Starting phenix.real_space_refine on Mon Apr 6 03:02:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjb_45626/04_2026/9cjb_45626.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjb_45626/04_2026/9cjb_45626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cjb_45626/04_2026/9cjb_45626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjb_45626/04_2026/9cjb_45626.map" model { file = "/net/cci-nas-00/data/ceres_data/9cjb_45626/04_2026/9cjb_45626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjb_45626/04_2026/9cjb_45626.cif" } resolution = 1.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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 Mo 2 10.26 5 Fe 32 7.16 5 S 130 5.16 5 C 9200 2.51 5 N 2438 2.21 5 O 3652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15454 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3053 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 367} Chain breaks: 3 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2997 Classifications: {'peptide': 380} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 361} Chain breaks: 3 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "B" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 367 Classifications: {'water': 367} Link IDs: {None: 366} Chain: "C" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 127 Classifications: {'water': 127} Link IDs: {None: 126} Chain: "D" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 354 Classifications: {'water': 354} Link IDs: {None: 353} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1711 SG CYS A 275 33.436 58.825 98.908 1.00 42.91 S ATOM 792 SG CYS A 154 51.645 46.052 99.775 1.00 21.69 S ATOM 3812 SG CYS B 95 49.843 43.171 95.682 1.00 34.69 S ATOM 87 SG CYS A 62 46.352 48.734 97.181 1.00 21.46 S ATOM 274 SG CYS A 88 52.012 48.516 93.759 1.00 24.98 S ATOM 274 SG CYS A 88 52.012 48.516 93.759 1.00 24.98 S ATOM 4265 SG CYS B 153 54.811 44.585 96.548 1.00 36.31 S ATOM 3632 SG CYS B 70 53.051 43.107 89.682 1.00 28.37 S ATOM 3812 SG CYS B 95 49.843 43.171 95.682 1.00 34.69 S ATOM 8938 SG CYS C 275 49.664 59.066 24.169 1.00 57.60 S ATOM 8019 SG CYS C 154 30.289 48.029 22.486 1.00 23.26 S ATOM 10983 SG CYS D 95 31.684 44.797 26.695 1.00 31.97 S ATOM 7314 SG CYS C 62 35.786 50.069 25.101 1.00 21.79 S ATOM 7501 SG CYS C 88 29.963 50.309 28.534 1.00 21.42 S ATOM 7501 SG CYS C 88 29.963 50.309 28.534 1.00 21.42 S ATOM 11436 SG CYS D 153 26.921 46.623 25.773 1.00 37.20 S ATOM 10803 SG CYS D 70 28.561 44.845 32.586 1.00 28.68 S ATOM 10983 SG CYS D 95 31.684 44.797 26.695 1.00 31.97 S Time building chain proxies: 4.34, per 1000 atoms: 0.28 Number of scatterers: 15454 At special positions: 0 Unit cell: (82.55, 95.55, 122.85, 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) Mo 2 41.97 Fe 32 26.01 S 130 16.00 O 3652 8.00 N 2438 7.00 C 9200 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 565.9 milliseconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 12 sheets defined 58.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.985A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.585A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.151A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.031A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.667A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 370 removed outlier: 4.109A pdb=" N TYR A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.713A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 3.975A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.034A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.821A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.198A pdb=" N THR B 263 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.134A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.995A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.092A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.963A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.643A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.068A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.118A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 290 removed outlier: 6.005A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 314 removed outlier: 4.333A pdb=" N LYS C 304 " --> pdb=" O PHE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 363 through 370 removed outlier: 4.174A pdb=" N TYR C 367 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 435 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.688A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.519A pdb=" N LYS C 474 " --> pdb=" O CYS C 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 81 removed outlier: 3.959A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.030A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.796A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 4.218A pdb=" N THR D 263 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.087A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.857A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.056A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.973A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.545A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.333A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.796A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.968A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.399A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.563A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.580A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE D 367 " --> pdb=" O PRO D 390 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 14589 1.57 - 1.91: 164 1.91 - 2.26: 42 2.26 - 2.61: 76 2.61 - 2.95: 18 Bond restraints: 14889 Sorted by residual: bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.955 -0.755 2.00e-02 2.50e+03 1.42e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.952 -0.752 2.00e-02 2.50e+03 1.41e+03 bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.916 -0.716 2.00e-02 2.50e+03 1.28e+03 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.907 -0.707 2.00e-02 2.50e+03 1.25e+03 bond pdb="FE6 CLF B 601 " pdb="FE7 CLF B 601 " ideal model delta sigma weight residual 2.200 2.889 -0.689 2.00e-02 2.50e+03 1.19e+03 ... (remaining 14884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.95: 20077 6.95 - 13.89: 2 13.89 - 20.84: 2 20.84 - 27.78: 0 27.78 - 34.73: 4 Bond angle restraints: 20085 Sorted by residual: angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.27 34.73 3.00e+00 1.11e-01 1.34e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.51 34.49 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE1 CLF B 601 " ideal model delta sigma weight residual 90.00 56.89 33.11 3.00e+00 1.11e-01 1.22e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 57.10 32.90 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 107.66 -17.66 3.00e+00 1.11e-01 3.47e+01 ... (remaining 20080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8196 17.96 - 35.93: 692 35.93 - 53.89: 132 53.89 - 71.85: 52 71.85 - 89.82: 24 Dihedral angle restraints: 9096 sinusoidal: 3920 harmonic: 5176 Sorted by residual: dihedral pdb=" CA PHE D 367 " pdb=" C PHE D 367 " pdb=" N ALA D 368 " pdb=" CA ALA D 368 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ILE C 75 " pdb=" C ILE C 75 " pdb=" N LYS C 76 " pdb=" CA LYS C 76 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1389 0.041 - 0.081: 481 0.081 - 0.121: 213 0.121 - 0.162: 24 0.162 - 0.202: 4 Chirality restraints: 2111 Sorted by residual: chirality pdb=" CA ILE C 416 " pdb=" N ILE C 416 " pdb=" C ILE C 416 " pdb=" CB ILE C 416 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LYS B 143 " pdb=" N LYS B 143 " pdb=" C LYS B 143 " pdb=" CB LYS B 143 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2108 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 450 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C PHE B 450 " 0.077 2.00e-02 2.50e+03 pdb=" O PHE B 450 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE B 451 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 449 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C LYS D 449 " 0.062 2.00e-02 2.50e+03 pdb=" O LYS D 449 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE D 450 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 447 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C TYR D 447 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR D 447 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY D 448 " 0.021 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 376 2.58 - 3.16: 13782 3.16 - 3.74: 29633 3.74 - 4.32: 43254 4.32 - 4.90: 64650 Nonbonded interactions: 151695 Sorted by model distance: nonbonded pdb="FE FE D 601 " pdb=" O HOH B 862 " model vdw 2.002 2.260 nonbonded pdb="FE FE D 601 " pdb=" O HOH B 861 " model vdw 2.048 2.260 nonbonded pdb="FE FE B 602 " pdb=" O HOH D 892 " model vdw 2.063 2.260 nonbonded pdb="FE FE B 602 " pdb=" O HOH D 745 " model vdw 2.075 2.260 nonbonded pdb=" O ARG B 108 " pdb="FE FE D 601 " model vdw 2.103 2.260 ... (remaining 151690 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 'A' and (resid 51 through 376 or resid 416 through 600)) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } 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: 16.910 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.920 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 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 : 0.026 0.755 14904 Z= 1.325 Angle : 0.871 34.727 20085 Z= 0.447 Chirality : 0.048 0.202 2111 Planarity : 0.005 0.044 2568 Dihedral : 15.040 89.818 5784 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.03 % Allowed : 8.11 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1790 helix: 1.35 (0.17), residues: 901 sheet: -0.47 (0.37), residues: 145 loop : 0.00 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.027 0.004 TYR D 88 PHE 0.019 0.002 PHE B 31 TRP 0.044 0.003 TRP A 444 HIS 0.008 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.02548 (14889) covalent geometry : angle 0.87100 (20085) hydrogen bonds : bond 0.13351 ( 712) hydrogen bonds : angle 6.70902 ( 2052) Misc. bond : bond 0.12599 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: C 441 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.5677 (ttp) REVERT: D 279 GLU cc_start: 0.8020 (mp0) cc_final: 0.7399 (tp30) REVERT: D 330 MET cc_start: 0.8972 (mtp) cc_final: 0.8764 (mtm) REVERT: D 503 GLU cc_start: 0.8227 (tt0) cc_final: 0.7806 (mt-10) outliers start: 16 outliers final: 6 residues processed: 185 average time/residue: 0.8677 time to fit residues: 172.4490 Evaluate side-chains 170 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain D residue 121 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0000 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 274 HIS C 321 GLN C 451 HIS D 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096729 restraints weight = 10297.506| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 0.84 r_work: 0.3066 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.284 14904 Z= 0.205 Angle : 0.749 28.931 20085 Z= 0.361 Chirality : 0.046 0.162 2111 Planarity : 0.004 0.042 2568 Dihedral : 5.186 57.605 2278 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.22 % Allowed : 9.59 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 1790 helix: 1.54 (0.17), residues: 901 sheet: -0.55 (0.38), residues: 149 loop : -0.12 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 350 TYR 0.024 0.002 TYR D 88 PHE 0.021 0.002 PHE B 31 TRP 0.031 0.002 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00405 (14889) covalent geometry : angle 0.74913 (20085) hydrogen bonds : bond 0.05437 ( 712) hydrogen bonds : angle 5.81873 ( 2052) Misc. bond : bond 0.12618 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8571 (mttp) cc_final: 0.8313 (mtpt) REVERT: B 42 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: B 154 MET cc_start: 0.9184 (ttt) cc_final: 0.8940 (ttt) REVERT: B 279 GLU cc_start: 0.7989 (mp0) cc_final: 0.7584 (mp0) REVERT: C 362 HIS cc_start: 0.4387 (OUTLIER) cc_final: 0.3987 (t-90) REVERT: D 315 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8393 (tttt) REVERT: D 330 MET cc_start: 0.8968 (mtp) cc_final: 0.8676 (mtm) REVERT: D 430 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8692 (tm) REVERT: D 503 GLU cc_start: 0.8169 (tt0) cc_final: 0.7805 (mt-10) outliers start: 19 outliers final: 5 residues processed: 183 average time/residue: 0.8461 time to fit residues: 166.7282 Evaluate side-chains 173 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 104 ASN C 98 ASN C 321 GLN D 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096015 restraints weight = 10128.881| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 0.82 r_work: 0.3061 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.2751 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 14904 Z= 0.204 Angle : 0.745 29.364 20085 Z= 0.356 Chirality : 0.046 0.147 2111 Planarity : 0.004 0.038 2568 Dihedral : 5.020 57.552 2267 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.12 % Allowed : 8.94 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 1790 helix: 1.50 (0.17), residues: 913 sheet: -0.70 (0.37), residues: 159 loop : -0.08 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.023 0.002 TYR A 229 PHE 0.018 0.002 PHE B 31 TRP 0.028 0.002 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00416 (14889) covalent geometry : angle 0.74460 (20085) hydrogen bonds : bond 0.05432 ( 712) hydrogen bonds : angle 5.72438 ( 2052) Misc. bond : bond 0.10857 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: A 368 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: A 473 LYS cc_start: 0.9181 (mttp) cc_final: 0.8464 (mptt) REVERT: B 26 LYS cc_start: 0.8764 (mttp) cc_final: 0.8488 (mtpt) REVERT: B 42 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8447 (tm-30) REVERT: C 362 HIS cc_start: 0.4366 (OUTLIER) cc_final: 0.4143 (t-90) REVERT: C 368 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: C 417 LYS cc_start: 0.5076 (OUTLIER) cc_final: 0.3722 (mmtt) REVERT: D 50 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8516 (mttp) REVERT: D 315 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8700 (tttt) REVERT: D 430 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8759 (tm) REVERT: D 503 GLU cc_start: 0.8729 (tt0) cc_final: 0.8192 (mt-10) outliers start: 33 outliers final: 12 residues processed: 189 average time/residue: 0.8318 time to fit residues: 169.7645 Evaluate side-chains 188 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 32 optimal weight: 0.0050 chunk 171 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 191 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 191 GLN C 321 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098508 restraints weight = 10176.396| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 0.84 r_work: 0.3093 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 14904 Z= 0.159 Angle : 0.709 29.193 20085 Z= 0.332 Chirality : 0.044 0.146 2111 Planarity : 0.004 0.031 2568 Dihedral : 4.862 58.401 2267 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.12 % Allowed : 9.14 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1790 helix: 1.60 (0.17), residues: 912 sheet: -0.72 (0.38), residues: 155 loop : -0.06 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.019 0.002 TYR A 229 PHE 0.014 0.001 PHE B 31 TRP 0.024 0.002 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00316 (14889) covalent geometry : angle 0.70922 (20085) hydrogen bonds : bond 0.04716 ( 712) hydrogen bonds : angle 5.59643 ( 2052) Misc. bond : bond 0.09207 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: A 364 ILE cc_start: 0.5709 (OUTLIER) cc_final: 0.5163 (pp) REVERT: A 368 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: A 473 LYS cc_start: 0.9049 (mttp) cc_final: 0.8383 (mptt) REVERT: B 26 LYS cc_start: 0.8538 (mttp) cc_final: 0.8308 (mtpt) REVERT: B 42 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: B 124 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8389 (t) REVERT: C 417 LYS cc_start: 0.5338 (OUTLIER) cc_final: 0.4023 (mmtt) REVERT: D 315 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8448 (tttt) REVERT: D 430 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8716 (tm) REVERT: D 461 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: D 503 GLU cc_start: 0.8148 (tt0) cc_final: 0.7747 (mt-10) outliers start: 33 outliers final: 9 residues processed: 194 average time/residue: 0.8367 time to fit residues: 175.0439 Evaluate side-chains 189 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 161 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 191 GLN A 362 HIS C 98 ASN C 321 GLN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096289 restraints weight = 10236.394| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 0.83 r_work: 0.3063 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2752 rms_B_bonded: 4.98 restraints_weight: 0.1250 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 14904 Z= 0.204 Angle : 0.742 29.361 20085 Z= 0.353 Chirality : 0.046 0.148 2111 Planarity : 0.004 0.045 2568 Dihedral : 4.967 56.492 2267 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.87 % Allowed : 9.33 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1790 helix: 1.53 (0.17), residues: 912 sheet: -0.69 (0.38), residues: 155 loop : -0.07 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.023 0.002 TYR A 229 PHE 0.016 0.002 PHE B 31 TRP 0.025 0.002 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00418 (14889) covalent geometry : angle 0.74181 (20085) hydrogen bonds : bond 0.05365 ( 712) hydrogen bonds : angle 5.66057 ( 2052) Misc. bond : bond 0.10485 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: A 368 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: A 427 GLU cc_start: 0.5837 (mm-30) cc_final: 0.5577 (mm-30) REVERT: A 473 LYS cc_start: 0.9207 (mttp) cc_final: 0.8488 (mptt) REVERT: B 26 LYS cc_start: 0.8745 (mttp) cc_final: 0.8485 (mtpt) REVERT: B 42 GLU cc_start: 0.8677 (tt0) cc_final: 0.8456 (tm-30) REVERT: D 315 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8716 (tttt) REVERT: D 430 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8755 (tm) REVERT: D 461 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: D 503 GLU cc_start: 0.8721 (tt0) cc_final: 0.8182 (mt-10) outliers start: 29 outliers final: 14 residues processed: 185 average time/residue: 0.8110 time to fit residues: 162.0394 Evaluate side-chains 186 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 92 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 0.0870 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 191 GLN C 98 ASN C 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099968 restraints weight = 10452.095| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.82 r_work: 0.3118 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 14904 Z= 0.141 Angle : 0.694 29.122 20085 Z= 0.322 Chirality : 0.043 0.149 2111 Planarity : 0.004 0.032 2568 Dihedral : 4.719 52.652 2267 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.74 % Allowed : 9.72 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 1790 helix: 1.67 (0.18), residues: 912 sheet: -0.76 (0.38), residues: 155 loop : -0.05 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.017 0.001 TYR B 88 PHE 0.011 0.001 PHE B 31 TRP 0.020 0.002 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00276 (14889) covalent geometry : angle 0.69444 (20085) hydrogen bonds : bond 0.04326 ( 712) hydrogen bonds : angle 5.50317 ( 2052) Misc. bond : bond 0.08196 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8335 (tp30) cc_final: 0.7221 (pm20) REVERT: A 364 ILE cc_start: 0.5260 (OUTLIER) cc_final: 0.4509 (pp) REVERT: A 368 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: A 473 LYS cc_start: 0.9058 (mttp) cc_final: 0.8417 (mptt) REVERT: B 26 LYS cc_start: 0.8551 (mttp) cc_final: 0.8344 (mtpt) REVERT: B 42 GLU cc_start: 0.8337 (tt0) cc_final: 0.8118 (tm-30) REVERT: B 279 GLU cc_start: 0.8012 (mp0) cc_final: 0.7544 (mp0) REVERT: C 372 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8275 (mtt) REVERT: D 222 LYS cc_start: 0.8323 (mptt) cc_final: 0.8006 (mmtt) REVERT: D 430 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8710 (tm) REVERT: D 461 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: D 503 GLU cc_start: 0.8141 (tt0) cc_final: 0.7773 (mt-10) outliers start: 27 outliers final: 11 residues processed: 191 average time/residue: 0.8093 time to fit residues: 166.6516 Evaluate side-chains 188 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 145 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099458 restraints weight = 10433.468| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 0.83 r_work: 0.3109 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 14904 Z= 0.151 Angle : 0.699 29.189 20085 Z= 0.325 Chirality : 0.044 0.149 2111 Planarity : 0.004 0.032 2568 Dihedral : 4.695 52.196 2267 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.93 % Allowed : 9.52 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1790 helix: 1.67 (0.17), residues: 912 sheet: -0.75 (0.38), residues: 155 loop : -0.02 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 284 TYR 0.019 0.002 TYR C 276 PHE 0.012 0.001 PHE B 31 TRP 0.019 0.002 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00302 (14889) covalent geometry : angle 0.69940 (20085) hydrogen bonds : bond 0.04466 ( 712) hydrogen bonds : angle 5.48907 ( 2052) Misc. bond : bond 0.08660 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: A 368 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: A 473 LYS cc_start: 0.9064 (mttp) cc_final: 0.8418 (mptt) REVERT: B 26 LYS cc_start: 0.8572 (mttp) cc_final: 0.8356 (mtpt) REVERT: B 42 GLU cc_start: 0.8348 (tt0) cc_final: 0.8124 (tm-30) REVERT: B 124 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 279 GLU cc_start: 0.8017 (mp0) cc_final: 0.7515 (mp0) REVERT: D 222 LYS cc_start: 0.8346 (mptt) cc_final: 0.8021 (mmtt) REVERT: D 299 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8040 (mt-10) REVERT: D 430 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8726 (tm) REVERT: D 461 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7785 (pt0) REVERT: D 503 GLU cc_start: 0.8147 (tt0) cc_final: 0.7768 (mt-10) outliers start: 30 outliers final: 13 residues processed: 191 average time/residue: 0.7947 time to fit residues: 164.1367 Evaluate side-chains 190 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 69 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 362 HIS C 191 GLN C 321 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102073 restraints weight = 10594.470| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 0.87 r_work: 0.3149 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 14904 Z= 0.129 Angle : 0.678 29.091 20085 Z= 0.311 Chirality : 0.043 0.147 2111 Planarity : 0.004 0.033 2568 Dihedral : 4.529 51.536 2267 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.35 % Allowed : 9.97 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1790 helix: 1.75 (0.18), residues: 915 sheet: -0.73 (0.38), residues: 160 loop : -0.01 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 284 TYR 0.017 0.001 TYR D 142 PHE 0.009 0.001 PHE D 237 TRP 0.015 0.001 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00255 (14889) covalent geometry : angle 0.67765 (20085) hydrogen bonds : bond 0.03928 ( 712) hydrogen bonds : angle 5.38472 ( 2052) Misc. bond : bond 0.07283 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8307 (tp30) cc_final: 0.7201 (pm20) REVERT: A 350 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.8073 (mtp-110) REVERT: A 368 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: A 473 LYS cc_start: 0.9049 (mttp) cc_final: 0.8332 (mptt) REVERT: B 26 LYS cc_start: 0.8545 (mttp) cc_final: 0.8327 (mtpt) REVERT: B 42 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: B 279 GLU cc_start: 0.7991 (mp0) cc_final: 0.7482 (mp0) REVERT: C 60 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7081 (ptp90) REVERT: C 277 ARG cc_start: 0.6281 (mtt90) cc_final: 0.4558 (ttt-90) REVERT: D 222 LYS cc_start: 0.8271 (mptt) cc_final: 0.7877 (mmtt) REVERT: D 430 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8701 (tm) REVERT: D 503 GLU cc_start: 0.8117 (tt0) cc_final: 0.7732 (mt-10) outliers start: 21 outliers final: 10 residues processed: 186 average time/residue: 0.8564 time to fit residues: 171.2309 Evaluate side-chains 180 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 61 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN C 321 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097891 restraints weight = 10416.322| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 0.86 r_work: 0.3083 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 14904 Z= 0.181 Angle : 0.722 29.313 20085 Z= 0.340 Chirality : 0.045 0.146 2111 Planarity : 0.004 0.044 2568 Dihedral : 4.572 53.193 2264 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 10.17 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1790 helix: 1.64 (0.17), residues: 916 sheet: -0.76 (0.38), residues: 155 loop : -0.01 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 284 TYR 0.022 0.002 TYR A 229 PHE 0.014 0.002 PHE A 109 TRP 0.020 0.002 TRP A 444 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00367 (14889) covalent geometry : angle 0.72181 (20085) hydrogen bonds : bond 0.04939 ( 712) hydrogen bonds : angle 5.53778 ( 2052) Misc. bond : bond 0.09771 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: A 350 ARG cc_start: 0.8604 (mtp-110) cc_final: 0.8123 (mtp-110) REVERT: A 473 LYS cc_start: 0.9066 (mttp) cc_final: 0.8395 (mptt) REVERT: B 26 LYS cc_start: 0.8576 (mttp) cc_final: 0.8347 (mtpt) REVERT: B 42 GLU cc_start: 0.8346 (tt0) cc_final: 0.8102 (tm-30) REVERT: B 417 LYS cc_start: 0.8271 (mmpt) cc_final: 0.8019 (mmpt) REVERT: D 222 LYS cc_start: 0.8366 (mptt) cc_final: 0.7998 (mmtt) REVERT: D 299 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8019 (mt-10) REVERT: D 430 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8730 (tm) REVERT: D 503 GLU cc_start: 0.8158 (tt0) cc_final: 0.7745 (mt-10) outliers start: 19 outliers final: 11 residues processed: 181 average time/residue: 0.8597 time to fit residues: 167.6979 Evaluate side-chains 182 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 103 optimal weight: 0.8980 chunk 88 optimal weight: 0.0870 chunk 127 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 122 optimal weight: 0.0040 chunk 155 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 191 GLN C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100891 restraints weight = 10622.653| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 0.87 r_work: 0.3130 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 14904 Z= 0.136 Angle : 0.687 29.130 20085 Z= 0.317 Chirality : 0.043 0.148 2111 Planarity : 0.004 0.032 2568 Dihedral : 4.399 50.495 2264 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.84 % Allowed : 10.62 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1790 helix: 1.72 (0.17), residues: 915 sheet: -0.78 (0.38), residues: 155 loop : -0.00 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 284 TYR 0.017 0.001 TYR D 142 PHE 0.010 0.001 PHE B 31 TRP 0.015 0.001 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00267 (14889) covalent geometry : angle 0.68668 (20085) hydrogen bonds : bond 0.04140 ( 712) hydrogen bonds : angle 5.42729 ( 2052) Misc. bond : bond 0.07895 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8328 (tp30) cc_final: 0.7198 (pm20) REVERT: A 372 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7559 (mtt) REVERT: B 26 LYS cc_start: 0.8546 (mttp) cc_final: 0.8323 (mtpt) REVERT: B 42 GLU cc_start: 0.8344 (tt0) cc_final: 0.8099 (tm-30) REVERT: B 279 GLU cc_start: 0.8002 (mp0) cc_final: 0.7545 (mp0) REVERT: B 417 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7975 (mmpt) REVERT: C 277 ARG cc_start: 0.6335 (mtt90) cc_final: 0.4620 (ttt180) REVERT: D 222 LYS cc_start: 0.8292 (mptt) cc_final: 0.7941 (mmtt) REVERT: D 299 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8029 (mt-10) REVERT: D 430 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8694 (tm) REVERT: D 503 GLU cc_start: 0.8138 (tt0) cc_final: 0.7740 (mt-10) outliers start: 13 outliers final: 9 residues processed: 179 average time/residue: 0.8900 time to fit residues: 171.1185 Evaluate side-chains 182 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 97 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 98 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 191 GLN C 98 ASN C 191 GLN C 321 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100372 restraints weight = 10461.188| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 0.87 r_work: 0.3122 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 14904 Z= 0.144 Angle : 0.693 29.167 20085 Z= 0.320 Chirality : 0.043 0.149 2111 Planarity : 0.004 0.048 2568 Dihedral : 4.398 49.184 2264 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.03 % Allowed : 10.49 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1790 helix: 1.71 (0.17), residues: 916 sheet: -0.70 (0.37), residues: 160 loop : -0.01 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 284 TYR 0.018 0.001 TYR B 88 PHE 0.011 0.001 PHE B 31 TRP 0.015 0.001 TRP A 444 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00286 (14889) covalent geometry : angle 0.69280 (20085) hydrogen bonds : bond 0.04281 ( 712) hydrogen bonds : angle 5.42796 ( 2052) Misc. bond : bond 0.08189 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6758.03 seconds wall clock time: 116 minutes 4.71 seconds (6964.71 seconds total)