Starting phenix.real_space_refine on Sat May 17 08:57:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfw_45565/05_2025/9cfw_45565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfw_45565/05_2025/9cfw_45565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cfw_45565/05_2025/9cfw_45565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfw_45565/05_2025/9cfw_45565.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfw_45565/05_2025/9cfw_45565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfw_45565/05_2025/9cfw_45565.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.048 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 95 5.16 5 C 9983 2.51 5 N 2714 2.21 5 O 3035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15838 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2896 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2896 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2896 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "P" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5874 Classifications: {'peptide': 720} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 693} Chain: "R" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.53, per 1000 atoms: 0.60 Number of scatterers: 15838 At special positions: 0 Unit cell: (188.44, 125.178, 138.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 8 15.00 Mg 3 11.99 O 3035 8.00 N 2714 7.00 C 9983 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: 4.29 Conformation dependent library (CDL) restraints added in 2.1 seconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 26 sheets defined 54.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.867A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.153A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.703A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.731A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 4.095A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.048A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.595A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 353 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.743A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.962A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.644A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.774A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.690A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.777A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.564A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.556A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.807A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.288A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.507A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.670A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 214 removed outlier: 3.851A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.766A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.347A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'P' and resid 1 through 8 removed outlier: 3.814A pdb=" N ALA P 4 " --> pdb=" O MET P 1 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR P 6 " --> pdb=" O SER P 3 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG P 8 " --> pdb=" O LEU P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 24 through 38 Processing helix chain 'P' and resid 58 through 61 removed outlier: 3.802A pdb=" N TYR P 61 " --> pdb=" O LEU P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 62 through 70 Processing helix chain 'P' and resid 80 through 96 removed outlier: 3.834A pdb=" N VAL P 84 " --> pdb=" O HIS P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 Processing helix chain 'P' and resid 128 through 142 Processing helix chain 'P' and resid 142 through 150 Processing helix chain 'P' and resid 189 through 194 removed outlier: 4.178A pdb=" N VAL P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 211 removed outlier: 4.394A pdb=" N TYR P 206 " --> pdb=" O PHE P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 218 Processing helix chain 'P' and resid 225 through 228 Processing helix chain 'P' and resid 229 through 234 removed outlier: 4.278A pdb=" N LYS P 234 " --> pdb=" O LEU P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 244 through 259 Processing helix chain 'P' and resid 262 through 281 Processing helix chain 'P' and resid 296 through 307 removed outlier: 4.713A pdb=" N LEU P 300 " --> pdb=" O THR P 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR P 302 " --> pdb=" O ASN P 298 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ARG P 305 " --> pdb=" O LYS P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 318 removed outlier: 3.750A pdb=" N GLU P 316 " --> pdb=" O THR P 312 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 367 removed outlier: 3.654A pdb=" N ILE P 362 " --> pdb=" O LEU P 358 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA P 367 " --> pdb=" O ASN P 363 " (cutoff:3.500A) Processing helix chain 'P' and resid 397 through 429 removed outlier: 3.589A pdb=" N GLU P 416 " --> pdb=" O GLN P 412 " (cutoff:3.500A) Processing helix chain 'P' and resid 441 through 450 removed outlier: 3.742A pdb=" N ASP P 446 " --> pdb=" O LYS P 442 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU P 447 " --> pdb=" O ILE P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 454 through 460 Processing helix chain 'P' and resid 470 through 482 Processing helix chain 'P' and resid 497 through 502 removed outlier: 4.035A pdb=" N LEU P 502 " --> pdb=" O ARG P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 528 removed outlier: 3.874A pdb=" N ASN P 528 " --> pdb=" O LEU P 524 " (cutoff:3.500A) Processing helix chain 'P' and resid 532 through 541 removed outlier: 3.670A pdb=" N LYS P 536 " --> pdb=" O PHE P 532 " (cutoff:3.500A) Processing helix chain 'P' and resid 544 through 551 Processing helix chain 'P' and resid 554 through 558 Processing helix chain 'P' and resid 564 through 582 Processing helix chain 'P' and resid 603 through 614 Processing helix chain 'P' and resid 615 through 625 Processing helix chain 'P' and resid 633 through 641 Processing helix chain 'P' and resid 642 through 648 Proline residue: P 645 - end of helix Processing helix chain 'P' and resid 654 through 666 Processing helix chain 'P' and resid 685 through 718 removed outlier: 4.113A pdb=" N GLN P 700 " --> pdb=" O GLU P 696 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER P 701 " --> pdb=" O VAL P 697 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG P 716 " --> pdb=" O GLY P 712 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 22 removed outlier: 4.288A pdb=" N GLU R 12 " --> pdb=" O GLU R 8 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU R 19 " --> pdb=" O GLU R 15 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE R 20 " --> pdb=" O ALA R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 removed outlier: 3.795A pdb=" N THR R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 54 Processing helix chain 'R' and resid 65 through 77 Processing helix chain 'R' and resid 82 through 92 Processing helix chain 'R' and resid 103 through 113 removed outlier: 3.721A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 130 removed outlier: 4.088A pdb=" N GLU R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.874A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.599A pdb=" N LYS B 68 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.458A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.892A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.659A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.928A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.568A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'P' and resid 43 through 45 removed outlier: 6.562A pdb=" N ALA P 100 " --> pdb=" O ALA P 586 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE P 588 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET P 102 " --> pdb=" O ILE P 588 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS P 590 " --> pdb=" O MET P 102 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER P 104 " --> pdb=" O CYS P 590 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET P 167 " --> pdb=" O LEU P 384 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY P 164 " --> pdb=" O SER P 184 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER P 184 " --> pdb=" O GLY P 164 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR P 166 " --> pdb=" O ILE P 182 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE P 182 " --> pdb=" O TYR P 166 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP P 168 " --> pdb=" O GLY P 180 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY P 180 " --> pdb=" O ASP P 168 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN P 170 " --> pdb=" O VAL P 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AC3, first strand: chain 'P' and resid 284 through 286 Processing sheet with id=AC4, first strand: chain 'P' and resid 320 through 325 Processing sheet with id=AC5, first strand: chain 'P' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'P' and resid 629 through 632 removed outlier: 3.635A pdb=" N TYR P 629 " --> pdb=" O ILE P 682 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 28 through 29 Processing sheet with id=AC8, first strand: chain 'R' and resid 100 through 102 791 hydrogen bonds defined for protein. 2112 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: 5.44 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4023 1.33 - 1.45: 3111 1.45 - 1.58: 8862 1.58 - 1.70: 4 1.70 - 1.82: 165 Bond restraints: 16165 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.343 0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.346 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C4 ADP P 801 " pdb=" C5 ADP P 801 " ideal model delta sigma weight residual 1.490 1.349 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.352 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 16160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 21230 4.02 - 8.04: 621 8.04 - 12.06: 23 12.06 - 16.08: 2 16.08 - 20.10: 1 Bond angle restraints: 21877 Sorted by residual: angle pdb=" O1B ADP C 401 " pdb=" PB ADP C 401 " pdb=" O2B ADP C 401 " ideal model delta sigma weight residual 119.90 99.80 20.10 3.00e+00 1.11e-01 4.49e+01 angle pdb=" C LEU R 113 " pdb=" N GLY R 114 " pdb=" CA GLY R 114 " ideal model delta sigma weight residual 120.10 125.52 -5.42 9.50e-01 1.11e+00 3.25e+01 angle pdb=" CA ASP R 65 " pdb=" CB ASP R 65 " pdb=" CG ASP R 65 " ideal model delta sigma weight residual 112.60 117.96 -5.36 1.00e+00 1.00e+00 2.87e+01 angle pdb=" CA ASN P 441 " pdb=" CB ASN P 441 " pdb=" CG ASN P 441 " ideal model delta sigma weight residual 112.60 117.86 -5.26 1.00e+00 1.00e+00 2.77e+01 angle pdb=" C ILE C 71 " pdb=" N GLU C 72 " pdb=" CA GLU C 72 " ideal model delta sigma weight residual 122.84 129.59 -6.75 1.30e+00 5.92e-01 2.70e+01 ... (remaining 21872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 9518 33.89 - 67.78: 221 67.78 - 101.66: 29 101.66 - 135.55: 4 135.55 - 169.44: 1 Dihedral angle restraints: 9773 sinusoidal: 4022 harmonic: 5751 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.43 -169.44 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 63.91 -123.92 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 61.45 -121.45 1 2.00e+01 2.50e-03 3.65e+01 ... (remaining 9770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1586 0.085 - 0.170: 663 0.170 - 0.255: 132 0.255 - 0.340: 22 0.340 - 0.424: 3 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA GLU R 115 " pdb=" N GLU R 115 " pdb=" C GLU R 115 " pdb=" CB GLU R 115 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CB THR R 45 " pdb=" CA THR R 45 " pdb=" OG1 THR R 45 " pdb=" CG2 THR R 45 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILE R 64 " pdb=" CA ILE R 64 " pdb=" CG1 ILE R 64 " pdb=" CG2 ILE R 64 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 2403 not shown) Planarity restraints: 2821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " -0.236 2.00e-02 2.50e+03 1.19e-01 3.57e+02 pdb=" CG TRP B 340 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " 0.112 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " 0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " 0.068 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " 0.136 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " -0.154 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.089 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 401 " 0.258 2.00e-02 2.50e+03 1.09e-01 3.26e+02 pdb=" C2 ADP B 401 " -0.053 2.00e-02 2.50e+03 pdb=" C4 ADP B 401 " -0.077 2.00e-02 2.50e+03 pdb=" C5 ADP B 401 " -0.053 2.00e-02 2.50e+03 pdb=" C6 ADP B 401 " 0.017 2.00e-02 2.50e+03 pdb=" C8 ADP B 401 " -0.089 2.00e-02 2.50e+03 pdb=" N1 ADP B 401 " 0.024 2.00e-02 2.50e+03 pdb=" N3 ADP B 401 " -0.073 2.00e-02 2.50e+03 pdb=" N6 ADP B 401 " 0.173 2.00e-02 2.50e+03 pdb=" N7 ADP B 401 " -0.067 2.00e-02 2.50e+03 pdb=" N9 ADP B 401 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " -0.181 2.00e-02 2.50e+03 9.25e-02 2.14e+02 pdb=" CG TRP D 340 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " 0.115 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " 0.023 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " 0.125 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " -0.093 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " -0.098 2.00e-02 2.50e+03 ... (remaining 2818 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 12 2.44 - 3.05: 9575 3.05 - 3.67: 23725 3.67 - 4.28: 36942 4.28 - 4.90: 61379 Nonbonded interactions: 131633 Sorted by model distance: nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.823 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.848 2.170 nonbonded pdb=" O1A ADP B 401 " pdb="MG MG B 402 " model vdw 1.895 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.906 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.923 2.170 ... (remaining 131628 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.870 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 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 : 0.013 0.147 16165 Z= 0.764 Angle : 1.833 20.099 21877 Z= 1.204 Chirality : 0.092 0.424 2406 Planarity : 0.017 0.178 2821 Dihedral : 14.921 169.437 6077 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 1.88 % Allowed : 4.41 % Favored : 93.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -1.69 (0.17), residues: 1971 helix: -1.89 (0.14), residues: 896 sheet: -0.76 (0.36), residues: 178 loop : -0.07 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.236 0.029 TRP B 340 HIS 0.016 0.004 HIS D 101 PHE 0.067 0.013 PHE B 262 TYR 0.172 0.023 TYR C 279 ARG 0.011 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.17211 ( 785) hydrogen bonds : angle 8.27068 ( 2112) covalent geometry : bond 0.01258 (16165) covalent geometry : angle 1.83294 (21877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7701 (mtp) cc_final: 0.6814 (mtm) REVERT: B 51 ASP cc_start: 0.8291 (m-30) cc_final: 0.8052 (t0) REVERT: B 60 SER cc_start: 0.8750 (t) cc_final: 0.8499 (p) REVERT: B 82 MET cc_start: 0.8573 (tpt) cc_final: 0.8328 (tpp) REVERT: B 190 MET cc_start: 0.8022 (mtm) cc_final: 0.7630 (mtp) REVERT: B 240 TYR cc_start: 0.7742 (t80) cc_final: 0.7531 (t80) REVERT: B 241 GLU cc_start: 0.7883 (tt0) cc_final: 0.7515 (mp0) REVERT: B 269 MET cc_start: 0.8780 (mtm) cc_final: 0.8526 (mtm) REVERT: B 299 MET cc_start: 0.8486 (mtp) cc_final: 0.8234 (mtp) REVERT: B 313 MET cc_start: 0.8645 (tpp) cc_final: 0.8332 (tpt) REVERT: B 334 GLU cc_start: 0.7589 (pm20) cc_final: 0.7091 (pm20) REVERT: B 355 MET cc_start: 0.8818 (tpp) cc_final: 0.8576 (mmm) REVERT: C 44 MET cc_start: 0.6554 (mtp) cc_final: 0.5859 (mtp) REVERT: C 47 MET cc_start: 0.7207 (tpp) cc_final: 0.6960 (ptt) REVERT: C 91 TYR cc_start: 0.8174 (t80) cc_final: 0.7779 (m-80) REVERT: C 162 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7956 (t0) REVERT: C 176 MET cc_start: 0.8132 (mmm) cc_final: 0.7889 (mmt) REVERT: C 221 LEU cc_start: 0.8704 (tp) cc_final: 0.8324 (pp) REVERT: C 291 LYS cc_start: 0.7820 (tttt) cc_final: 0.6854 (mttt) REVERT: C 326 LYS cc_start: 0.8952 (tppp) cc_final: 0.8212 (pmtt) REVERT: D 51 ASP cc_start: 0.8482 (m-30) cc_final: 0.8097 (p0) REVERT: D 162 ASN cc_start: 0.8207 (t0) cc_final: 0.7010 (t0) REVERT: D 227 MET cc_start: 0.7494 (tpt) cc_final: 0.6882 (tpt) REVERT: D 313 MET cc_start: 0.7997 (tpp) cc_final: 0.7791 (tpp) REVERT: D 317 ILE cc_start: 0.8443 (tp) cc_final: 0.8238 (pt) REVERT: P 36 PHE cc_start: 0.8618 (t80) cc_final: 0.8293 (t80) REVERT: P 64 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8766 (pp30) REVERT: P 65 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.7572 (m90) REVERT: P 66 MET cc_start: 0.8549 (mtt) cc_final: 0.7826 (mtm) REVERT: P 364 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7874 (mtt-85) REVERT: P 394 GLN cc_start: 0.8853 (mp10) cc_final: 0.8586 (pm20) REVERT: P 412 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: P 539 MET cc_start: 0.8498 (tpp) cc_final: 0.8194 (mmm) REVERT: P 547 MET cc_start: 0.8314 (mmm) cc_final: 0.8001 (mmm) outliers start: 32 outliers final: 9 residues processed: 264 average time/residue: 1.3883 time to fit residues: 402.9068 Evaluate side-chains 148 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 64 GLN Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 412 GLN Chi-restraints excluded: chain R residue 45 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 0.0870 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 0.0980 chunk 79 optimal weight: 0.4980 chunk 154 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS C 49 GLN C 246 GLN D 59 GLN P 320 HIS P 395 HIS P 441 ASN P 487 HIS R 108 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.122254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.095595 restraints weight = 37565.637| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.51 r_work: 0.3659 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16165 Z= 0.146 Angle : 0.702 12.047 21877 Z= 0.354 Chirality : 0.044 0.198 2406 Planarity : 0.004 0.058 2821 Dihedral : 9.614 171.933 2243 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.35 % Allowed : 10.65 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.24 (0.19), residues: 1971 helix: -0.37 (0.16), residues: 915 sheet: -0.52 (0.30), residues: 249 loop : 0.54 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 340 HIS 0.008 0.001 HIS R 108 PHE 0.025 0.002 PHE P 414 TYR 0.020 0.002 TYR P 633 ARG 0.008 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 785) hydrogen bonds : angle 5.54027 ( 2112) covalent geometry : bond 0.00319 (16165) covalent geometry : angle 0.70249 (21877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8307 (m-30) cc_final: 0.8062 (t0) REVERT: B 72 GLU cc_start: 0.5636 (OUTLIER) cc_final: 0.5247 (pt0) REVERT: B 123 MET cc_start: 0.8869 (mmp) cc_final: 0.8626 (mmm) REVERT: B 190 MET cc_start: 0.8631 (mtm) cc_final: 0.8376 (mtp) REVERT: B 205 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7983 (mp0) REVERT: B 326 LYS cc_start: 0.7614 (pmtt) cc_final: 0.7130 (tmmt) REVERT: C 291 LYS cc_start: 0.8629 (tttt) cc_final: 0.8069 (mttt) REVERT: C 370 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8152 (m) REVERT: D 123 MET cc_start: 0.8263 (tpp) cc_final: 0.8033 (tpp) REVERT: D 227 MET cc_start: 0.8174 (tpt) cc_final: 0.7840 (tpt) REVERT: P 1 MET cc_start: 0.8670 (pmt) cc_final: 0.8454 (pmm) REVERT: P 65 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7453 (m90) REVERT: P 112 THR cc_start: 0.8006 (m) cc_final: 0.7763 (p) REVERT: P 412 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: P 539 MET cc_start: 0.8097 (tpp) cc_final: 0.7498 (mmm) REVERT: P 675 MET cc_start: 0.7966 (mmm) cc_final: 0.7702 (tpt) REVERT: P 715 TRP cc_start: 0.9130 (m100) cc_final: 0.8810 (m100) REVERT: R 77 MET cc_start: 0.8223 (mmp) cc_final: 0.7672 (mmm) REVERT: R 138 ASN cc_start: 0.8781 (p0) cc_final: 0.8479 (p0) outliers start: 40 outliers final: 16 residues processed: 203 average time/residue: 1.2660 time to fit residues: 285.8437 Evaluate side-chains 147 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 412 GLN Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 108 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 150 optimal weight: 1.9990 chunk 166 optimal weight: 0.0470 chunk 151 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 59 GLN R 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.121084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.094456 restraints weight = 37770.709| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.52 r_work: 0.3638 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16165 Z= 0.146 Angle : 0.658 12.898 21877 Z= 0.323 Chirality : 0.043 0.166 2406 Planarity : 0.004 0.036 2821 Dihedral : 8.626 173.322 2229 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.47 % Allowed : 12.59 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.13 (0.19), residues: 1971 helix: 0.04 (0.17), residues: 935 sheet: -0.34 (0.32), residues: 239 loop : 0.58 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP P 648 HIS 0.015 0.001 HIS R 108 PHE 0.026 0.002 PHE R 13 TYR 0.017 0.002 TYR C 91 ARG 0.006 0.001 ARG R 38 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 785) hydrogen bonds : angle 5.18666 ( 2112) covalent geometry : bond 0.00336 (16165) covalent geometry : angle 0.65797 (21877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8421 (m-30) cc_final: 0.8082 (t0) REVERT: B 190 MET cc_start: 0.8654 (mtm) cc_final: 0.8374 (mtp) REVERT: B 326 LYS cc_start: 0.7614 (pmtt) cc_final: 0.7126 (tmmt) REVERT: B 355 MET cc_start: 0.8909 (mmm) cc_final: 0.8527 (mtm) REVERT: C 66 THR cc_start: 0.8325 (m) cc_final: 0.8109 (p) REVERT: C 72 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6138 (pt0) REVERT: C 291 LYS cc_start: 0.8620 (tttt) cc_final: 0.8063 (mttt) REVERT: D 72 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5921 (pt0) REVERT: D 123 MET cc_start: 0.8321 (tpp) cc_final: 0.8087 (tpp) REVERT: D 227 MET cc_start: 0.8201 (tpt) cc_final: 0.7805 (tpt) REVERT: P 66 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7350 (mtm) REVERT: P 112 THR cc_start: 0.8084 (m) cc_final: 0.7827 (p) REVERT: P 412 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: P 468 GLU cc_start: 0.8210 (tp30) cc_final: 0.7719 (mp0) REVERT: P 650 MET cc_start: 0.8254 (mpt) cc_final: 0.7989 (mmp) REVERT: P 675 MET cc_start: 0.8111 (mmm) cc_final: 0.7813 (tpt) REVERT: R 1 MET cc_start: 0.3079 (ptp) cc_final: 0.2141 (pmm) REVERT: R 37 MET cc_start: 0.8059 (ptp) cc_final: 0.7714 (ptp) REVERT: R 38 ARG cc_start: 0.7624 (mpt-90) cc_final: 0.7355 (mmt90) REVERT: R 64 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7769 (mp) REVERT: R 72 MET cc_start: 0.8656 (pp-130) cc_final: 0.8182 (pp-130) REVERT: R 75 ARG cc_start: 0.8623 (ttm110) cc_final: 0.8402 (ttm170) REVERT: R 77 MET cc_start: 0.7718 (mmp) cc_final: 0.7301 (mmm) REVERT: R 112 ASN cc_start: 0.9420 (m-40) cc_final: 0.9129 (m110) REVERT: R 138 ASN cc_start: 0.8764 (p0) cc_final: 0.8457 (p0) REVERT: R 145 MET cc_start: 0.9293 (ppp) cc_final: 0.8883 (pp-130) outliers start: 42 outliers final: 17 residues processed: 169 average time/residue: 1.3035 time to fit residues: 244.2731 Evaluate side-chains 147 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 412 GLN Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 47 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 128 optimal weight: 0.0040 chunk 100 optimal weight: 0.8980 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 371 HIS D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.121611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.094784 restraints weight = 37791.417| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.54 r_work: 0.3639 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16165 Z= 0.144 Angle : 0.623 11.281 21877 Z= 0.304 Chirality : 0.043 0.214 2406 Planarity : 0.004 0.035 2821 Dihedral : 7.919 177.095 2223 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.94 % Allowed : 12.29 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1971 helix: 0.33 (0.17), residues: 935 sheet: -0.27 (0.32), residues: 239 loop : 0.64 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.047 0.002 PHE R 13 TYR 0.018 0.001 TYR D 166 ARG 0.005 0.000 ARG P 711 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 785) hydrogen bonds : angle 4.99896 ( 2112) covalent geometry : bond 0.00335 (16165) covalent geometry : angle 0.62264 (21877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8416 (m-30) cc_final: 0.8059 (t0) REVERT: B 190 MET cc_start: 0.8677 (mtm) cc_final: 0.8435 (mtp) REVERT: B 326 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7150 (tmmt) REVERT: B 355 MET cc_start: 0.8920 (mmm) cc_final: 0.8559 (mtm) REVERT: C 291 LYS cc_start: 0.8620 (tttt) cc_final: 0.8010 (mptp) REVERT: C 370 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (m) REVERT: D 72 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5958 (pt0) REVERT: D 227 MET cc_start: 0.8182 (tpt) cc_final: 0.7873 (tpt) REVERT: D 286 ASP cc_start: 0.6556 (t0) cc_final: 0.6321 (p0) REVERT: P 65 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7563 (t70) REVERT: P 66 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7179 (mtp) REVERT: P 112 THR cc_start: 0.8133 (m) cc_final: 0.7882 (p) REVERT: P 412 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: P 468 GLU cc_start: 0.8196 (tp30) cc_final: 0.7726 (mp0) REVERT: P 650 MET cc_start: 0.8498 (mpt) cc_final: 0.8161 (mpp) REVERT: P 675 MET cc_start: 0.7760 (mmm) cc_final: 0.7465 (tpt) REVERT: R 1 MET cc_start: 0.2518 (ptp) cc_final: 0.1395 (pmm) REVERT: R 37 MET cc_start: 0.8112 (ptp) cc_final: 0.7887 (ptp) REVERT: R 64 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7797 (mp) REVERT: R 72 MET cc_start: 0.8697 (pp-130) cc_final: 0.8350 (pp-130) REVERT: R 77 MET cc_start: 0.7732 (mmp) cc_final: 0.7270 (mmm) REVERT: R 93 PHE cc_start: 0.8378 (m-10) cc_final: 0.7985 (m-80) REVERT: R 138 ASN cc_start: 0.8432 (p0) cc_final: 0.8214 (p0) REVERT: R 145 MET cc_start: 0.9274 (ppp) cc_final: 0.8897 (pp-130) outliers start: 50 outliers final: 17 residues processed: 172 average time/residue: 1.2061 time to fit residues: 231.8454 Evaluate side-chains 151 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 412 GLN Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 54 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 172 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN P 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.122155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.095412 restraints weight = 38029.229| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.53 r_work: 0.3639 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16165 Z= 0.137 Angle : 0.606 9.862 21877 Z= 0.295 Chirality : 0.042 0.148 2406 Planarity : 0.004 0.036 2821 Dihedral : 7.690 179.640 2223 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.88 % Allowed : 13.00 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1971 helix: 0.53 (0.17), residues: 927 sheet: -0.18 (0.32), residues: 239 loop : 0.66 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP P 651 HIS 0.003 0.001 HIS D 161 PHE 0.045 0.002 PHE R 13 TYR 0.021 0.001 TYR D 166 ARG 0.004 0.000 ARG P 711 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 785) hydrogen bonds : angle 4.84801 ( 2112) covalent geometry : bond 0.00316 (16165) covalent geometry : angle 0.60638 (21877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8446 (m-30) cc_final: 0.8114 (t0) REVERT: B 190 MET cc_start: 0.8667 (mtm) cc_final: 0.8409 (mtp) REVERT: B 205 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: B 326 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7311 (tmmt) REVERT: C 47 MET cc_start: 0.7623 (tpp) cc_final: 0.7093 (pmm) REVERT: C 82 MET cc_start: 0.7935 (tpt) cc_final: 0.7541 (tpt) REVERT: C 132 MET cc_start: 0.8099 (ppp) cc_final: 0.7849 (ttp) REVERT: C 291 LYS cc_start: 0.8610 (tttt) cc_final: 0.8003 (mptp) REVERT: C 370 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8306 (m) REVERT: D 72 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5964 (pt0) REVERT: D 107 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: D 227 MET cc_start: 0.8182 (tpt) cc_final: 0.7835 (tpt) REVERT: P 65 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7610 (t70) REVERT: P 66 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7832 (ptp) REVERT: P 112 THR cc_start: 0.8154 (m) cc_final: 0.7919 (p) REVERT: P 468 GLU cc_start: 0.8129 (tp30) cc_final: 0.7728 (mp0) REVERT: P 501 SER cc_start: 0.8220 (p) cc_final: 0.7994 (p) REVERT: P 598 GLN cc_start: 0.8939 (tt0) cc_final: 0.8363 (tm-30) REVERT: P 650 MET cc_start: 0.8494 (mpt) cc_final: 0.8171 (mpp) REVERT: P 675 MET cc_start: 0.7760 (mmm) cc_final: 0.7451 (tpt) REVERT: R 1 MET cc_start: 0.2742 (ptp) cc_final: 0.1912 (pmm) REVERT: R 77 MET cc_start: 0.7279 (mmp) cc_final: 0.6859 (mmt) REVERT: R 138 ASN cc_start: 0.8449 (p0) cc_final: 0.8146 (p0) REVERT: R 145 MET cc_start: 0.9255 (ppp) cc_final: 0.8929 (pp-130) outliers start: 49 outliers final: 20 residues processed: 170 average time/residue: 1.2173 time to fit residues: 231.0637 Evaluate side-chains 153 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 372 GLU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN P 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.119684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.092651 restraints weight = 37991.777| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.54 r_work: 0.3601 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16165 Z= 0.203 Angle : 0.670 11.041 21877 Z= 0.324 Chirality : 0.044 0.174 2406 Planarity : 0.004 0.049 2821 Dihedral : 7.472 173.155 2220 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.82 % Allowed : 13.94 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.47 (0.19), residues: 1971 helix: 0.44 (0.17), residues: 924 sheet: -0.23 (0.31), residues: 245 loop : 0.62 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP P 648 HIS 0.004 0.001 HIS D 161 PHE 0.044 0.002 PHE R 13 TYR 0.024 0.002 TYR D 166 ARG 0.009 0.001 ARG R 107 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 785) hydrogen bonds : angle 4.98925 ( 2112) covalent geometry : bond 0.00477 (16165) covalent geometry : angle 0.66980 (21877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8390 (m-30) cc_final: 0.8016 (t0) REVERT: B 190 MET cc_start: 0.8682 (mtm) cc_final: 0.8425 (mtp) REVERT: B 205 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: B 241 GLU cc_start: 0.7890 (tt0) cc_final: 0.7374 (mm-30) REVERT: B 326 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7364 (tmmt) REVERT: C 47 MET cc_start: 0.7558 (tpp) cc_final: 0.7316 (tpt) REVERT: C 82 MET cc_start: 0.8016 (tpt) cc_final: 0.7544 (tpt) REVERT: C 291 LYS cc_start: 0.8634 (tttt) cc_final: 0.7968 (mptp) REVERT: C 370 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8359 (m) REVERT: D 165 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8746 (mp) REVERT: D 227 MET cc_start: 0.8096 (tpt) cc_final: 0.7868 (tpt) REVERT: P 65 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.7754 (t70) REVERT: P 66 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7958 (ptp) REVERT: P 112 THR cc_start: 0.8253 (m) cc_final: 0.8012 (p) REVERT: P 468 GLU cc_start: 0.8108 (tp30) cc_final: 0.7746 (mp0) REVERT: P 598 GLN cc_start: 0.8969 (tt0) cc_final: 0.8398 (tm-30) REVERT: P 650 MET cc_start: 0.8485 (mpt) cc_final: 0.8138 (mmp) REVERT: R 1 MET cc_start: 0.2750 (ptp) cc_final: 0.1852 (pmm) REVERT: R 138 ASN cc_start: 0.8723 (p0) cc_final: 0.8312 (p0) REVERT: R 145 MET cc_start: 0.9309 (ppp) cc_final: 0.8939 (pp-130) outliers start: 48 outliers final: 23 residues processed: 165 average time/residue: 1.3317 time to fit residues: 244.4083 Evaluate side-chains 152 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 169 optimal weight: 0.0670 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 101 HIS D 59 GLN P 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.121089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.094243 restraints weight = 37868.629| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.54 r_work: 0.3632 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16165 Z= 0.147 Angle : 0.644 12.221 21877 Z= 0.307 Chirality : 0.042 0.146 2406 Planarity : 0.004 0.036 2821 Dihedral : 7.298 171.148 2220 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.88 % Allowed : 14.41 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1971 helix: 0.54 (0.17), residues: 923 sheet: -0.22 (0.31), residues: 247 loop : 0.67 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 648 HIS 0.003 0.001 HIS D 161 PHE 0.043 0.002 PHE R 13 TYR 0.018 0.001 TYR D 166 ARG 0.006 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 785) hydrogen bonds : angle 4.83468 ( 2112) covalent geometry : bond 0.00345 (16165) covalent geometry : angle 0.64425 (21877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8366 (m-30) cc_final: 0.8005 (t0) REVERT: B 190 MET cc_start: 0.8662 (mtm) cc_final: 0.8423 (mtp) REVERT: B 241 GLU cc_start: 0.7849 (tt0) cc_final: 0.7352 (mm-30) REVERT: C 82 MET cc_start: 0.7899 (tpt) cc_final: 0.7560 (tpt) REVERT: C 291 LYS cc_start: 0.8582 (tttt) cc_final: 0.7824 (mmtt) REVERT: C 370 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8306 (m) REVERT: D 72 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5948 (pt0) REVERT: D 165 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8726 (mp) REVERT: P 9 ASP cc_start: 0.8110 (p0) cc_final: 0.7842 (p0) REVERT: P 65 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7621 (t70) REVERT: P 66 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7950 (ptp) REVERT: P 112 THR cc_start: 0.8255 (m) cc_final: 0.8027 (p) REVERT: P 264 ASP cc_start: 0.8781 (p0) cc_final: 0.8397 (t70) REVERT: P 468 GLU cc_start: 0.8091 (tp30) cc_final: 0.7746 (mp0) REVERT: P 598 GLN cc_start: 0.8943 (tt0) cc_final: 0.8377 (tm-30) REVERT: P 650 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8266 (mpp) REVERT: P 675 MET cc_start: 0.7668 (mmm) cc_final: 0.7427 (tpt) REVERT: R 1 MET cc_start: 0.1976 (ptp) cc_final: 0.1202 (pmm) REVERT: R 37 MET cc_start: 0.7995 (tmm) cc_final: 0.7715 (ppp) REVERT: R 73 MET cc_start: 0.6780 (mmm) cc_final: 0.6252 (mmm) REVERT: R 77 MET cc_start: 0.7326 (mmm) cc_final: 0.6738 (mmm) REVERT: R 87 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8091 (mmm160) REVERT: R 138 ASN cc_start: 0.8594 (p0) cc_final: 0.8143 (p0) REVERT: R 145 MET cc_start: 0.9273 (ppp) cc_final: 0.8888 (pp-130) outliers start: 49 outliers final: 21 residues processed: 164 average time/residue: 1.2729 time to fit residues: 232.0558 Evaluate side-chains 150 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 312 THR Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain P residue 650 MET Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 108 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.119463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.092469 restraints weight = 37685.052| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.52 r_work: 0.3604 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16165 Z= 0.187 Angle : 0.668 12.739 21877 Z= 0.321 Chirality : 0.044 0.160 2406 Planarity : 0.004 0.036 2821 Dihedral : 7.255 163.451 2220 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.59 % Allowed : 15.24 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 1971 helix: 0.51 (0.17), residues: 919 sheet: -0.21 (0.31), residues: 247 loop : 0.61 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 340 HIS 0.004 0.001 HIS D 161 PHE 0.045 0.002 PHE R 13 TYR 0.022 0.001 TYR D 166 ARG 0.005 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 785) hydrogen bonds : angle 4.91405 ( 2112) covalent geometry : bond 0.00442 (16165) covalent geometry : angle 0.66826 (21877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8359 (m-30) cc_final: 0.7993 (t0) REVERT: B 190 MET cc_start: 0.8672 (mtm) cc_final: 0.8437 (mtp) REVERT: B 241 GLU cc_start: 0.7919 (tt0) cc_final: 0.7404 (mm-30) REVERT: C 82 MET cc_start: 0.7983 (tpt) cc_final: 0.7535 (tpt) REVERT: C 291 LYS cc_start: 0.8616 (tttt) cc_final: 0.7850 (mmtt) REVERT: C 370 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8350 (m) REVERT: D 165 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8717 (mp) REVERT: P 65 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7652 (t70) REVERT: P 66 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8049 (ptp) REVERT: P 72 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7769 (m) REVERT: P 112 THR cc_start: 0.8312 (m) cc_final: 0.8084 (p) REVERT: P 264 ASP cc_start: 0.8821 (p0) cc_final: 0.8419 (t70) REVERT: P 468 GLU cc_start: 0.8021 (tp30) cc_final: 0.7794 (mp0) REVERT: P 598 GLN cc_start: 0.8986 (tt0) cc_final: 0.8410 (tm-30) REVERT: P 650 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8287 (mpp) REVERT: P 675 MET cc_start: 0.7558 (mmm) cc_final: 0.7320 (tpt) REVERT: R 1 MET cc_start: 0.2468 (ptp) cc_final: 0.1980 (pmm) REVERT: R 73 MET cc_start: 0.6863 (mmm) cc_final: 0.6615 (mmm) REVERT: R 75 ARG cc_start: 0.6897 (ptt180) cc_final: 0.6623 (ptt180) REVERT: R 77 MET cc_start: 0.7212 (mmm) cc_final: 0.6871 (mmm) REVERT: R 87 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8083 (mmm160) REVERT: R 110 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.6088 (mmm) REVERT: R 138 ASN cc_start: 0.8522 (p0) cc_final: 0.8049 (p0) REVERT: R 145 MET cc_start: 0.9276 (ppp) cc_final: 0.8887 (pp-130) outliers start: 44 outliers final: 23 residues processed: 162 average time/residue: 1.2700 time to fit residues: 230.9590 Evaluate side-chains 152 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain P residue 650 MET Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 110 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 115 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 chunk 44 optimal weight: 0.0370 chunk 128 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 59 GLN ** P 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.121194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.094404 restraints weight = 37871.031| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.52 r_work: 0.3634 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16165 Z= 0.145 Angle : 0.660 13.753 21877 Z= 0.313 Chirality : 0.042 0.152 2406 Planarity : 0.004 0.036 2821 Dihedral : 7.068 158.918 2220 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.00 % Allowed : 15.94 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.63 (0.19), residues: 1971 helix: 0.61 (0.17), residues: 920 sheet: -0.17 (0.31), residues: 247 loop : 0.64 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP P 249 HIS 0.003 0.001 HIS D 161 PHE 0.019 0.001 PHE R 13 TYR 0.018 0.001 TYR D 166 ARG 0.006 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 785) hydrogen bonds : angle 4.77689 ( 2112) covalent geometry : bond 0.00338 (16165) covalent geometry : angle 0.65997 (21877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8377 (m-30) cc_final: 0.7994 (t0) REVERT: B 190 MET cc_start: 0.8651 (mtm) cc_final: 0.8388 (mtp) REVERT: B 241 GLU cc_start: 0.7876 (tt0) cc_final: 0.7382 (mm-30) REVERT: B 355 MET cc_start: 0.8842 (mmm) cc_final: 0.8640 (mtp) REVERT: C 82 MET cc_start: 0.7908 (tpt) cc_final: 0.7435 (tpt) REVERT: C 132 MET cc_start: 0.8052 (ppp) cc_final: 0.7693 (ttp) REVERT: C 291 LYS cc_start: 0.8568 (tttt) cc_final: 0.7810 (mmtt) REVERT: C 370 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (m) REVERT: D 72 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5745 (pt0) REVERT: D 167 GLU cc_start: 0.7798 (pt0) cc_final: 0.6950 (tm-30) REVERT: D 325 MET cc_start: 0.8432 (mmp) cc_final: 0.8220 (mmt) REVERT: P 9 ASP cc_start: 0.8099 (p0) cc_final: 0.7861 (p0) REVERT: P 65 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7803 (t70) REVERT: P 66 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8074 (ptp) REVERT: P 72 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7840 (m) REVERT: P 112 THR cc_start: 0.8308 (m) cc_final: 0.8086 (p) REVERT: P 264 ASP cc_start: 0.8742 (p0) cc_final: 0.8363 (t70) REVERT: P 468 GLU cc_start: 0.8053 (tp30) cc_final: 0.7730 (mp0) REVERT: P 598 GLN cc_start: 0.8949 (tt0) cc_final: 0.8393 (tm-30) REVERT: P 650 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8320 (mpp) REVERT: P 675 MET cc_start: 0.7652 (mmm) cc_final: 0.7403 (tpt) REVERT: R 75 ARG cc_start: 0.6816 (ptt180) cc_final: 0.6425 (ptm-80) REVERT: R 77 MET cc_start: 0.7705 (mmm) cc_final: 0.6944 (mmm) REVERT: R 87 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8100 (mmm160) REVERT: R 110 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.6110 (mmm) REVERT: R 138 ASN cc_start: 0.8474 (p0) cc_final: 0.7969 (p0) REVERT: R 145 MET cc_start: 0.9255 (ppp) cc_final: 0.8861 (pp-130) outliers start: 34 outliers final: 22 residues processed: 156 average time/residue: 1.2488 time to fit residues: 217.1281 Evaluate side-chains 151 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain P residue 650 MET Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 110 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 62 optimal weight: 0.9990 chunk 136 optimal weight: 0.0050 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 118 optimal weight: 0.0020 chunk 26 optimal weight: 0.3980 chunk 187 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 59 GLN P 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.121484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.094960 restraints weight = 37813.421| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.50 r_work: 0.3656 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16165 Z= 0.121 Angle : 0.646 10.879 21877 Z= 0.311 Chirality : 0.042 0.170 2406 Planarity : 0.004 0.044 2821 Dihedral : 6.866 154.825 2220 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.00 % Allowed : 16.12 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.78 (0.19), residues: 1971 helix: 0.71 (0.18), residues: 919 sheet: -0.05 (0.32), residues: 241 loop : 0.73 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP P 648 HIS 0.002 0.001 HIS D 161 PHE 0.046 0.001 PHE R 13 TYR 0.017 0.001 TYR P 44 ARG 0.005 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 785) hydrogen bonds : angle 4.69341 ( 2112) covalent geometry : bond 0.00274 (16165) covalent geometry : angle 0.64620 (21877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8278 (m-30) cc_final: 0.7979 (t0) REVERT: B 72 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5780 (pt0) REVERT: B 190 MET cc_start: 0.8641 (mtm) cc_final: 0.8402 (mtp) REVERT: B 241 GLU cc_start: 0.7834 (tt0) cc_final: 0.7320 (mm-30) REVERT: B 360 GLN cc_start: 0.8029 (tp40) cc_final: 0.7780 (tp-100) REVERT: C 82 MET cc_start: 0.7777 (tpt) cc_final: 0.7418 (tpt) REVERT: C 291 LYS cc_start: 0.8536 (tttt) cc_final: 0.7881 (mptp) REVERT: D 72 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5700 (pt0) REVERT: D 167 GLU cc_start: 0.7670 (pt0) cc_final: 0.6779 (tm-30) REVERT: D 325 MET cc_start: 0.8442 (mmp) cc_final: 0.8235 (mmt) REVERT: P 1 MET cc_start: 0.7955 (mpp) cc_final: 0.7270 (mmt) REVERT: P 65 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7792 (t70) REVERT: P 66 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8112 (ptp) REVERT: P 72 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7785 (p) REVERT: P 112 THR cc_start: 0.8276 (m) cc_final: 0.8065 (p) REVERT: P 264 ASP cc_start: 0.8773 (p0) cc_final: 0.8379 (t70) REVERT: P 468 GLU cc_start: 0.8001 (tp30) cc_final: 0.7733 (mp0) REVERT: P 598 GLN cc_start: 0.8928 (tt0) cc_final: 0.8369 (tm-30) REVERT: P 650 MET cc_start: 0.8403 (mpt) cc_final: 0.8121 (mpp) REVERT: P 675 MET cc_start: 0.7631 (mmm) cc_final: 0.7324 (tpt) REVERT: R 1 MET cc_start: 0.4454 (pmm) cc_final: 0.4127 (pmm) REVERT: R 77 MET cc_start: 0.7434 (mmm) cc_final: 0.6884 (mmm) REVERT: R 87 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8278 (mmm160) REVERT: R 110 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.6182 (mmm) REVERT: R 138 ASN cc_start: 0.8377 (p0) cc_final: 0.7873 (p0) REVERT: R 145 MET cc_start: 0.9230 (ppp) cc_final: 0.8819 (pp-130) outliers start: 34 outliers final: 16 residues processed: 156 average time/residue: 1.3340 time to fit residues: 230.9064 Evaluate side-chains 143 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 110 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 191 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 144 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.121602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.094954 restraints weight = 37553.738| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.51 r_work: 0.3637 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16165 Z= 0.142 Angle : 0.667 15.328 21877 Z= 0.317 Chirality : 0.042 0.167 2406 Planarity : 0.004 0.080 2821 Dihedral : 6.740 149.476 2220 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.76 % Allowed : 16.88 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.78 (0.19), residues: 1971 helix: 0.74 (0.18), residues: 915 sheet: -0.03 (0.33), residues: 235 loop : 0.68 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP P 715 HIS 0.003 0.001 HIS D 161 PHE 0.017 0.001 PHE R 13 TYR 0.019 0.001 TYR P 44 ARG 0.011 0.000 ARG R 38 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 785) hydrogen bonds : angle 4.77040 ( 2112) covalent geometry : bond 0.00330 (16165) covalent geometry : angle 0.66720 (21877) =============================================================================== Job complete usr+sys time: 10525.91 seconds wall clock time: 182 minutes 38.08 seconds (10958.08 seconds total)