Starting phenix.real_space_refine on Fri Jun 13 16:16:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrr_63340/06_2025/9lrr_63340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrr_63340/06_2025/9lrr_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_63340/06_2025/9lrr_63340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrr_63340/06_2025/9lrr_63340.map" model { file = "/net/cci-nas-00/data/ceres_data/9lrr_63340/06_2025/9lrr_63340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrr_63340/06_2025/9lrr_63340.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 32 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 9.61, per 1000 atoms: 0.63 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: 4.52 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.84 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: 5.00 Time building geometry restraints manager: 5.13 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: 0.010 Normalize map: mean=0, sd=1: 2.270 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.110 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 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 : 2.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP B 103 HIS 0.002 0.001 HIS F 97 PHE 0.014 0.001 PHE D 50 TYR 0.012 0.001 TYR D 141 ARG 0.004 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.12877 ( 744) hydrogen bonds : angle 5.35126 ( 2097) metal coordination : bond 0.00549 ( 7) metal coordination : angle 23.28663 ( 12) covalent geometry : bond 0.00347 (15446) covalent geometry : angle 0.60267 (20934) *********************** 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 : 1.631 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: 0.5483 (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: 1.4219 time to fit residues: 404.6845 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 : 1.641 ------------------------------------------------------------------------------- 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 159 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 285 GLN A 362 ASN C 143 ASN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.179907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119133 restraints weight = 12994.347| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.16 r_work: 0.2810 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 15453 Z= 0.371 Angle : 0.904 43.707 20946 Z= 0.437 Chirality : 0.057 0.194 2355 Planarity : 0.007 0.072 2616 Dihedral : 10.083 123.658 2377 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.30 % Allowed : 11.05 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 1909 helix: 0.80 (0.17), residues: 886 sheet: 0.34 (0.38), residues: 171 loop : -0.54 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 260 HIS 0.009 0.003 HIS A 223 PHE 0.028 0.004 PHE C 235 TYR 0.022 0.003 TYR D 141 ARG 0.010 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.08302 ( 744) hydrogen bonds : angle 5.20387 ( 2097) metal coordination : bond 0.02071 ( 7) metal coordination : angle 14.44823 ( 12) covalent geometry : bond 0.00920 (15446) covalent geometry : angle 0.83526 (20934) *********************** 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 229 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.626 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8066 (ptp90) cc_final: 0.7196 (mtm-85) REVERT: A 98 ASP cc_start: 0.8490 (m-30) cc_final: 0.8155 (m-30) REVERT: A 116 ASP cc_start: 0.7899 (m-30) cc_final: 0.7693 (m-30) REVERT: A 147 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 259 GLN cc_start: 0.7878 (mm110) cc_final: 0.7485 (mt0) REVERT: A 333 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7824 (mt-10) REVERT: A 433 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: B 42 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7884 (mtpt) REVERT: B 130 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7952 (mp) REVERT: B 154 GLU cc_start: 0.7884 (pm20) cc_final: 0.7460 (pm20) REVERT: B 380 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: B 406 LYS cc_start: 0.8580 (mtmt) cc_final: 0.7828 (mtmt) REVERT: C 48 LYS cc_start: 0.7635 (mmmt) cc_final: 0.6773 (mttt) REVERT: C 56 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7211 (mm-30) REVERT: C 58 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6780 (tttm) REVERT: C 84 VAL cc_start: 0.7151 (t) cc_final: 0.6865 (m) REVERT: D 99 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7804 (mtmt) REVERT: D 164 GLU cc_start: 0.8171 (tt0) cc_final: 0.7842 (tt0) REVERT: E 10 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6987 (tttt) REVERT: E 197 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5910 (pp30) REVERT: F 49 THR cc_start: 0.5928 (m) cc_final: 0.5687 (p) REVERT: F 118 ASP cc_start: 0.5534 (m-30) cc_final: 0.5232 (m-30) REVERT: F 214 MET cc_start: 0.5801 (ttm) cc_final: 0.5341 (ttm) REVERT: F 293 PHE cc_start: 0.6027 (m-80) cc_final: 0.5249 (m-80) REVERT: F 300 LYS cc_start: 0.6553 (mttm) cc_final: 0.6203 (mtmt) REVERT: F 302 LYS cc_start: 0.6428 (mmmt) cc_final: 0.5946 (mttp) REVERT: F 317 MET cc_start: 0.7057 (ptp) cc_final: 0.6025 (pp-130) REVERT: F 322 ASP cc_start: 0.6266 (m-30) cc_final: 0.5843 (m-30) REVERT: F 349 THR cc_start: 0.6460 (p) cc_final: 0.5988 (m) REVERT: F 382 MET cc_start: 0.5807 (pmm) cc_final: 0.5060 (ttp) REVERT: F 392 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7689 (mtmm) REVERT: F 399 GLU cc_start: 0.7178 (mp0) cc_final: 0.6849 (mm-30) outliers start: 36 outliers final: 11 residues processed: 211 average time/residue: 1.4960 time to fit residues: 343.9546 Evaluate side-chains 197 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 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 130 LEU 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 176 LEU 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 5 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 197 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 127 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 285 GLN B 13 HIS C 198 ASN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.185181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.125890 restraints weight = 13033.783| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.63 r_work: 0.2884 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15453 Z= 0.123 Angle : 0.583 32.169 20946 Z= 0.282 Chirality : 0.043 0.159 2355 Planarity : 0.005 0.045 2616 Dihedral : 9.095 96.591 2377 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.79 % Allowed : 12.07 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1909 helix: 1.32 (0.18), residues: 887 sheet: 0.59 (0.39), residues: 164 loop : -0.36 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 103 HIS 0.004 0.001 HIS C 216 PHE 0.017 0.001 PHE D 50 TYR 0.021 0.001 TYR D 141 ARG 0.003 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 744) hydrogen bonds : angle 4.65578 ( 2097) metal coordination : bond 0.01061 ( 7) metal coordination : angle 10.50258 ( 12) covalent geometry : bond 0.00269 (15446) covalent geometry : angle 0.52626 (20934) *********************** 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 227 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 46 ARG cc_start: 0.7826 (ptp90) cc_final: 0.7129 (mtm-85) REVERT: A 98 ASP cc_start: 0.8394 (m-30) cc_final: 0.8072 (m-30) REVERT: A 147 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8216 (mt-10) REVERT: A 259 GLN cc_start: 0.7930 (mm110) cc_final: 0.7540 (mt0) REVERT: A 333 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7805 (mt-10) REVERT: A 433 GLN cc_start: 0.8288 (mt0) cc_final: 0.7946 (mm-40) REVERT: B 42 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7871 (mtpt) REVERT: B 154 GLU cc_start: 0.7841 (pm20) cc_final: 0.7354 (pm20) REVERT: B 406 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7780 (mtmt) REVERT: C 48 LYS cc_start: 0.7528 (mmmt) cc_final: 0.6629 (mttt) REVERT: C 58 LYS cc_start: 0.7038 (mmtt) cc_final: 0.6790 (tttm) REVERT: C 84 VAL cc_start: 0.7111 (t) cc_final: 0.6901 (m) REVERT: D 99 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7690 (mtmt) REVERT: D 164 GLU cc_start: 0.8163 (tt0) cc_final: 0.7811 (tt0) REVERT: E 10 LYS cc_start: 0.7324 (ttpt) cc_final: 0.6997 (ttpt) REVERT: E 17 MET cc_start: 0.8409 (tpt) cc_final: 0.8011 (tpt) REVERT: F 49 THR cc_start: 0.5749 (m) cc_final: 0.5420 (p) REVERT: F 118 ASP cc_start: 0.5550 (OUTLIER) cc_final: 0.5303 (m-30) REVERT: F 214 MET cc_start: 0.5850 (ttm) cc_final: 0.5461 (ttm) REVERT: F 293 PHE cc_start: 0.5888 (m-80) cc_final: 0.5188 (m-80) REVERT: F 300 LYS cc_start: 0.6494 (mttm) cc_final: 0.6150 (mtmt) REVERT: F 302 LYS cc_start: 0.6419 (mmmt) cc_final: 0.6006 (mttp) REVERT: F 317 MET cc_start: 0.7052 (ptp) cc_final: 0.6026 (pp-130) REVERT: F 322 ASP cc_start: 0.6303 (m-30) cc_final: 0.5857 (m-30) REVERT: F 382 MET cc_start: 0.5711 (pmm) cc_final: 0.4996 (ttp) REVERT: F 399 GLU cc_start: 0.7106 (mp0) cc_final: 0.6751 (mm-30) outliers start: 28 outliers final: 9 residues processed: 214 average time/residue: 1.4843 time to fit residues: 347.0130 Evaluate side-chains 197 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 B residue 42 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 153 VAL 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 98 LEU Chi-restraints excluded: chain F residue 118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 161 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 153 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 285 GLN B 13 HIS F 142 ASN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.181309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138804 restraints weight = 13010.584| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.38 r_work: 0.3016 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15453 Z= 0.239 Angle : 0.696 26.682 20946 Z= 0.348 Chirality : 0.049 0.167 2355 Planarity : 0.006 0.055 2616 Dihedral : 9.694 124.584 2374 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.13 % Allowed : 11.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1909 helix: 0.93 (0.18), residues: 884 sheet: 0.40 (0.39), residues: 168 loop : -0.49 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 103 HIS 0.006 0.002 HIS B 328 PHE 0.022 0.002 PHE B 213 TYR 0.021 0.002 TYR D 141 ARG 0.006 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.06883 ( 744) hydrogen bonds : angle 4.90049 ( 2097) metal coordination : bond 0.01275 ( 7) metal coordination : angle 8.51041 ( 12) covalent geometry : bond 0.00581 (15446) covalent geometry : angle 0.66555 (20934) *********************** 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 235 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8654 (mp) REVERT: A 46 ARG cc_start: 0.8240 (ptp90) cc_final: 0.7329 (mtm-85) REVERT: A 98 ASP cc_start: 0.8552 (m-30) cc_final: 0.8248 (m-30) REVERT: A 147 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8408 (mt-10) REVERT: A 172 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: A 259 GLN cc_start: 0.8107 (mm110) cc_final: 0.7770 (mt0) REVERT: A 333 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8055 (mt-10) REVERT: A 433 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: A 444 LYS cc_start: 0.7861 (tppp) cc_final: 0.7641 (tttt) REVERT: B 42 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8073 (mtpt) REVERT: B 154 GLU cc_start: 0.8082 (pm20) cc_final: 0.7591 (pm20) REVERT: B 380 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: B 406 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7973 (mtmt) REVERT: C 48 LYS cc_start: 0.7897 (mmmt) cc_final: 0.6927 (mttt) REVERT: C 56 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7397 (mm-30) REVERT: D 145 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8210 (mp) REVERT: E 10 LYS cc_start: 0.7608 (ttpt) cc_final: 0.7309 (ttpp) REVERT: F 118 ASP cc_start: 0.5965 (OUTLIER) cc_final: 0.5612 (m-30) REVERT: F 214 MET cc_start: 0.6334 (ttm) cc_final: 0.6019 (ttm) REVERT: F 293 PHE cc_start: 0.6458 (m-80) cc_final: 0.5705 (m-80) REVERT: F 300 LYS cc_start: 0.6783 (mttm) cc_final: 0.6431 (mtmt) REVERT: F 302 LYS cc_start: 0.6612 (mmmt) cc_final: 0.6264 (mttm) REVERT: F 317 MET cc_start: 0.7134 (ptp) cc_final: 0.6298 (pp-130) REVERT: F 322 ASP cc_start: 0.6392 (m-30) cc_final: 0.6024 (m-30) REVERT: F 382 MET cc_start: 0.5867 (pmm) cc_final: 0.5120 (ttp) REVERT: F 399 GLU cc_start: 0.7274 (mp0) cc_final: 0.6981 (mm-30) outliers start: 49 outliers final: 21 residues processed: 213 average time/residue: 1.3415 time to fit residues: 313.6441 Evaluate side-chains 211 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 130 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 43 LEU 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 200 LYS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 115 MET 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 Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 133 optimal weight: 3.9990 chunk 136 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 155 optimal weight: 0.0000 chunk 77 optimal weight: 0.5980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 13 HIS F 142 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.185948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.127453 restraints weight = 13283.051| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.17 r_work: 0.2895 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15453 Z= 0.103 Angle : 0.522 22.714 20946 Z= 0.262 Chirality : 0.041 0.154 2355 Planarity : 0.004 0.043 2616 Dihedral : 8.889 89.620 2374 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.23 % Allowed : 12.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1909 helix: 1.41 (0.18), residues: 888 sheet: 0.57 (0.39), residues: 163 loop : -0.38 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS C 216 PHE 0.016 0.001 PHE D 50 TYR 0.020 0.001 TYR D 141 ARG 0.002 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 744) hydrogen bonds : angle 4.51432 ( 2097) metal coordination : bond 0.00656 ( 7) metal coordination : angle 7.42469 ( 12) covalent geometry : bond 0.00210 (15446) covalent geometry : angle 0.49111 (20934) *********************** 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 225 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 46 ARG cc_start: 0.7825 (ptp90) cc_final: 0.7071 (mtm-85) REVERT: A 98 ASP cc_start: 0.8395 (m-30) cc_final: 0.8078 (m-30) REVERT: A 147 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8223 (mt-10) REVERT: A 172 GLU cc_start: 0.7955 (tt0) cc_final: 0.7623 (mp0) REVERT: A 259 GLN cc_start: 0.7934 (mm110) cc_final: 0.7569 (mt0) REVERT: A 333 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7809 (mt-10) REVERT: A 433 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: B 42 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7898 (mtpt) REVERT: B 107 MET cc_start: 0.8575 (ttp) cc_final: 0.8358 (ttm) REVERT: B 154 GLU cc_start: 0.7771 (pm20) cc_final: 0.7310 (pm20) REVERT: B 406 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7771 (mtmt) REVERT: C 48 LYS cc_start: 0.7594 (mmmt) cc_final: 0.6692 (mttt) REVERT: D 99 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7751 (mtmt) REVERT: E 10 LYS cc_start: 0.7365 (ttpt) cc_final: 0.7042 (ttpp) REVERT: E 191 MET cc_start: 0.8789 (mtm) cc_final: 0.8523 (mtp) REVERT: F 118 ASP cc_start: 0.5476 (OUTLIER) cc_final: 0.5157 (m-30) REVERT: F 214 MET cc_start: 0.5562 (ttm) cc_final: 0.5311 (ttm) REVERT: F 293 PHE cc_start: 0.5921 (m-80) cc_final: 0.5145 (m-80) REVERT: F 300 LYS cc_start: 0.6537 (mttm) cc_final: 0.6183 (mtmt) REVERT: F 302 LYS cc_start: 0.6445 (mmmt) cc_final: 0.6193 (mttm) REVERT: F 317 MET cc_start: 0.7097 (ptp) cc_final: 0.6104 (pp-130) REVERT: F 322 ASP cc_start: 0.6256 (m-30) cc_final: 0.5858 (m-30) REVERT: F 382 MET cc_start: 0.5839 (pmm) cc_final: 0.5173 (ttp) REVERT: F 399 GLU cc_start: 0.7130 (mp0) cc_final: 0.6820 (mm-30) outliers start: 35 outliers final: 18 residues processed: 210 average time/residue: 1.4566 time to fit residues: 333.7115 Evaluate side-chains 207 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 318 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 43 LEU 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 99 LYS 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 118 ASP Chi-restraints excluded: chain F residue 259 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 8 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 13 HIS C 40 ASN ** 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 = 0.3953 r_free = 0.3953 target = 0.182664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.141063 restraints weight = 13117.758| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.40 r_work: 0.3021 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15453 Z= 0.226 Angle : 0.667 21.032 20946 Z= 0.337 Chirality : 0.048 0.171 2355 Planarity : 0.006 0.053 2616 Dihedral : 9.600 119.475 2374 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.87 % Allowed : 12.52 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1909 helix: 0.99 (0.18), residues: 885 sheet: 0.38 (0.39), residues: 168 loop : -0.48 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.006 0.002 HIS C 141 PHE 0.021 0.002 PHE B 213 TYR 0.021 0.002 TYR D 141 ARG 0.006 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.06657 ( 744) hydrogen bonds : angle 4.83402 ( 2097) metal coordination : bond 0.01128 ( 7) metal coordination : angle 6.74536 ( 12) covalent geometry : bond 0.00548 (15446) covalent geometry : angle 0.64733 (20934) *********************** 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 230 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 31 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8712 (mp) REVERT: A 46 ARG cc_start: 0.8215 (ptp90) cc_final: 0.7494 (ptp90) REVERT: A 98 ASP cc_start: 0.8586 (m-30) cc_final: 0.8307 (m-30) REVERT: A 147 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8470 (mt-10) REVERT: A 172 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: A 259 GLN cc_start: 0.8116 (mm110) cc_final: 0.7810 (mt0) REVERT: A 333 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8066 (mt-10) REVERT: A 433 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: A 444 LYS cc_start: 0.7919 (tppp) cc_final: 0.7685 (tttt) REVERT: B 42 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8091 (mtpt) REVERT: B 49 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8615 (t70) REVERT: B 154 GLU cc_start: 0.8042 (pm20) cc_final: 0.7592 (pm20) REVERT: B 380 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: B 406 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8013 (mtmt) REVERT: C 48 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7070 (mttt) REVERT: C 56 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: D 99 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8138 (mtmt) REVERT: E 1 MET cc_start: 0.6649 (tpp) cc_final: 0.6337 (tpt) REVERT: E 10 LYS cc_start: 0.7683 (ttpt) cc_final: 0.7305 (tttt) REVERT: F 118 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5650 (m-30) REVERT: F 214 MET cc_start: 0.6302 (ttm) cc_final: 0.6071 (ttm) REVERT: F 293 PHE cc_start: 0.6595 (m-80) cc_final: 0.5853 (m-80) REVERT: F 300 LYS cc_start: 0.6803 (mttm) cc_final: 0.6454 (mtmt) REVERT: F 302 LYS cc_start: 0.6538 (mmmt) cc_final: 0.6300 (mttm) REVERT: F 317 MET cc_start: 0.7235 (ptp) cc_final: 0.6440 (pp-130) REVERT: F 322 ASP cc_start: 0.6332 (m-30) cc_final: 0.6035 (m-30) REVERT: F 382 MET cc_start: 0.6003 (pmm) cc_final: 0.5272 (ttp) REVERT: F 399 GLU cc_start: 0.7371 (mp0) cc_final: 0.7085 (mm-30) outliers start: 45 outliers final: 21 residues processed: 212 average time/residue: 1.4204 time to fit residues: 330.1829 Evaluate side-chains 216 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 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 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 43 LEU 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 99 LYS 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 118 ASP Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 13 HIS C 40 ASN C 116 GLN F 142 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 = 0.3984 r_free = 0.3984 target = 0.185900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.125278 restraints weight = 13164.797| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.96 r_work: 0.2886 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15453 Z= 0.117 Angle : 0.533 18.025 20946 Z= 0.271 Chirality : 0.042 0.156 2355 Planarity : 0.005 0.043 2616 Dihedral : 9.038 95.573 2374 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.55 % Allowed : 12.71 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1909 helix: 1.28 (0.18), residues: 888 sheet: 0.61 (0.39), residues: 163 loop : -0.39 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 PHE 0.017 0.001 PHE D 50 TYR 0.021 0.001 TYR D 141 ARG 0.004 0.000 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 744) hydrogen bonds : angle 4.56077 ( 2097) metal coordination : bond 0.00593 ( 7) metal coordination : angle 5.93506 ( 12) covalent geometry : bond 0.00254 (15446) covalent geometry : angle 0.51379 (20934) *********************** 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 223 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8540 (mp) REVERT: A 46 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7080 (mtm-85) REVERT: A 98 ASP cc_start: 0.8397 (m-30) cc_final: 0.8083 (m-30) REVERT: A 172 GLU cc_start: 0.7936 (tt0) cc_final: 0.7584 (mp0) REVERT: A 259 GLN cc_start: 0.7904 (mm110) cc_final: 0.7580 (mt0) REVERT: A 333 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7770 (mt-10) REVERT: A 433 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: A 444 LYS cc_start: 0.7636 (tppp) cc_final: 0.7414 (tttt) REVERT: B 49 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8435 (t70) REVERT: B 154 GLU cc_start: 0.7732 (pm20) cc_final: 0.7250 (pm20) REVERT: B 380 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: B 406 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7753 (mtmt) REVERT: C 48 LYS cc_start: 0.7662 (mmmt) cc_final: 0.6670 (mttt) REVERT: C 56 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: D 99 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7738 (mtmt) REVERT: E 1 MET cc_start: 0.6328 (tpp) cc_final: 0.6095 (tpt) REVERT: E 10 LYS cc_start: 0.7330 (ttpt) cc_final: 0.7001 (ttpp) REVERT: F 118 ASP cc_start: 0.5432 (m-30) cc_final: 0.5094 (m-30) REVERT: F 214 MET cc_start: 0.5476 (ttm) cc_final: 0.5139 (ttm) REVERT: F 293 PHE cc_start: 0.5981 (m-80) cc_final: 0.5134 (m-80) REVERT: F 300 LYS cc_start: 0.6610 (mttm) cc_final: 0.6242 (mtmt) REVERT: F 302 LYS cc_start: 0.6500 (mmmt) cc_final: 0.6244 (mttm) REVERT: F 317 MET cc_start: 0.7068 (ptp) cc_final: 0.6074 (pp-130) REVERT: F 322 ASP cc_start: 0.6173 (m-30) cc_final: 0.5798 (m-30) REVERT: F 382 MET cc_start: 0.5779 (pmm) cc_final: 0.5193 (ttp) REVERT: F 399 GLU cc_start: 0.7137 (mp0) cc_final: 0.6834 (mm-30) outliers start: 40 outliers final: 22 residues processed: 210 average time/residue: 1.5321 time to fit residues: 351.4558 Evaluate side-chains 208 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 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 43 LEU 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 200 LYS 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 99 LYS 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 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 11 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 13 HIS C 40 ASN ** 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 = 0.4089 r_free = 0.4089 target = 0.191524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136110 restraints weight = 13826.922| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.46 r_work: 0.3295 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2188 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= 0.201 Angle : 0.625 17.447 20946 Z= 0.318 Chirality : 0.046 0.165 2355 Planarity : 0.005 0.050 2616 Dihedral : 9.472 112.000 2374 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.36 % Allowed : 12.96 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1909 helix: 1.05 (0.18), residues: 886 sheet: 0.39 (0.38), residues: 174 loop : -0.46 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 103 HIS 0.007 0.001 HIS B 328 PHE 0.021 0.002 PHE B 213 TYR 0.021 0.002 TYR D 141 ARG 0.004 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.06195 ( 744) hydrogen bonds : angle 4.74546 ( 2097) metal coordination : bond 0.00934 ( 7) metal coordination : angle 5.72457 ( 12) covalent geometry : bond 0.00482 (15446) covalent geometry : angle 0.61002 (20934) *********************** 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 217 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7782 (mp) REVERT: A 31 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 46 ARG cc_start: 0.7984 (ptp90) cc_final: 0.7345 (ptp90) REVERT: A 98 ASP cc_start: 0.8458 (m-30) cc_final: 0.8183 (m-30) REVERT: A 172 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: A 333 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7953 (mt-10) REVERT: A 433 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: A 444 LYS cc_start: 0.7800 (tppp) cc_final: 0.7563 (tttt) REVERT: B 42 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7668 (mtpp) REVERT: B 49 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8565 (t70) REVERT: B 154 GLU cc_start: 0.7751 (pm20) cc_final: 0.7293 (pm20) REVERT: B 380 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: B 406 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7929 (mtmt) REVERT: C 48 LYS cc_start: 0.7916 (mmmt) cc_final: 0.6997 (mttt) REVERT: C 56 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: D 99 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7940 (mtmt) REVERT: E 1 MET cc_start: 0.6428 (tpp) cc_final: 0.6137 (tpt) REVERT: E 10 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7129 (tttt) REVERT: F 118 ASP cc_start: 0.5677 (m-30) cc_final: 0.5343 (m-30) REVERT: F 214 MET cc_start: 0.5483 (ttm) cc_final: 0.5127 (ttm) REVERT: F 289 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.5299 (ttt90) REVERT: F 293 PHE cc_start: 0.6122 (m-80) cc_final: 0.5209 (m-80) REVERT: F 300 LYS cc_start: 0.6717 (mttm) cc_final: 0.6341 (mtmt) REVERT: F 302 LYS cc_start: 0.6527 (mmmt) cc_final: 0.6264 (mttm) REVERT: F 317 MET cc_start: 0.7107 (ptp) cc_final: 0.6130 (pp-130) REVERT: F 322 ASP cc_start: 0.6203 (m-30) cc_final: 0.5850 (m-30) REVERT: F 382 MET cc_start: 0.5835 (pmm) cc_final: 0.5390 (ptm) REVERT: F 399 GLU cc_start: 0.7142 (mp0) cc_final: 0.6850 (mm-30) outliers start: 37 outliers final: 20 residues processed: 205 average time/residue: 1.4634 time to fit residues: 327.8646 Evaluate side-chains 205 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 42 LYS 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 43 LEU 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 99 LYS 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 259 THR Chi-restraints excluded: chain F residue 289 ARG 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 8 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 13 HIS C 40 ASN C 116 GLN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.191477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136955 restraints weight = 13831.991| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.47 r_work: 0.3223 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15453 Z= 0.197 Angle : 0.625 16.542 20946 Z= 0.319 Chirality : 0.046 0.168 2355 Planarity : 0.005 0.048 2616 Dihedral : 9.567 112.278 2374 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.55 % Allowed : 12.90 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1909 helix: 0.96 (0.18), residues: 892 sheet: 0.33 (0.38), residues: 174 loop : -0.53 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 PHE 0.020 0.002 PHE B 213 TYR 0.022 0.002 TYR D 141 ARG 0.004 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.06134 ( 744) hydrogen bonds : angle 4.75892 ( 2097) metal coordination : bond 0.00841 ( 7) metal coordination : angle 5.52739 ( 12) covalent geometry : bond 0.00475 (15446) covalent geometry : angle 0.61150 (20934) *********************** 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 219 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7802 (mp) REVERT: A 31 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 46 ARG cc_start: 0.8045 (ptp90) cc_final: 0.7404 (ptp90) REVERT: A 98 ASP cc_start: 0.8503 (m-30) cc_final: 0.8230 (m-30) REVERT: A 172 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: A 333 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8008 (mt-10) REVERT: A 433 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: A 444 LYS cc_start: 0.7781 (tppp) cc_final: 0.7545 (tttt) REVERT: B 42 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7713 (mtpp) REVERT: B 49 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8590 (t70) REVERT: B 154 GLU cc_start: 0.7788 (pm20) cc_final: 0.7328 (pm20) REVERT: B 380 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: B 406 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7949 (mtmt) REVERT: C 48 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7088 (mttt) REVERT: C 56 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: C 68 ASN cc_start: 0.7203 (m-40) cc_final: 0.6972 (m110) REVERT: D 99 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8017 (mtmt) REVERT: E 1 MET cc_start: 0.6386 (tpp) cc_final: 0.6109 (tpt) REVERT: E 10 LYS cc_start: 0.7568 (ttpt) cc_final: 0.7186 (tttt) REVERT: F 118 ASP cc_start: 0.5674 (OUTLIER) cc_final: 0.5258 (m-30) REVERT: F 293 PHE cc_start: 0.6249 (m-80) cc_final: 0.5262 (m-80) REVERT: F 300 LYS cc_start: 0.6776 (mttm) cc_final: 0.6381 (mtmt) REVERT: F 302 LYS cc_start: 0.6449 (mmmt) cc_final: 0.6197 (mttm) REVERT: F 317 MET cc_start: 0.7109 (ptp) cc_final: 0.6131 (pp-130) REVERT: F 322 ASP cc_start: 0.6217 (m-30) cc_final: 0.5847 (m-30) REVERT: F 382 MET cc_start: 0.5808 (pmm) cc_final: 0.5235 (ttp) REVERT: F 399 GLU cc_start: 0.7220 (mp0) cc_final: 0.6916 (mm-30) outliers start: 40 outliers final: 19 residues processed: 206 average time/residue: 1.4242 time to fit residues: 321.3027 Evaluate side-chains 208 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 42 LYS Chi-restraints excluded: chain B residue 49 ASP 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 B residue 406 LYS Chi-restraints excluded: chain C residue 43 LEU 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 99 LYS 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 118 ASP 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 107 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 156 optimal weight: 30.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 285 GLN B 13 HIS C 40 ASN F 140 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 = 0.4105 r_free = 0.4105 target = 0.193188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137991 restraints weight = 13858.774| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.43 r_work: 0.3258 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15453 Z= 0.135 Angle : 0.554 15.468 20946 Z= 0.282 Chirality : 0.043 0.163 2355 Planarity : 0.005 0.044 2616 Dihedral : 9.146 97.024 2374 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.11 % Allowed : 13.47 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1909 helix: 1.20 (0.18), residues: 887 sheet: 0.51 (0.39), residues: 169 loop : -0.46 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 PHE 0.017 0.002 PHE D 50 TYR 0.022 0.001 TYR D 141 ARG 0.003 0.000 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.05177 ( 744) hydrogen bonds : angle 4.58960 ( 2097) metal coordination : bond 0.00547 ( 7) metal coordination : angle 5.35708 ( 12) covalent geometry : bond 0.00306 (15446) covalent geometry : angle 0.53879 (20934) ********************** 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 217 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.685 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 46 ARG cc_start: 0.7939 (ptp90) cc_final: 0.7344 (ptp90) REVERT: A 98 ASP cc_start: 0.8469 (m-30) cc_final: 0.8193 (m-30) REVERT: A 172 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: A 333 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8020 (mt-10) REVERT: A 433 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: A 444 LYS cc_start: 0.7779 (tppp) cc_final: 0.7540 (tttt) REVERT: B 42 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7716 (mtpp) REVERT: B 49 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8516 (t70) REVERT: B 154 GLU cc_start: 0.7761 (pm20) cc_final: 0.7310 (pm20) REVERT: B 380 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: B 406 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7917 (mtmt) REVERT: C 48 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7021 (mttt) REVERT: C 56 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: D 99 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7973 (mtmt) REVERT: D 145 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8151 (mp) REVERT: E 1 MET cc_start: 0.6410 (tpp) cc_final: 0.6204 (tpt) REVERT: E 10 LYS cc_start: 0.7561 (ttpt) cc_final: 0.7174 (tttt) REVERT: F 118 ASP cc_start: 0.5700 (OUTLIER) cc_final: 0.5281 (m-30) REVERT: F 293 PHE cc_start: 0.6170 (m-80) cc_final: 0.5229 (m-80) REVERT: F 300 LYS cc_start: 0.6774 (mttm) cc_final: 0.6381 (mtmt) REVERT: F 302 LYS cc_start: 0.6508 (mmmt) cc_final: 0.6285 (mttm) REVERT: F 317 MET cc_start: 0.7087 (ptp) cc_final: 0.6172 (pp-130) REVERT: F 322 ASP cc_start: 0.6199 (m-30) cc_final: 0.5934 (m-30) REVERT: F 382 MET cc_start: 0.5718 (pmm) cc_final: 0.5185 (ttp) REVERT: F 399 GLU cc_start: 0.7191 (mp0) cc_final: 0.6889 (mm-30) outliers start: 33 outliers final: 18 residues processed: 205 average time/residue: 1.9640 time to fit residues: 439.5130 Evaluate side-chains 208 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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 384 MET Chi-restraints excluded: chain A residue 433 GLN 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 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 43 LEU 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 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 99 LYS 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 118 ASP 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 81 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 0.0370 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 285 GLN B 13 HIS C 40 ASN C 116 GLN F 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.196150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142619 restraints weight = 13856.511| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.48 r_work: 0.3301 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15453 Z= 0.099 Angle : 0.501 13.718 20946 Z= 0.255 Chirality : 0.041 0.156 2355 Planarity : 0.004 0.043 2616 Dihedral : 8.598 87.263 2374 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.85 % Allowed : 14.18 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1909 helix: 1.47 (0.18), residues: 890 sheet: 0.61 (0.39), residues: 169 loop : -0.34 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.016 0.001 PHE D 50 TYR 0.021 0.001 TYR D 141 ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 744) hydrogen bonds : angle 4.37005 ( 2097) metal coordination : bond 0.00435 ( 7) metal coordination : angle 5.07360 ( 12) covalent geometry : bond 0.00207 (15446) covalent geometry : angle 0.48602 (20934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12981.94 seconds wall clock time: 225 minutes 38.88 seconds (13538.88 seconds total)