 12.20 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.60 (0.19), residues: 1909 helix: 1.15 (0.18), residues: 900 sheet: 0.61 (0.39), residues: 169 loop : -0.41 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 55 TYR 0.020 0.002 TYR D 141 PHE 0.019 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (15446) covalent geometry : angle 0.59235 / 0.31 (20934) hydrogen bonds : bond 0.05970 / 3.85 ( 744) hydrogen bonds : angle 4.67978 / 3.29 ( 2097) metal coordination : bond 0.00935 / 0.53 ( 7) metal coordination : angle 5.60801 / 3.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 31 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8646 (mp) REVERT: A 46 ARG cc_start: 0.8094 (ptp90) cc_final: 0.7401 (ptp90) REVERT: A 98 ASP cc_start: 0.8483 (m-30) cc_final: 0.8178 (m-30) REVERT: A 172 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: A 433 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: A 444 LYS cc_start: 0.7737 (tppp) cc_final: 0.7477 (tttt) REVERT: B 42 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7912 (mtpp) REVERT: B 49 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8594 (t70) REVERT: B 154 GLU cc_start: 0.7766 (pm20) cc_final: 0.7317 (pm20) REVERT: B 380 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: B 406 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7935 (mtmt) REVERT: C 48 LYS cc_start: 0.7936 (mmmt) cc_final: 0.7005 (mttt) REVERT: C 56 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: E 1 MET cc_start: 0.6305 (tpp) cc_final: 0.5989 (tpt) REVERT: E 10 LYS cc_start: 0.7523 (ttpt) cc_final: 0.7143 (tttt) REVERT: F 293 PHE cc_start: 0.6037 (m-80) cc_final: 0.5347 (m-80) REVERT: F 317 MET cc_start: 0.7088 (ptp) cc_final: 0.6180 (pp-130) REVERT: F 382 MET cc_start: 0.5967 (pmm) cc_final: 0.5482 (ptm) REVERT: F 399 GLU cc_start: 0.7204 (mp0) cc_final: 0.6902 (mm-30) outliers start: 36 outliers final: 19 residues processed: 202 average time/residue: 0.6307 time to fit residues: 139.8798 Evaluate side-chains 205 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.0020 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN B 13 HIS C 40 ASN F 142 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.193247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137918 restraints weight = 13810.167| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.45 r_work: 0.3251 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15453 Z= 0.152 Angle : 0.564 15.966 20946 Z= 0.288 Chirality : 0.044 0.161 2355 Planarity : 0.005 0.045 2616 Dihedral : 9.048 101.619 2374 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.23 % Allowed : 12.39 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.60 (0.19), residues: 1909 helix: 1.16 (0.18), residues: 900 sheet: 0.61 (0.39), residues: 169 loop : -0.40 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.021 0.001 TYR D 141 PHE 0.017 0.002 PHE B 213 TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (15446) covalent geometry : angle 0.54878 / 0.29 (20934) hydrogen bonds : bond 0.05460 / 3.52 ( 744) hydrogen bonds : angle 4.62396 / 3.25 ( 2097) metal coordination : bond 0.00691 / 0.41 ( 7) metal coordination : angle 5.44078 / 3.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 46 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7419 (ptp90) REVERT: A 98 ASP cc_start: 0.8486 (m-30) cc_final: 0.8191 (m-30) REVERT: A 172 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: A 433 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: A 444 LYS cc_start: 0.7729 (tppp) cc_final: 0.7469 (tttt) REVERT: B 42 LYS cc_start: 0.8490 (mtpt) cc_final: 0.7911 (mtpp) REVERT: B 49 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8549 (t70) REVERT: B 154 GLU cc_start: 0.7784 (pm20) cc_final: 0.7337 (pm20) REVERT: B 380 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: B 406 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7924 (mtmt) REVERT: C 48 LYS cc_start: 0.7915 (mmmt) cc_final: 0.6996 (mttt) REVERT: C 56 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: D 145 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8134 (mp) REVERT: E 1 MET cc_start: 0.6321 (tpp) cc_final: 0.6109 (tpt) REVERT: E 10 LYS cc_start: 0.7514 (ttpt) cc_final: 0.7136 (tttt) REVERT: E 191 MET cc_start: 0.8802 (mtm) cc_final: 0.8514 (mtp) REVERT: F 293 PHE cc_start: 0.6088 (m-80) cc_final: 0.5370 (m-80) REVERT: F 317 MET cc_start: 0.7093 (ptp) cc_final: 0.6186 (pp-130) REVERT: F 382 MET cc_start: 0.5927 (pmm) cc_final: 0.5460 (ptm) REVERT: F 399 GLU cc_start: 0.7215 (mp0) cc_final: 0.6916 (mm-30) outliers start: 35 outliers final: 21 residues processed: 198 average time/residue: 0.6302 time to fit residues: 137.2795 Evaluate side-chains 203 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN B 13 HIS C 40 ASN F 142 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.191893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137391 restraints weight = 13903.229| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.50 r_work: 0.3303 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15453 Z= 0.213 Angle : 0.638 16.077 20946 Z= 0.325 Chirality : 0.047 0.163 2355 Planarity : 0.005 0.053 2616 Dihedral : 9.428 113.906 2374 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.11 % Allowed : 12.64 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1909 helix: 0.95 (0.18), residues: 898 sheet: 0.39 (0.38), residues: 176 loop : -0.47 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 55 TYR 0.020 0.002 TYR D 141 PHE 0.019 0.002 PHE B 213 TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (15446) covalent geometry : angle 0.62460 / 0.32 (20934) hydrogen bonds : bond 0.06304 / 4.06 ( 744) hydrogen bonds : angle 4.76213 / 3.36 ( 2097) metal coordination : bond 0.00997 / 0.53 ( 7) metal coordination : angle 5.44676 / 3.79 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8632 (mp) REVERT: A 46 ARG cc_start: 0.8154 (ptp90) cc_final: 0.7440 (ptp90) REVERT: A 98 ASP cc_start: 0.8468 (m-30) cc_final: 0.8188 (m-30) REVERT: A 172 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: A 433 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: A 444 LYS cc_start: 0.7780 (tppp) cc_final: 0.7534 (tttt) REVERT: B 42 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7911 (mtpp) REVERT: B 49 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8571 (t70) REVERT: B 154 GLU cc_start: 0.7710 (pm20) cc_final: 0.7253 (pm20) REVERT: B 380 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: B 406 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7919 (mtmt) REVERT: C 48 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7079 (mttt) REVERT: C 56 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: C 68 ASN cc_start: 0.7146 (m-40) cc_final: 0.6943 (m110) REVERT: D 145 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8136 (mp) REVERT: E 10 LYS cc_start: 0.7497 (ttpt) cc_final: 0.7122 (tttt) REVERT: F 293 PHE cc_start: 0.6108 (m-80) cc_final: 0.5334 (m-80) REVERT: F 317 MET cc_start: 0.7048 (ptp) cc_final: 0.6172 (pp-130) REVERT: F 382 MET cc_start: 0.5769 (pmm) cc_final: 0.5239 (ttp) REVERT: F 399 GLU cc_start: 0.7191 (mp0) cc_final: 0.6888 (mm-30) outliers start: 33 outliers final: 20 residues processed: 204 average time/residue: 0.6213 time to fit residues: 138.9693 Evaluate side-chains 206 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 7 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 178 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 285 GLN B 13 HIS C 40 ASN C 116 GLN F 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.194485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139679 restraints weight = 13869.982| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.48 r_work: 0.3338 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15453 Z= 0.117 Angle : 0.526 15.097 20946 Z= 0.270 Chirality : 0.042 0.155 2355 Planarity : 0.004 0.044 2616 Dihedral : 8.994 95.432 2374 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.98 % Allowed : 13.03 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.67 (0.19), residues: 1909 helix: 1.24 (0.18), residues: 898 sheet: 0.59 (0.39), residues: 171 loop : -0.39 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.021 0.001 TYR D 141 PHE 0.016 0.001 PHE D 50 TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (15446) covalent geometry : angle 0.51081 / 0.27 (20934) hydrogen bonds : bond 0.04890 / 3.17 ( 744) hydrogen bonds : angle 4.56087 / 3.20 ( 2097) metal coordination : bond 0.00509 / 0.31 ( 7) metal coordination : angle 5.30829 / 3.65 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5529.33 seconds wall clock time: 94 minutes 51.99 seconds (5691.99 seconds total)