Starting phenix.real_space_refine on Sat May 17 03:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrr_63340/05_2025/9lrr_63340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrr_63340/05_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_63340/05_2025/9lrr_63340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrr_63340/05_2025/9lrr_63340.map" model { file = "/net/cci-nas-00/data/ceres_data/9lrr_63340/05_2025/9lrr_63340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrr_63340/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.12, per 1000 atoms: 0.60 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: 4.25 Conformation dependent library (CDL) restraints added in 1.9 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: 1.61 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: 5.05 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 6107 1.40 - 1.60: 9166 1.60 - 1.80: 79 1.80 - 2.00: 86 2.00 - 2.20: 8 Bond restraints: 15446 Sorted by residual: bond pdb=" C12 IQT B 505 " pdb=" C13 IQT B 505 " ideal model delta sigma weight residual 1.454 1.278 0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C1 IQT B 505 " pdb=" C7 IQT B 505 " ideal model delta sigma weight residual 1.479 1.376 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C6 IQT B 505 " pdb=" C7 IQT B 505 " ideal model delta sigma weight residual 1.333 1.398 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 15441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 20434 1.78 - 3.57: 456 3.57 - 5.35: 41 5.35 - 7.14: 2 7.14 - 8.92: 1 Bond angle restraints: 20934 Sorted by residual: angle pdb=" C SER D 102 " pdb=" CA SER D 102 " pdb=" CB SER D 102 " ideal model delta sigma weight residual 116.34 110.44 5.90 1.40e+00 5.10e-01 1.77e+01 angle pdb=" N VAL D 165 " pdb=" CA VAL D 165 " pdb=" C VAL D 165 " ideal model delta sigma weight residual 111.62 108.38 3.24 7.90e-01 1.60e+00 1.68e+01 angle pdb=" N PHE A 136 " pdb=" CA PHE A 136 " pdb=" CB PHE A 136 " ideal model delta sigma weight residual 114.17 110.07 4.10 1.14e+00 7.69e-01 1.29e+01 angle pdb=" CB MET F 382 " pdb=" CG MET F 382 " pdb=" SD MET F 382 " ideal model delta sigma weight residual 112.70 121.62 -8.92 3.00e+00 1.11e-01 8.85e+00 angle pdb=" C VAL A 424 " pdb=" CA VAL A 424 " pdb=" CB VAL A 424 " ideal model delta sigma weight residual 112.19 108.81 3.38 1.15e+00 7.56e-01 8.63e+00 ... (remaining 20929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 9009 34.66 - 69.33: 189 69.33 - 103.99: 16 103.99 - 138.65: 0 138.65 - 173.31: 3 Dihedral angle restraints: 9217 sinusoidal: 3778 harmonic: 5439 Sorted by residual: dihedral pdb=" C14 IQT B 505 " pdb=" C15 IQT B 505 " pdb=" C16 IQT B 505 " pdb=" C17 IQT B 505 " ideal model delta sinusoidal sigma weight residual 87.07 -99.62 -173.31 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C14 IQT B 505 " pdb=" C15 IQT B 505 " pdb=" C16 IQT B 505 " pdb=" O4 IQT B 505 " ideal model delta sinusoidal sigma weight residual 157.21 -29.56 -173.23 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C13 IQT B 505 " pdb=" C14 IQT B 505 " pdb=" C15 IQT B 505 " pdb=" C16 IQT B 505 " ideal model delta sinusoidal sigma weight residual 108.58 -52.23 160.81 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 9214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1509 0.031 - 0.062: 469 0.062 - 0.093: 236 0.093 - 0.124: 128 0.124 - 0.155: 13 Chirality restraints: 2355 Sorted by residual: chirality pdb=" CB THR C 249 " pdb=" CA THR C 249 " pdb=" OG1 THR C 249 " pdb=" CG2 THR C 249 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA PRO F 381 " pdb=" N PRO F 381 " pdb=" C PRO F 381 " pdb=" CB PRO F 381 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE F 154 " pdb=" N ILE F 154 " pdb=" C ILE F 154 " pdb=" CB ILE F 154 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2352 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 IQT B 505 " -0.205 2.00e-02 2.50e+03 1.88e-01 3.52e+02 pdb=" C13 IQT B 505 " 0.210 2.00e-02 2.50e+03 pdb=" C14 IQT B 505 " 0.163 2.00e-02 2.50e+03 pdb=" C15 IQT B 505 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IQT B 505 " 0.084 2.00e-02 2.50e+03 1.84e-01 3.39e+02 pdb=" C11 IQT B 505 " -0.234 2.00e-02 2.50e+03 pdb=" C12 IQT B 505 " 0.252 2.00e-02 2.50e+03 pdb=" C13 IQT B 505 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 IQT B 505 " -0.086 2.00e-02 2.50e+03 6.94e-02 6.02e+01 pdb=" C8 IQT B 505 " 0.039 2.00e-02 2.50e+03 pdb=" C9 IQT B 505 " -0.064 2.00e-02 2.50e+03 pdb=" N1 IQT B 505 " 0.105 2.00e-02 2.50e+03 pdb=" O5 IQT B 505 " 0.006 2.00e-02 2.50e+03 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 87 2.58 - 3.16: 12549 3.16 - 3.74: 22510 3.74 - 4.32: 33122 4.32 - 4.90: 55761 Nonbonded interactions: 124029 Sorted by model distance: nonbonded pdb=" OG1 THR C 225 " pdb=" O3P FMN C 301 " model vdw 1.995 3.040 nonbonded pdb=" O PRO F 31 " pdb=" OG1 THR F 32 " model vdw 2.022 3.040 nonbonded pdb=" N GLU F 206 " pdb=" OE1 GLU F 206 " model vdw 2.053 3.120 nonbonded pdb=" O HOH A 503 " pdb=" O HOH A 518 " model vdw 2.106 3.040 nonbonded pdb=" O HOH A 508 " pdb=" O HOH A 514 " model vdw 2.126 3.040 ... (remaining 124024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.100 Set scattering table: 0.140 Process input model: 38.480 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- 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 : 1.749 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: 1.3674 time to fit residues: 389.5401 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 : 1.546 ------------------------------------------------------------------------------- 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** C 198 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 = 0.3932 r_free = 0.3932 target = 0.180432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120801 restraints weight = 13001.850| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.50 r_work: 0.2968 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 15453 Z= 0.374 Angle : 0.904 42.757 20946 Z= 0.438 Chirality : 0.058 0.206 2355 Planarity : 0.007 0.071 2616 Dihedral : 10.154 125.844 2377 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.30 % Allowed : 11.11 % Favored : 86.59 % 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: 0.18 (0.19), residues: 1909 helix: 0.78 (0.17), residues: 886 sheet: 0.32 (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 327 HIS 0.010 0.003 HIS A 223 PHE 0.028 0.004 PHE C 235 TYR 0.022 0.003 TYR D 141 ARG 0.009 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.08363 ( 744) hydrogen bonds : angle 5.21399 ( 2097) metal coordination : bond 0.02082 ( 7) metal coordination : angle 14.16708 ( 12) covalent geometry : bond 0.00927 (15446) covalent geometry : angle 0.83841 (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 230 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8014 (ptp90) cc_final: 0.7113 (mtm-85) REVERT: A 98 ASP cc_start: 0.8476 (m-30) cc_final: 0.8139 (m-30) REVERT: A 116 ASP cc_start: 0.7847 (m-30) cc_final: 0.7628 (m-30) REVERT: A 147 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 259 GLN cc_start: 0.7778 (mm110) cc_final: 0.7430 (mt0) REVERT: A 333 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7781 (mt-10) REVERT: A 433 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: B 42 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7894 (mtpt) REVERT: B 107 MET cc_start: 0.8625 (ttp) cc_final: 0.8406 (ttm) REVERT: B 154 GLU cc_start: 0.7756 (pm20) cc_final: 0.7304 (pm20) REVERT: B 380 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: B 406 LYS cc_start: 0.8563 (mtmt) cc_final: 0.7809 (mtmt) REVERT: C 48 LYS cc_start: 0.7601 (mmmt) cc_final: 0.6748 (mttt) REVERT: C 56 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: C 58 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6821 (tttm) REVERT: C 84 VAL cc_start: 0.7167 (t) cc_final: 0.6894 (m) REVERT: D 99 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7770 (mtmt) REVERT: D 164 GLU cc_start: 0.8158 (tt0) cc_final: 0.7837 (tt0) REVERT: E 10 LYS cc_start: 0.7321 (ttpt) cc_final: 0.6928 (tttt) REVERT: E 17 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8182 (tpt) REVERT: E 197 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6105 (pp30) REVERT: F 49 THR cc_start: 0.5949 (m) cc_final: 0.5706 (p) REVERT: F 118 ASP cc_start: 0.5557 (m-30) cc_final: 0.5283 (m-30) REVERT: F 214 MET cc_start: 0.5784 (ttm) cc_final: 0.5325 (ttm) REVERT: F 293 PHE cc_start: 0.5956 (m-80) cc_final: 0.5171 (m-80) REVERT: F 300 LYS cc_start: 0.6504 (mttm) cc_final: 0.6152 (mtmt) REVERT: F 302 LYS cc_start: 0.6405 (mmmt) cc_final: 0.5929 (mttp) REVERT: F 317 MET cc_start: 0.7043 (ptp) cc_final: 0.6020 (pp-130) REVERT: F 322 ASP cc_start: 0.6236 (m-30) cc_final: 0.5805 (m-30) REVERT: F 349 THR cc_start: 0.6420 (p) cc_final: 0.5957 (m) REVERT: F 382 MET cc_start: 0.5776 (pmm) cc_final: 0.5075 (ttp) REVERT: F 392 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7664 (mtmm) REVERT: F 399 GLU cc_start: 0.7126 (mp0) cc_final: 0.6797 (mm-30) outliers start: 36 outliers final: 12 residues processed: 212 average time/residue: 1.3710 time to fit residues: 317.4147 Evaluate side-chains 198 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 17 MET 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: 0.9990 chunk 132 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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 = 0.3976 r_free = 0.3976 target = 0.185130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137745 restraints weight = 13036.422| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.60 r_work: 0.2944 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15453 Z= 0.118 Angle : 0.584 32.600 20946 Z= 0.281 Chirality : 0.042 0.157 2355 Planarity : 0.005 0.044 2616 Dihedral : 9.128 96.859 2377 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.85 % Allowed : 12.13 % Favored : 86.02 % 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: 0.72 (0.19), residues: 1909 helix: 1.32 (0.18), residues: 887 sheet: 0.59 (0.39), residues: 164 loop : -0.37 (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 C 216 PHE 0.018 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 0.05001 ( 744) hydrogen bonds : angle 4.66188 ( 2097) metal coordination : bond 0.01042 ( 7) metal coordination : angle 10.64588 ( 12) covalent geometry : bond 0.00251 (15446) covalent geometry : angle 0.52542 (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: 29 poor density : 198 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8599 (mp) REVERT: A 46 ARG cc_start: 0.7970 (ptp90) cc_final: 0.7270 (mtm-85) REVERT: A 98 ASP cc_start: 0.8498 (m-30) cc_final: 0.8194 (m-30) REVERT: A 147 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8357 (mt-10) REVERT: A 259 GLN cc_start: 0.8070 (mm110) cc_final: 0.7711 (mt0) REVERT: A 333 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7991 (mt-10) REVERT: A 433 GLN cc_start: 0.8446 (mt0) cc_final: 0.8171 (tt0) REVERT: A 444 LYS cc_start: 0.7804 (tppp) cc_final: 0.7557 (tttt) REVERT: B 42 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8005 (mtpt) REVERT: B 107 MET cc_start: 0.8697 (ttp) cc_final: 0.8475 (ttm) REVERT: B 154 GLU cc_start: 0.8045 (pm20) cc_final: 0.7547 (pm20) REVERT: B 406 LYS cc_start: 0.8599 (mtmt) cc_final: 0.7936 (mtmt) REVERT: C 48 LYS cc_start: 0.7768 (mmmt) cc_final: 0.6881 (mttt) REVERT: C 58 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6868 (tttm) REVERT: C 84 VAL cc_start: 0.7175 (t) cc_final: 0.6971 (m) REVERT: D 99 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7915 (mtmt) REVERT: D 164 GLU cc_start: 0.8317 (tt0) cc_final: 0.7978 (tt0) REVERT: E 10 LYS cc_start: 0.7592 (ttpt) cc_final: 0.7280 (ttpt) REVERT: F 49 THR cc_start: 0.5737 (m) cc_final: 0.5407 (p) REVERT: F 118 ASP cc_start: 0.5752 (OUTLIER) cc_final: 0.5491 (m-30) REVERT: F 214 MET cc_start: 0.6150 (ttm) cc_final: 0.5751 (ttm) REVERT: F 293 PHE cc_start: 0.6094 (m-80) cc_final: 0.5430 (m-80) REVERT: F 300 LYS cc_start: 0.6617 (mttm) cc_final: 0.6272 (mtmt) REVERT: F 302 LYS cc_start: 0.6444 (mmmt) cc_final: 0.6170 (mttm) REVERT: F 317 MET cc_start: 0.7116 (ptp) cc_final: 0.6148 (pp-130) REVERT: F 322 ASP cc_start: 0.6352 (m-30) cc_final: 0.5906 (m-30) REVERT: F 382 MET cc_start: 0.5782 (pmm) cc_final: 0.5032 (ttp) REVERT: F 399 GLU cc_start: 0.7211 (mp0) cc_final: 0.6867 (mm-30) outliers start: 29 outliers final: 9 residues processed: 213 average time/residue: 1.3557 time to fit residues: 316.7323 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 : 1.585 ------------------------------------------------------------------------------- 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: 0.4980 chunk 138 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 chunk 153 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 overall best weight: 2.0982 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.183264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.120516 restraints weight = 13002.577| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.28 r_work: 0.2848 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15453 Z= 0.186 Angle : 0.634 26.278 20946 Z= 0.316 Chirality : 0.046 0.162 2355 Planarity : 0.005 0.050 2616 Dihedral : 9.326 112.018 2374 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.75 % Allowed : 11.75 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.54 (0.19), residues: 1909 helix: 1.12 (0.18), residues: 884 sheet: 0.57 (0.39), residues: 163 loop : -0.43 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS C 141 PHE 0.020 0.002 PHE B 213 TYR 0.021 0.002 TYR D 141 ARG 0.004 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.06123 ( 744) hydrogen bonds : angle 4.76331 ( 2097) metal coordination : bond 0.01065 ( 7) metal coordination : angle 8.44138 ( 12) covalent geometry : bond 0.00444 (15446) covalent geometry : angle 0.60076 (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 230 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 46 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7128 (mtm-85) REVERT: A 98 ASP cc_start: 0.8418 (m-30) cc_final: 0.8091 (m-30) REVERT: A 147 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8296 (mt-10) REVERT: A 172 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: A 259 GLN cc_start: 0.7901 (mm110) cc_final: 0.7549 (mt0) REVERT: A 333 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7814 (mt-10) REVERT: A 433 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 444 LYS cc_start: 0.7661 (tppp) cc_final: 0.7446 (tttt) REVERT: B 42 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7919 (mtpt) REVERT: B 154 GLU cc_start: 0.7822 (pm20) cc_final: 0.7278 (pm20) REVERT: B 380 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: B 406 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7815 (mtmt) REVERT: C 48 LYS cc_start: 0.7569 (mmmt) cc_final: 0.6667 (mttt) REVERT: C 56 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: C 58 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6815 (tttm) REVERT: D 145 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7980 (mp) REVERT: E 10 LYS cc_start: 0.7363 (ttpt) cc_final: 0.7049 (ttpp) REVERT: E 17 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8220 (tpt) REVERT: F 118 ASP cc_start: 0.5553 (OUTLIER) cc_final: 0.5212 (m-30) REVERT: F 214 MET cc_start: 0.5749 (ttm) cc_final: 0.5426 (ttm) REVERT: F 293 PHE cc_start: 0.6000 (m-80) cc_final: 0.5213 (m-80) REVERT: F 300 LYS cc_start: 0.6557 (mttm) cc_final: 0.6206 (mtmt) REVERT: F 302 LYS cc_start: 0.6565 (mmmt) cc_final: 0.6236 (mttm) REVERT: F 317 MET cc_start: 0.7062 (ptp) cc_final: 0.6040 (pp-130) REVERT: F 322 ASP cc_start: 0.6292 (m-30) cc_final: 0.5873 (m-30) REVERT: F 382 MET cc_start: 0.5797 (pmm) cc_final: 0.5061 (ttp) REVERT: F 399 GLU cc_start: 0.7174 (mp0) cc_final: 0.6880 (mm-30) outliers start: 43 outliers final: 18 residues processed: 211 average time/residue: 1.2916 time to fit residues: 299.6228 Evaluate side-chains 211 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 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 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 145 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 17 MET 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: 4.9990 chunk 136 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 171 optimal weight: 30.0000 chunk 155 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 40 ASN 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 = 0.3955 r_free = 0.3955 target = 0.182967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.142043 restraints weight = 13255.502| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.46 r_work: 0.3003 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15453 Z= 0.170 Angle : 0.605 23.914 20946 Z= 0.304 Chirality : 0.045 0.162 2355 Planarity : 0.005 0.048 2616 Dihedral : 9.295 107.907 2374 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.62 % Allowed : 11.88 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.19), residues: 1909 helix: 1.13 (0.18), residues: 885 sheet: 0.52 (0.39), residues: 163 loop : -0.44 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 PHE 0.019 0.002 PHE B 213 TYR 0.021 0.002 TYR D 141 ARG 0.003 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.05810 ( 744) hydrogen bonds : angle 4.70978 ( 2097) metal coordination : bond 0.00951 ( 7) metal coordination : angle 7.63081 ( 12) covalent geometry : bond 0.00402 (15446) covalent geometry : angle 0.57706 (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 227 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8657 (mp) REVERT: A 46 ARG cc_start: 0.8182 (ptp90) cc_final: 0.7328 (mtm-85) REVERT: A 98 ASP cc_start: 0.8537 (m-30) cc_final: 0.8250 (m-30) REVERT: A 147 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8362 (mt-10) REVERT: A 172 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: A 259 GLN cc_start: 0.8016 (mm110) cc_final: 0.7775 (mt0) REVERT: A 333 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8047 (mt-10) REVERT: A 433 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: A 444 LYS cc_start: 0.7894 (tppp) cc_final: 0.7652 (tttt) REVERT: B 42 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8103 (mtpt) REVERT: B 49 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8532 (t70) REVERT: B 154 GLU cc_start: 0.7986 (pm20) cc_final: 0.7586 (pm20) REVERT: B 380 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: B 406 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7962 (mtmt) REVERT: C 48 LYS cc_start: 0.7920 (mmmt) cc_final: 0.6960 (mttt) REVERT: C 56 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: E 10 LYS cc_start: 0.7728 (ttpt) cc_final: 0.7450 (ttpp) REVERT: E 17 MET cc_start: 0.8588 (tpt) cc_final: 0.8347 (tpt) REVERT: F 118 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5638 (m-30) REVERT: F 214 MET cc_start: 0.6212 (ttm) cc_final: 0.5967 (ttm) REVERT: F 293 PHE cc_start: 0.6479 (m-80) cc_final: 0.5736 (m-80) REVERT: F 300 LYS cc_start: 0.6798 (mttm) cc_final: 0.6445 (mtmt) REVERT: F 302 LYS cc_start: 0.6586 (mmmt) cc_final: 0.6295 (mttm) REVERT: F 317 MET cc_start: 0.7178 (ptp) cc_final: 0.6377 (pp-130) REVERT: F 322 ASP cc_start: 0.6365 (m-30) cc_final: 0.6042 (m-30) REVERT: F 382 MET cc_start: 0.5879 (pmm) cc_final: 0.5123 (ttp) REVERT: F 399 GLU cc_start: 0.7289 (mp0) cc_final: 0.6991 (mm-30) outliers start: 41 outliers final: 21 residues processed: 210 average time/residue: 1.4134 time to fit residues: 324.3982 Evaluate side-chains 212 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 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 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 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 8 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 153 optimal weight: 0.0000 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 40 ASN 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 = 0.3965 r_free = 0.3965 target = 0.184490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.142228 restraints weight = 13152.118| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.47 r_work: 0.2978 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1976 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= 0.107 Angle : 0.519 20.185 20946 Z= 0.262 Chirality : 0.041 0.153 2355 Planarity : 0.004 0.045 2616 Dihedral : 8.837 90.632 2374 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.68 % Allowed : 12.32 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.19), residues: 1909 helix: 1.42 (0.18), residues: 888 sheet: 0.61 (0.40), residues: 163 loop : -0.35 (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 B 328 PHE 0.017 0.001 PHE D 50 TYR 0.020 0.001 TYR D 141 ARG 0.003 0.000 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 744) hydrogen bonds : angle 4.48815 ( 2097) metal coordination : bond 0.00611 ( 7) metal coordination : angle 6.66747 ( 12) covalent geometry : bond 0.00224 (15446) covalent geometry : angle 0.49383 (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 229 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 46 ARG cc_start: 0.8001 (ptp90) cc_final: 0.7291 (mtm-85) REVERT: A 98 ASP cc_start: 0.8501 (m-30) cc_final: 0.8197 (m-30) REVERT: A 172 GLU cc_start: 0.8139 (tt0) cc_final: 0.7827 (mp0) REVERT: A 259 GLN cc_start: 0.8063 (mm110) cc_final: 0.7739 (mt0) REVERT: A 333 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7995 (mt-10) REVERT: A 433 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: A 444 LYS cc_start: 0.7807 (tppp) cc_final: 0.7569 (tttt) REVERT: B 49 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8366 (t70) REVERT: B 154 GLU cc_start: 0.7940 (pm20) cc_final: 0.7522 (pm20) REVERT: B 406 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7920 (mtmt) REVERT: C 48 LYS cc_start: 0.7892 (mmmt) cc_final: 0.6926 (mttt) REVERT: C 56 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: E 1 MET cc_start: 0.6434 (tpp) cc_final: 0.6188 (tpt) REVERT: E 10 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7340 (ttpp) REVERT: E 17 MET cc_start: 0.8485 (tpt) cc_final: 0.8262 (tpt) REVERT: F 13 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7333 (mp) REVERT: F 118 ASP cc_start: 0.5570 (OUTLIER) cc_final: 0.5243 (m-30) REVERT: F 293 PHE cc_start: 0.6083 (m-80) cc_final: 0.5286 (m-80) REVERT: F 300 LYS cc_start: 0.6624 (mttm) cc_final: 0.6257 (mtmt) REVERT: F 302 LYS cc_start: 0.6454 (mmmt) cc_final: 0.6230 (mttm) REVERT: F 317 MET cc_start: 0.7152 (ptp) cc_final: 0.6174 (pp-130) REVERT: F 322 ASP cc_start: 0.6213 (m-30) cc_final: 0.5843 (m-30) REVERT: F 382 MET cc_start: 0.5940 (pmm) cc_final: 0.5245 (ttp) REVERT: F 399 GLU cc_start: 0.7256 (mp0) cc_final: 0.6951 (mm-30) outliers start: 42 outliers final: 23 residues processed: 212 average time/residue: 1.2952 time to fit residues: 301.5412 Evaluate side-chains 212 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.809 ------------------------------------------------------------------------------- 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 A residue 433 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 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 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 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 = 0.3948 r_free = 0.3948 target = 0.182221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141952 restraints weight = 13159.168| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.37 r_work: 0.3101 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15453 Z= 0.252 Angle : 0.688 19.672 20946 Z= 0.349 Chirality : 0.049 0.171 2355 Planarity : 0.006 0.058 2616 Dihedral : 9.687 121.950 2374 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.94 % Allowed : 12.39 % 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: 0.35 (0.19), residues: 1909 helix: 0.95 (0.18), residues: 886 sheet: 0.34 (0.39), residues: 168 loop : -0.46 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 103 HIS 0.006 0.002 HIS A 223 PHE 0.023 0.003 PHE B 213 TYR 0.021 0.002 TYR D 141 ARG 0.006 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.06867 ( 744) hydrogen bonds : angle 4.85756 ( 2097) metal coordination : bond 0.01271 ( 7) metal coordination : angle 6.31790 ( 12) covalent geometry : bond 0.00616 (15446) covalent geometry : angle 0.67174 (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 231 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 31 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (mp) REVERT: A 46 ARG cc_start: 0.8212 (ptp90) cc_final: 0.7456 (ptp90) REVERT: A 98 ASP cc_start: 0.8552 (m-30) cc_final: 0.8262 (m-30) REVERT: A 172 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: A 259 GLN cc_start: 0.8085 (mm110) cc_final: 0.7781 (mt0) REVERT: A 333 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8087 (mt-10) REVERT: A 433 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: A 444 LYS cc_start: 0.7876 (tppp) cc_final: 0.7662 (tttt) REVERT: B 42 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7735 (mtpp) REVERT: B 49 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8641 (t70) REVERT: B 154 GLU cc_start: 0.8011 (pm20) cc_final: 0.7547 (pm20) REVERT: B 380 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: B 406 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8008 (mtmt) REVERT: C 48 LYS cc_start: 0.7901 (mmmt) cc_final: 0.6921 (mttt) REVERT: C 56 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: E 1 MET cc_start: 0.6399 (tpp) cc_final: 0.6072 (tpt) REVERT: E 10 LYS cc_start: 0.7578 (ttpt) cc_final: 0.7180 (tttt) REVERT: F 118 ASP cc_start: 0.5923 (OUTLIER) cc_final: 0.5581 (m-30) REVERT: F 293 PHE cc_start: 0.6407 (m-80) cc_final: 0.5554 (m-80) REVERT: F 300 LYS cc_start: 0.6767 (mttm) cc_final: 0.6389 (mtmt) REVERT: F 302 LYS cc_start: 0.6493 (mmmt) cc_final: 0.6248 (mttm) REVERT: F 317 MET cc_start: 0.7194 (ptp) cc_final: 0.6317 (pp-130) REVERT: F 322 ASP cc_start: 0.6278 (m-30) cc_final: 0.5955 (m-30) REVERT: F 382 MET cc_start: 0.5768 (pmm) cc_final: 0.5197 (ttp) REVERT: F 399 GLU cc_start: 0.7260 (mp0) cc_final: 0.6956 (mm-30) outliers start: 46 outliers final: 22 residues processed: 213 average time/residue: 1.3552 time to fit residues: 316.1809 Evaluate side-chains 211 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 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 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 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 11 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 183 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 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 B 91 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.191464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.136138 restraints weight = 13844.698| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.45 r_work: 0.3249 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 0.060 15453 Z= 0.198 Angle : 0.629 18.148 20946 Z= 0.320 Chirality : 0.046 0.168 2355 Planarity : 0.005 0.050 2616 Dihedral : 9.634 114.816 2374 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.55 % Allowed : 12.96 % Favored : 84.48 % 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: 0.31 (0.19), residues: 1909 helix: 0.93 (0.18), residues: 892 sheet: 0.31 (0.38), residues: 174 loop : -0.53 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 103 HIS 0.006 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 0.06170 ( 744) hydrogen bonds : angle 4.77259 ( 2097) metal coordination : bond 0.00948 ( 7) metal coordination : angle 5.90258 ( 12) covalent geometry : bond 0.00475 (15446) covalent geometry : angle 0.61270 (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 218 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 31 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 46 ARG cc_start: 0.8111 (ptp90) cc_final: 0.7432 (ptp90) REVERT: A 98 ASP cc_start: 0.8474 (m-30) cc_final: 0.8198 (m-30) REVERT: A 172 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: A 333 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7937 (mt-10) REVERT: A 433 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: A 444 LYS cc_start: 0.7781 (tppp) cc_final: 0.7533 (tttt) REVERT: B 42 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7682 (mtpp) REVERT: B 49 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8583 (t70) REVERT: B 154 GLU cc_start: 0.7721 (pm20) cc_final: 0.7261 (pm20) REVERT: B 380 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: B 406 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7908 (mtmt) REVERT: C 48 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7021 (mttt) REVERT: C 56 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: E 1 MET cc_start: 0.6465 (tpp) cc_final: 0.6185 (tpt) REVERT: E 10 LYS cc_start: 0.7499 (ttpt) cc_final: 0.7112 (tttt) REVERT: F 118 ASP cc_start: 0.5771 (OUTLIER) cc_final: 0.5411 (m-30) REVERT: F 293 PHE cc_start: 0.6232 (m-80) cc_final: 0.5398 (m-80) REVERT: F 300 LYS cc_start: 0.6754 (mttm) cc_final: 0.6383 (mtmt) REVERT: F 302 LYS cc_start: 0.6496 (mmmt) cc_final: 0.6246 (mttm) REVERT: F 317 MET cc_start: 0.7090 (ptp) cc_final: 0.6101 (pp-130) REVERT: F 322 ASP cc_start: 0.6200 (m-30) cc_final: 0.5891 (m-30) REVERT: F 382 MET cc_start: 0.5852 (pmm) cc_final: 0.5309 (ttp) REVERT: F 399 GLU cc_start: 0.7223 (mp0) cc_final: 0.6929 (mm-30) outliers start: 40 outliers final: 23 residues processed: 204 average time/residue: 1.3575 time to fit residues: 304.1035 Evaluate side-chains 209 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 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 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 241 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 8 optimal weight: 0.2980 chunk 103 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 B 91 GLN C 40 ASN 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 = 0.4107 r_free = 0.4107 target = 0.193574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137195 restraints weight = 13858.450| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.43 r_work: 0.3287 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15453 Z= 0.125 Angle : 0.541 16.281 20946 Z= 0.277 Chirality : 0.042 0.160 2355 Planarity : 0.005 0.044 2616 Dihedral : 9.155 96.426 2374 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 13.09 % 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: 0.60 (0.19), residues: 1909 helix: 1.22 (0.18), residues: 892 sheet: 0.50 (0.39), residues: 169 loop : -0.45 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 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 0.05018 ( 744) hydrogen bonds : angle 4.58360 ( 2097) metal coordination : bond 0.00588 ( 7) metal coordination : angle 5.47898 ( 12) covalent geometry : bond 0.00279 (15446) covalent geometry : angle 0.52513 (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 214 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.731 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8573 (mp) REVERT: A 46 ARG cc_start: 0.7958 (ptp90) cc_final: 0.7328 (ptp90) REVERT: A 98 ASP cc_start: 0.8415 (m-30) cc_final: 0.8139 (m-30) REVERT: A 172 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 333 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7901 (mt-10) REVERT: A 433 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: A 444 LYS cc_start: 0.7727 (tppp) cc_final: 0.7484 (tttt) REVERT: B 42 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7635 (mtpp) REVERT: B 49 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8425 (t70) REVERT: B 154 GLU cc_start: 0.7654 (pm20) cc_final: 0.7208 (pm20) REVERT: B 380 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: B 406 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7844 (mtmt) REVERT: C 48 LYS cc_start: 0.7865 (mmmt) cc_final: 0.6955 (mttt) REVERT: C 56 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: E 1 MET cc_start: 0.6421 (tpp) cc_final: 0.6096 (tpt) REVERT: E 10 LYS cc_start: 0.7493 (ttpt) cc_final: 0.7102 (tttt) REVERT: F 118 ASP cc_start: 0.5723 (m-30) cc_final: 0.5377 (m-30) REVERT: F 293 PHE cc_start: 0.6147 (m-80) cc_final: 0.5224 (m-80) REVERT: F 300 LYS cc_start: 0.6737 (mttm) cc_final: 0.6361 (mtmt) REVERT: F 302 LYS cc_start: 0.6472 (mmmt) cc_final: 0.6210 (mttm) REVERT: F 317 MET cc_start: 0.7087 (ptp) cc_final: 0.6129 (pp-130) REVERT: F 322 ASP cc_start: 0.6162 (m-30) cc_final: 0.5934 (m-30) REVERT: F 382 MET cc_start: 0.5780 (pmm) cc_final: 0.5240 (ttp) REVERT: F 399 GLU cc_start: 0.7156 (mp0) cc_final: 0.6866 (mm-30) outliers start: 35 outliers final: 22 residues processed: 203 average time/residue: 1.3680 time to fit residues: 303.8454 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 : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 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 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 241 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 107 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.0170 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 7 optimal weight: 0.0020 chunk 116 optimal weight: 0.9980 chunk 156 optimal weight: 40.0000 overall best weight: 0.9428 ------------------------------------------------------------------------------- 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 B 91 GLN C 40 ASN F 142 ASN F 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.194070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139422 restraints weight = 13885.014| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.45 r_work: 0.3274 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15453 Z= 0.118 Angle : 0.528 15.252 20946 Z= 0.270 Chirality : 0.042 0.157 2355 Planarity : 0.005 0.044 2616 Dihedral : 8.945 93.203 2374 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.98 % Allowed : 13.54 % Favored : 84.48 % 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: 0.67 (0.19), residues: 1909 helix: 1.29 (0.18), residues: 898 sheet: 0.53 (0.39), residues: 169 loop : -0.45 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.004 0.001 HIS B 328 PHE 0.017 0.001 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 0.04799 ( 744) hydrogen bonds : angle 4.51420 ( 2097) metal coordination : bond 0.00497 ( 7) metal coordination : angle 5.28706 ( 12) covalent geometry : bond 0.00259 (15446) covalent geometry : angle 0.51271 (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 208 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 31 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 46 ARG cc_start: 0.7957 (ptp90) cc_final: 0.7330 (ptp90) REVERT: A 98 ASP cc_start: 0.8462 (m-30) cc_final: 0.8170 (m-30) REVERT: A 172 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 333 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7950 (mt-10) REVERT: A 433 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: A 444 LYS cc_start: 0.7762 (tppp) cc_final: 0.7518 (tttt) REVERT: B 42 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7681 (mtpp) REVERT: B 154 GLU cc_start: 0.7671 (pm20) cc_final: 0.7226 (pm20) REVERT: B 380 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: B 406 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7890 (mtmt) REVERT: C 48 LYS cc_start: 0.7848 (mmmt) cc_final: 0.6930 (mttt) REVERT: C 56 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: E 1 MET cc_start: 0.6349 (tpp) cc_final: 0.6101 (tpt) REVERT: E 10 LYS cc_start: 0.7529 (ttpt) cc_final: 0.7145 (tttt) REVERT: F 118 ASP cc_start: 0.5635 (m-30) cc_final: 0.5236 (m-30) REVERT: F 140 ASN cc_start: 0.4991 (t0) cc_final: 0.4553 (t0) REVERT: F 293 PHE cc_start: 0.6141 (m-80) cc_final: 0.5261 (m-80) REVERT: F 300 LYS cc_start: 0.6742 (mttm) cc_final: 0.6363 (mtmt) REVERT: F 302 LYS cc_start: 0.6469 (mmmt) cc_final: 0.6211 (mttm) REVERT: F 317 MET cc_start: 0.7065 (ptp) cc_final: 0.6148 (pp-130) REVERT: F 382 MET cc_start: 0.5620 (pmm) cc_final: 0.5090 (ttp) REVERT: F 399 GLU cc_start: 0.7188 (mp0) cc_final: 0.6893 (mm-30) outliers start: 31 outliers final: 21 residues processed: 199 average time/residue: 1.3721 time to fit residues: 298.7311 Evaluate side-chains 204 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 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 241 ASP Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 147 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 B 91 GLN C 40 ASN F 142 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.195304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139924 restraints weight = 13881.397| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.44 r_work: 0.3314 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2171 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= 0.102 Angle : 0.503 14.249 20946 Z= 0.257 Chirality : 0.041 0.156 2355 Planarity : 0.004 0.044 2616 Dihedral : 8.697 87.026 2374 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.72 % Allowed : 13.60 % 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: 0.83 (0.19), residues: 1909 helix: 1.47 (0.18), residues: 890 sheet: 0.57 (0.39), residues: 171 loop : -0.41 (0.21), residues: 848 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 0.017 0.001 PHE D 50 TYR 0.021 0.001 TYR D 141 ARG 0.003 0.000 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 744) hydrogen bonds : angle 4.41231 ( 2097) metal coordination : bond 0.00419 ( 7) metal coordination : angle 5.11090 ( 12) covalent geometry : bond 0.00214 (15446) covalent geometry : angle 0.48753 (20934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11895.31 seconds wall clock time: 205 minutes 9.58 seconds (12309.58 seconds total)