Starting phenix.real_space_refine on Mon Apr 6 16:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut9_26763/04_2026/7ut9_26763.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut9_26763/04_2026/7ut9_26763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ut9_26763/04_2026/7ut9_26763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut9_26763/04_2026/7ut9_26763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ut9_26763/04_2026/7ut9_26763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut9_26763/04_2026/7ut9_26763.map" } resolution = 2.44 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= 0.001 sd= 0.023 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: 8 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 36 7.16 5 P 5 5.49 5 Mg 2 5.21 5 S 181 5.16 5 C 12745 2.51 5 N 3410 2.21 5 O 3862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 20243 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} 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: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3776 Classifications: {'peptide': 475} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 453} 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: "E" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2052 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "F" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2053 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "E" 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: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'ATP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 34.262 57.217 64.970 1.00 3.39 S ATOM 1170 SG CYS A 154 54.877 56.074 54.775 1.00 19.77 S ATOM 4549 SG CYS B 95 52.780 59.611 50.941 1.00 25.54 S ATOM 465 SG CYS A 62 48.929 58.465 56.120 1.00 17.76 S ATOM 652 SG CYS A 88 54.054 62.355 56.378 1.00 7.61 S ATOM 652 SG CYS A 88 54.054 62.355 56.378 1.00 7.61 S ATOM 5002 SG CYS B 153 58.100 59.286 52.807 1.00 21.02 S ATOM 4369 SG CYS B 70 55.979 65.708 50.649 1.00 20.59 S ATOM 4549 SG CYS B 95 52.780 59.611 50.941 1.00 25.54 S ATOM 10039 SG CYS C 275 48.830 133.419 59.051 1.00 26.79 S ATOM 9120 SG CYS C 154 30.583 132.368 44.804 1.00 30.68 S ATOM 12499 SG CYS D 95 33.084 128.059 42.439 1.00 15.17 S ATOM 8415 SG CYS C 62 36.117 130.108 48.002 1.00 30.20 S ATOM 8602 SG CYS C 88 30.718 126.526 48.089 1.00 0.00 S ATOM 8602 SG CYS C 88 30.718 126.526 48.089 1.00 0.00 S ATOM 12952 SG CYS D 153 27.789 128.704 43.261 1.00 26.21 S ATOM 12319 SG CYS D 70 29.847 122.054 42.546 1.00 19.19 S ATOM 12499 SG CYS D 95 33.084 128.059 42.439 1.00 15.17 S ATOM 16598 SG CYS E 97 63.147 47.099 53.984 1.00 9.13 S ATOM 16869 SG CYS E 132 68.504 46.279 56.879 1.00 31.04 S ATOM 18655 SG CYS F 97 67.834 51.892 53.755 1.00 22.17 S ATOM 18926 SG CYS F 132 68.611 46.982 50.334 1.00 43.71 S Time building chain proxies: 4.92, per 1000 atoms: 0.24 Number of scatterers: 20243 At special positions: 0 Unit cell: (115.23, 160.32, 102.705, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 2 41.97 Fe 36 26.01 S 181 16.00 P 5 15.00 Mg 2 11.99 O 3862 8.00 N 3410 7.00 C 12745 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 F 301 " pdb="FE4 SF4 F 301 " - pdb=" SG CYS F 132 " pdb="FE3 SF4 F 301 " - pdb=" SG CYS F 97 " pdb="FE1 SF4 F 301 " - pdb=" SG CYS E 97 " pdb="FE2 SF4 F 301 " - pdb=" SG CYS E 132 " Number of angles added : 12 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4638 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 14 sheets defined 56.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.507A pdb=" N SER A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.567A pdb=" N GLN A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) 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: 3.831A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.785A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.152A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.488A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 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: 3.538A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.968A 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 removed outlier: 3.513A pdb=" N GLN A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.531A pdb=" N HIS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.115A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.634A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.572A pdb=" N GLY A 455 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.567A pdb=" N TRP A 472 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 473 " --> pdb=" O PRO A 470 " (cutoff:3.500A) 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 80 removed outlier: 4.012A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.871A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 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 233 through 247 removed outlier: 3.916A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.096A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.568A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.610A 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: 3.515A pdb=" N GLY B 416 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 413 through 417' Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 460 through 463 removed outlier: 3.529A pdb=" N GLU B 463 " --> pdb=" O LYS B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.622A pdb=" N ARG B 481 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.561A pdb=" N ASN B 518 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.778A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 69 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: 3.853A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 4.183A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.147A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.543A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C 245 " --> pdb=" O LEU C 241 " (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: 5.683A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 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 358 through 363 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.710A pdb=" N TYR C 387 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 435 removed outlier: 3.957A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.627A pdb=" N GLY C 455 " --> pdb=" O HIS C 451 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.724A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) 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 80 removed outlier: 3.987A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.997A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.873A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (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 321 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.222A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.730A 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: 3.688A 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 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 459 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 removed outlier: 3.659A pdb=" N ASN D 518 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 97 through 112 Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 154 through 175 removed outlier: 3.519A pdb=" N MET E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS E 170 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 removed outlier: 4.035A pdb=" N LEU E 195 " --> pdb=" O ARG E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 223 Processing helix chain 'E' and resid 234 through 250 removed outlier: 3.504A pdb=" N ASP E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 271 Processing helix chain 'F' and resid 14 through 27 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 56 through 65 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 97 through 113 removed outlier: 3.506A pdb=" N GLY F 101 " --> pdb=" O CYS F 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 154 through 171 removed outlier: 3.639A pdb=" N VAL F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS F 170 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 removed outlier: 3.692A pdb=" N LEU F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 223 removed outlier: 3.512A pdb=" N ARG F 219 " --> pdb=" O ASN F 215 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 222 " --> pdb=" O GLN F 218 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 234 through 249 Processing helix chain 'F' and resid 260 through 271 removed outlier: 4.332A pdb=" N LEU F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N MET F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 10.593A pdb=" N LEU A 399 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A 375 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N TYR A 401 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.853A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.346A pdb=" N ILE A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 252 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A 227 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER A 254 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 removed outlier: 8.820A pdb=" N VAL B 114 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.687A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.650A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 10.021A pdb=" N LEU C 399 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 375 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N TYR C 401 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 3.503A pdb=" N SER C 152 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.494A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 270 " --> pdb=" O ASP C 222 " (cutoff:3.500A) 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: 6.603A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.379A 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: 8.714A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78 removed outlier: 6.084A pdb=" N VAL E 33 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL E 86 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE E 35 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET E 34 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASP E 125 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL E 36 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN E 4 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR E 148 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA E 6 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL E 150 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR E 8 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N SER E 152 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE E 147 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU E 182 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE E 149 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N CYS E 184 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS E 151 " --> pdb=" O CYS E 184 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN E 206 " --> pdb=" O GLY E 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 77 through 78 removed outlier: 7.957A pdb=" N ASP F 125 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL F 36 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N CYS F 5 " --> pdb=" O TYR F 124 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE F 147 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY F 181 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N MET F 207 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU F 182 " --> pdb=" O MET F 207 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS F 209 " --> pdb=" O LEU F 182 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2736 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: 4.16 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 19835 1.54 - 1.89: 708 1.89 - 2.23: 28 2.23 - 2.58: 101 2.58 - 2.93: 19 Bond restraints: 20691 Sorted by residual: bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.935 -0.735 2.00e-02 2.50e+03 1.35e+03 bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.929 -0.729 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.848 -0.648 2.00e-02 2.50e+03 1.05e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.826 -0.626 2.00e-02 2.50e+03 9.79e+02 bond pdb="FE7 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.809 -0.609 2.00e-02 2.50e+03 9.26e+02 ... (remaining 20686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.98: 27899 6.98 - 13.95: 24 13.95 - 20.93: 2 20.93 - 27.90: 0 27.90 - 34.88: 4 Bond angle restraints: 27929 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 55.12 34.88 3.00e+00 1.11e-01 1.35e+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 55.87 34.13 3.00e+00 1.11e-01 1.29e+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 57.05 32.95 3.00e+00 1.11e-01 1.21e+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 57.95 32.05 3.00e+00 1.11e-01 1.14e+02 angle pdb=" PA ATP F 303 " pdb=" O3A ATP F 303 " pdb=" PB ATP F 303 " ideal model delta sigma weight residual 136.83 128.39 8.44 1.00e+00 1.00e+00 7.12e+01 ... (remaining 27924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.54: 11836 30.54 - 61.08: 770 61.08 - 91.62: 75 91.62 - 122.16: 1 122.16 - 152.70: 1 Dihedral angle restraints: 12683 sinusoidal: 5419 harmonic: 7264 Sorted by residual: dihedral pdb=" O1B ADP E 302 " pdb=" O3A ADP E 302 " pdb=" PB ADP E 302 " pdb=" PA ADP E 302 " ideal model delta sinusoidal sigma weight residual 300.00 147.30 152.70 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C5' ADP E 302 " pdb=" O5' ADP E 302 " pdb=" PA ADP E 302 " pdb=" O2A ADP E 302 " ideal model delta sinusoidal sigma weight residual -60.00 -165.52 105.52 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" CA ARG E 224 " pdb=" C ARG E 224 " pdb=" N MET E 225 " pdb=" CA MET E 225 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 12680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2590 0.066 - 0.131: 371 0.131 - 0.196: 18 0.196 - 0.262: 3 0.262 - 0.327: 1 Chirality restraints: 2983 Sorted by residual: chirality pdb=" CG LEU E 267 " pdb=" CB LEU E 267 " pdb=" CD1 LEU E 267 " pdb=" CD2 LEU E 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA TYR E 230 " pdb=" N TYR E 230 " pdb=" C TYR E 230 " pdb=" CB TYR E 230 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA THR E 17 " pdb=" N THR E 17 " pdb=" C THR E 17 " pdb=" CB THR E 17 " both_signs ideal model delta sigma weight residual False 2.53 2.74 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2980 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 152 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 152 " -0.068 2.00e-02 2.50e+03 pdb=" O SER A 152 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU A 153 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 229 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C GLU E 229 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU E 229 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR E 230 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 332 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO C 333 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.047 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1714 2.74 - 3.28: 20250 3.28 - 3.82: 36867 3.82 - 4.36: 44888 4.36 - 4.90: 74685 Nonbonded interactions: 178404 Sorted by model distance: nonbonded pdb=" O1 HCA A 501 " pdb=" O7 HCA A 501 " model vdw 2.201 3.040 nonbonded pdb=" OE1 GLU B 109 " pdb="FE FE D 601 " model vdw 2.210 2.260 nonbonded pdb=" OG1 THR F 66 " pdb=" OD1 ASP F 69 " model vdw 2.214 3.040 nonbonded pdb=" OG SER E 16 " pdb="MG MG E 301 " model vdw 2.224 2.170 nonbonded pdb=" NZ LYS A 146 " pdb=" O GLU B 33 " model vdw 2.225 3.120 ... (remaining 178399 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 6 through 502) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } ncs_group { reference = (chain 'E' and (resid 2 through 271 or resid 301)) selection = (chain 'F' and (resid 2 through 271 or resid 302)) } 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=0.00 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: 5.040 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 22.050 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.021 0.735 20711 Z= 1.069 Angle : 0.816 34.876 27941 Z= 0.405 Chirality : 0.045 0.327 2983 Planarity : 0.004 0.086 3592 Dihedral : 18.474 152.696 8045 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.29 % Favored : 96.48 % Rotamer: Outliers : 3.62 % Allowed : 25.14 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.25 (0.17), residues: 2526 helix: 1.12 (0.15), residues: 1213 sheet: -0.47 (0.33), residues: 254 loop : -0.72 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 389 TYR 0.018 0.001 TYR A 276 PHE 0.013 0.001 PHE F 210 TRP 0.023 0.001 TRP C 335 HIS 0.019 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.02061 (20691) covalent geometry : angle 0.80642 (27929) hydrogen bonds : bond 0.15389 ( 950) hydrogen bonds : angle 6.49161 ( 2736) metal coordination : bond 0.06440 ( 4) metal coordination : angle 6.19824 ( 12) Misc. bond : bond 0.12916 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 599 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.8304 (ptp) cc_final: 0.8004 (ptp) REVERT: B 499 ASN cc_start: 0.8444 (m-40) cc_final: 0.7562 (m110) REVERT: C 78 MET cc_start: 0.8246 (mtp) cc_final: 0.7952 (mmm) REVERT: D 338 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8129 (mm-40) REVERT: D 499 ASN cc_start: 0.8513 (m-40) cc_final: 0.7925 (m110) outliers start: 78 outliers final: 63 residues processed: 660 average time/residue: 0.6881 time to fit residues: 503.9575 Evaluate side-chains 652 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 589 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.0040 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 457 HIS B 492 GLN C 271 ASN C 451 HIS D 104 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN F 188 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.153219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127540 restraints weight = 23489.600| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.27 r_work: 0.3518 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 20711 Z= 0.187 Angle : 0.720 28.742 27941 Z= 0.334 Chirality : 0.046 0.269 2983 Planarity : 0.005 0.059 3592 Dihedral : 9.322 140.696 3271 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 5.52 % Allowed : 22.08 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.26 (0.17), residues: 2526 helix: 1.10 (0.15), residues: 1238 sheet: -0.54 (0.35), residues: 234 loop : -0.71 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.018 0.001 TYR D 142 PHE 0.013 0.002 PHE A 431 TRP 0.021 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00410 (20691) covalent geometry : angle 0.70899 (27929) hydrogen bonds : bond 0.04875 ( 950) hydrogen bonds : angle 5.42814 ( 2736) metal coordination : bond 0.00927 ( 4) metal coordination : angle 6.14949 ( 12) Misc. bond : bond 0.10776 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 600 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.6843 (mmp-170) REVERT: B 102 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8275 (t80) REVERT: D 499 ASN cc_start: 0.8469 (m-40) cc_final: 0.8064 (m110) REVERT: E 58 MET cc_start: 0.7666 (mmm) cc_final: 0.7333 (mmm) REVERT: E 179 LEU cc_start: 0.8736 (tp) cc_final: 0.8531 (mt) REVERT: F 76 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7134 (tt) outliers start: 119 outliers final: 67 residues processed: 663 average time/residue: 0.6653 time to fit residues: 491.2277 Evaluate side-chains 656 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 586 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 63 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 35 ASN A 145 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 457 HIS B 492 GLN C 98 ASN C 145 ASN C 199 ASN C 271 ASN C 298 ASN C 468 ASN C 469 ASN D 163 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.152801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127043 restraints weight = 23539.640| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.27 r_work: 0.3511 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 20711 Z= 0.199 Angle : 0.722 29.042 27941 Z= 0.335 Chirality : 0.046 0.260 2983 Planarity : 0.004 0.048 3592 Dihedral : 8.354 135.292 3211 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 5.80 % Allowed : 21.85 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.19 (0.16), residues: 2526 helix: 1.07 (0.15), residues: 1240 sheet: -0.49 (0.36), residues: 226 loop : -0.81 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.020 0.002 TYR D 142 PHE 0.014 0.002 PHE A 431 TRP 0.022 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00449 (20691) covalent geometry : angle 0.71092 (27929) hydrogen bonds : bond 0.04875 ( 950) hydrogen bonds : angle 5.30541 ( 2736) metal coordination : bond 0.01129 ( 4) metal coordination : angle 6.14402 ( 12) Misc. bond : bond 0.10333 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 599 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 439 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.6952 (mmp-170) REVERT: B 102 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.8305 (t80) REVERT: B 118 MET cc_start: 0.8431 (mtp) cc_final: 0.8226 (mtm) REVERT: C 210 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7522 (mtt180) REVERT: C 362 HIS cc_start: 0.5343 (OUTLIER) cc_final: 0.4721 (m90) REVERT: C 441 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7309 (mmp) REVERT: D 360 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8280 (t) REVERT: D 400 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7637 (mtmm) REVERT: E 239 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6767 (mt-10) REVERT: F 112 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6370 (mm-30) REVERT: F 253 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7490 (pt) outliers start: 125 outliers final: 74 residues processed: 659 average time/residue: 0.6640 time to fit residues: 488.5385 Evaluate side-chains 664 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 584 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 246 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 76 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 145 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 457 HIS B 492 GLN C 199 ASN C 271 ASN C 384 ASN D 104 ASN D 163 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN E 21 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.152736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127021 restraints weight = 23531.577| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.27 r_work: 0.3511 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 20711 Z= 0.195 Angle : 0.719 29.048 27941 Z= 0.333 Chirality : 0.046 0.268 2983 Planarity : 0.004 0.044 3592 Dihedral : 8.178 133.843 3209 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 5.38 % Allowed : 22.45 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.19 (0.16), residues: 2526 helix: 1.09 (0.15), residues: 1241 sheet: -0.50 (0.34), residues: 246 loop : -0.84 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 389 TYR 0.021 0.002 TYR C 91 PHE 0.014 0.002 PHE A 431 TRP 0.022 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00442 (20691) covalent geometry : angle 0.70813 (27929) hydrogen bonds : bond 0.04759 ( 950) hydrogen bonds : angle 5.24663 ( 2736) metal coordination : bond 0.01135 ( 4) metal coordination : angle 6.14369 ( 12) Misc. bond : bond 0.09800 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 600 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6949 (mmp-170) REVERT: B 102 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8299 (t80) REVERT: C 321 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: C 362 HIS cc_start: 0.5340 (OUTLIER) cc_final: 0.4815 (m90) REVERT: C 441 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7270 (mmp) REVERT: D 400 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7617 (mtmm) REVERT: E 239 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6778 (mt-10) REVERT: F 253 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7562 (pt) outliers start: 116 outliers final: 76 residues processed: 658 average time/residue: 0.6940 time to fit residues: 507.3800 Evaluate side-chains 675 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 593 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 204 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 149 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 35 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 457 HIS B 492 GLN C 98 ASN C 199 ASN C 271 ASN D 104 ASN D 163 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.153111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127447 restraints weight = 23430.380| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.26 r_work: 0.3517 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 20711 Z= 0.177 Angle : 0.711 29.051 27941 Z= 0.327 Chirality : 0.045 0.286 2983 Planarity : 0.004 0.041 3592 Dihedral : 7.899 133.605 3200 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 5.15 % Allowed : 22.26 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.22 (0.17), residues: 2526 helix: 1.13 (0.15), residues: 1241 sheet: -0.67 (0.35), residues: 244 loop : -0.79 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.022 0.001 TYR C 91 PHE 0.013 0.001 PHE A 431 TRP 0.021 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00397 (20691) covalent geometry : angle 0.69959 (27929) hydrogen bonds : bond 0.04551 ( 950) hydrogen bonds : angle 5.18480 ( 2736) metal coordination : bond 0.01054 ( 4) metal coordination : angle 6.07922 ( 12) Misc. bond : bond 0.09347 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 603 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7769 (mtpp) REVERT: A 439 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.6851 (mmp-170) REVERT: B 102 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8296 (t80) REVERT: C 362 HIS cc_start: 0.5371 (OUTLIER) cc_final: 0.4851 (m90) REVERT: C 441 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7272 (mmp) REVERT: D 400 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7578 (mtmm) REVERT: E 179 LEU cc_start: 0.8747 (tp) cc_final: 0.8522 (mt) REVERT: E 207 MET cc_start: 0.6878 (tmt) cc_final: 0.6665 (tmt) REVERT: F 253 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7531 (pt) outliers start: 111 outliers final: 71 residues processed: 658 average time/residue: 0.6811 time to fit residues: 497.2445 Evaluate side-chains 677 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 600 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 65 optimal weight: 0.3980 chunk 105 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 145 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 457 HIS B 492 GLN C 271 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126140 restraints weight = 23268.640| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.25 r_work: 0.3499 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.229 20711 Z= 0.254 Angle : 0.754 29.045 27941 Z= 0.351 Chirality : 0.048 0.336 2983 Planarity : 0.005 0.050 3592 Dihedral : 7.896 132.981 3194 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 5.71 % Allowed : 22.31 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.10 (0.16), residues: 2526 helix: 1.01 (0.15), residues: 1235 sheet: -0.42 (0.34), residues: 253 loop : -0.91 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.026 0.002 TYR C 91 PHE 0.018 0.002 PHE A 431 TRP 0.022 0.002 TRP C 335 HIS 0.010 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00594 (20691) covalent geometry : angle 0.74308 (27929) hydrogen bonds : bond 0.05236 ( 950) hydrogen bonds : angle 5.30525 ( 2736) metal coordination : bond 0.01594 ( 4) metal coordination : angle 6.19871 ( 12) Misc. bond : bond 0.10862 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 604 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7758 (mtpp) REVERT: A 408 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 439 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.6941 (mmp-170) REVERT: B 118 MET cc_start: 0.8445 (mtp) cc_final: 0.8240 (mtm) REVERT: C 362 HIS cc_start: 0.5430 (OUTLIER) cc_final: 0.4946 (m90) REVERT: C 441 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7267 (mmp) REVERT: D 360 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8272 (t) REVERT: E 29 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6539 (mpt) REVERT: E 207 MET cc_start: 0.6965 (tmt) cc_final: 0.6737 (tmt) REVERT: E 209 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6643 (m90) REVERT: E 241 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7808 (mtt-85) REVERT: E 246 LYS cc_start: 0.7627 (tttm) cc_final: 0.7252 (tttm) REVERT: E 266 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6495 (mt-10) REVERT: F 253 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7719 (pt) outliers start: 123 outliers final: 85 residues processed: 666 average time/residue: 0.6940 time to fit residues: 512.2398 Evaluate side-chains 686 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 592 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 209 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 241 ARG Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 186 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 218 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 35 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS B 492 GLN C 98 ASN C 271 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN D 104 ASN D 163 ASN D 167 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN D 492 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127129 restraints weight = 23496.733| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.25 r_work: 0.3512 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 20711 Z= 0.184 Angle : 0.726 29.044 27941 Z= 0.333 Chirality : 0.046 0.340 2983 Planarity : 0.004 0.041 3592 Dihedral : 7.751 133.684 3194 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.87 % Rotamer: Outliers : 5.61 % Allowed : 22.82 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.21 (0.17), residues: 2526 helix: 1.08 (0.15), residues: 1242 sheet: -0.34 (0.34), residues: 251 loop : -0.84 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 284 TYR 0.027 0.002 TYR C 91 PHE 0.013 0.001 PHE A 431 TRP 0.023 0.002 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00418 (20691) covalent geometry : angle 0.71456 (27929) hydrogen bonds : bond 0.04653 ( 950) hydrogen bonds : angle 5.19889 ( 2736) metal coordination : bond 0.01101 ( 4) metal coordination : angle 6.16023 ( 12) Misc. bond : bond 0.09463 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 595 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7755 (mtpp) REVERT: A 439 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.6897 (mmp-170) REVERT: B 118 MET cc_start: 0.8433 (mtp) cc_final: 0.8200 (mtm) REVERT: C 362 HIS cc_start: 0.5405 (OUTLIER) cc_final: 0.4903 (m90) REVERT: C 441 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7301 (mmp) REVERT: E 29 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6583 (mpt) REVERT: E 207 MET cc_start: 0.6992 (tmt) cc_final: 0.6763 (tmt) REVERT: E 209 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.6619 (m90) REVERT: E 241 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7810 (mtt-85) REVERT: E 246 LYS cc_start: 0.7552 (tttm) cc_final: 0.7092 (tttm) REVERT: E 266 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6526 (mt-10) REVERT: F 253 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7731 (pt) outliers start: 121 outliers final: 82 residues processed: 658 average time/residue: 0.6754 time to fit residues: 493.5678 Evaluate side-chains 681 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 591 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 209 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 241 ARG Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 6 optimal weight: 0.9990 chunk 171 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 145 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS B 492 GLN C 98 ASN C 199 ASN C 271 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 163 ASN D 167 ASN D 225 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.153294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127605 restraints weight = 23423.401| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.27 r_work: 0.3520 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 20711 Z= 0.166 Angle : 0.715 29.052 27941 Z= 0.329 Chirality : 0.046 0.335 2983 Planarity : 0.004 0.043 3592 Dihedral : 7.372 132.032 3187 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 4.96 % Allowed : 23.61 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.28 (0.17), residues: 2526 helix: 1.16 (0.15), residues: 1240 sheet: -0.40 (0.34), residues: 261 loop : -0.80 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 284 TYR 0.028 0.001 TYR C 91 PHE 0.012 0.001 PHE A 431 TRP 0.022 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00369 (20691) covalent geometry : angle 0.70488 (27929) hydrogen bonds : bond 0.04423 ( 950) hydrogen bonds : angle 5.14158 ( 2736) metal coordination : bond 0.00950 ( 4) metal coordination : angle 5.91425 ( 12) Misc. bond : bond 0.08822 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 597 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7754 (mtpp) REVERT: A 439 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6906 (mmp-170) REVERT: C 362 HIS cc_start: 0.5390 (OUTLIER) cc_final: 0.4890 (m90) REVERT: C 441 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7299 (mmp) REVERT: E 29 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6529 (mpt) REVERT: E 179 LEU cc_start: 0.8754 (tp) cc_final: 0.8520 (mt) REVERT: E 207 MET cc_start: 0.6948 (tmt) cc_final: 0.6730 (tmt) REVERT: E 209 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6597 (m90) REVERT: E 241 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7808 (mtt-85) REVERT: E 246 LYS cc_start: 0.7672 (tttm) cc_final: 0.7215 (tttm) REVERT: E 266 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6446 (mt-10) REVERT: F 253 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7732 (pt) outliers start: 107 outliers final: 80 residues processed: 653 average time/residue: 0.6785 time to fit residues: 491.9632 Evaluate side-chains 683 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 595 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 209 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 241 ARG Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 224 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 0.0010 chunk 129 optimal weight: 0.6980 chunk 234 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 139 optimal weight: 0.2980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 35 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS B 492 GLN C 98 ASN C 145 ASN C 271 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 469 ASN D 104 ASN D 163 ASN D 167 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128316 restraints weight = 23350.019| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.27 r_work: 0.3530 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 20711 Z= 0.148 Angle : 0.721 29.070 27941 Z= 0.329 Chirality : 0.045 0.335 2983 Planarity : 0.004 0.041 3592 Dihedral : 7.208 129.952 3186 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 4.59 % Allowed : 24.21 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.34 (0.17), residues: 2526 helix: 1.22 (0.15), residues: 1242 sheet: -0.46 (0.34), residues: 251 loop : -0.76 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.029 0.001 TYR C 91 PHE 0.011 0.001 PHE A 431 TRP 0.021 0.002 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00325 (20691) covalent geometry : angle 0.71116 (27929) hydrogen bonds : bond 0.04157 ( 950) hydrogen bonds : angle 5.08385 ( 2736) metal coordination : bond 0.00804 ( 4) metal coordination : angle 5.65883 ( 12) Misc. bond : bond 0.08021 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 599 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7805 (mtpp) REVERT: A 439 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.6895 (mmp-170) REVERT: B 253 LEU cc_start: 0.8061 (tp) cc_final: 0.7756 (tp) REVERT: C 243 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: C 362 HIS cc_start: 0.5384 (OUTLIER) cc_final: 0.4872 (m90) REVERT: C 441 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7289 (mmp) REVERT: D 499 ASN cc_start: 0.8490 (m-40) cc_final: 0.8157 (m110) REVERT: E 29 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6523 (mpt) REVERT: E 59 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6972 (tm-30) REVERT: E 179 LEU cc_start: 0.8730 (tp) cc_final: 0.8503 (mt) REVERT: E 207 MET cc_start: 0.6974 (tmt) cc_final: 0.6744 (tmt) REVERT: E 209 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6584 (m90) REVERT: E 246 LYS cc_start: 0.7674 (tttm) cc_final: 0.7222 (tttm) REVERT: E 266 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6532 (mt-10) REVERT: F 253 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (pt) outliers start: 99 outliers final: 74 residues processed: 654 average time/residue: 0.6852 time to fit residues: 497.5455 Evaluate side-chains 675 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 593 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 209 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 160 optimal weight: 0.0170 chunk 243 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 162 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 145 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 457 HIS B 492 GLN C 98 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 469 ASN D 104 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128013 restraints weight = 23522.510| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.25 r_work: 0.3525 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 20711 Z= 0.171 Angle : 0.732 29.074 27941 Z= 0.338 Chirality : 0.046 0.337 2983 Planarity : 0.004 0.043 3592 Dihedral : 7.192 129.360 3186 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 3.99 % Allowed : 24.86 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % 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: 0.27 (0.17), residues: 2526 helix: 1.16 (0.15), residues: 1242 sheet: -0.46 (0.34), residues: 251 loop : -0.80 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 284 TYR 0.031 0.001 TYR C 91 PHE 0.012 0.001 PHE A 431 TRP 0.021 0.002 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00388 (20691) covalent geometry : angle 0.72206 (27929) hydrogen bonds : bond 0.04366 ( 950) hydrogen bonds : angle 5.12410 ( 2736) metal coordination : bond 0.01016 ( 4) metal coordination : angle 5.87873 ( 12) Misc. bond : bond 0.08642 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 593 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7799 (mtpp) REVERT: A 439 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.6973 (mmp-170) REVERT: B 253 LEU cc_start: 0.7949 (tp) cc_final: 0.7729 (tp) REVERT: C 243 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: C 362 HIS cc_start: 0.5407 (OUTLIER) cc_final: 0.4914 (m90) REVERT: C 441 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7285 (mmp) REVERT: E 29 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6532 (mpt) REVERT: E 179 LEU cc_start: 0.8741 (tp) cc_final: 0.8518 (mt) REVERT: E 207 MET cc_start: 0.6912 (tmt) cc_final: 0.6693 (tmt) REVERT: E 209 HIS cc_start: 0.6926 (OUTLIER) cc_final: 0.6598 (m90) REVERT: E 246 LYS cc_start: 0.7656 (tttm) cc_final: 0.7200 (tttm) REVERT: E 266 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6526 (mt-10) REVERT: F 253 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7735 (pt) outliers start: 86 outliers final: 70 residues processed: 644 average time/residue: 0.6945 time to fit residues: 496.7239 Evaluate side-chains 663 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 585 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 209 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 262 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 182 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 104 optimal weight: 0.0980 chunk 206 optimal weight: 0.2980 chunk 120 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 110 optimal weight: 0.0070 chunk 147 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 35 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS B 492 GLN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 163 ASN D 278 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.154940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.129302 restraints weight = 23485.234| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.28 r_work: 0.3544 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 20711 Z= 0.130 Angle : 0.721 29.070 27941 Z= 0.330 Chirality : 0.045 0.333 2983 Planarity : 0.004 0.042 3592 Dihedral : 6.939 125.114 3183 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 3.66 % Allowed : 25.83 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2526 helix: 1.25 (0.15), residues: 1241 sheet: -0.41 (0.34), residues: 251 loop : -0.75 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 284 TYR 0.029 0.001 TYR C 91 PHE 0.013 0.001 PHE A 409 TRP 0.022 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00276 (20691) covalent geometry : angle 0.71208 (27929) hydrogen bonds : bond 0.03824 ( 950) hydrogen bonds : angle 5.02116 ( 2736) metal coordination : bond 0.00556 ( 4) metal coordination : angle 5.40164 ( 12) Misc. bond : bond 0.06972 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10837.83 seconds wall clock time: 184 minutes 22.70 seconds (11062.70 seconds total)