Starting phenix.real_space_refine on Fri Feb 6 02:58:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pxb_13696/02_2026/7pxb_13696_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pxb_13696/02_2026/7pxb_13696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pxb_13696/02_2026/7pxb_13696_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pxb_13696/02_2026/7pxb_13696_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pxb_13696/02_2026/7pxb_13696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pxb_13696/02_2026/7pxb_13696.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 67 5.16 5 C 13992 2.51 5 N 3842 2.21 5 O 4361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22286 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3650 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain breaks: 3 Chain: "B" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3719 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain breaks: 1 Chain: "C" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3629 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 2 Chain: "D" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3542 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3719 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain breaks: 1 Chain: "F" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3723 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 22, 'TRANS': 454} Chain breaks: 1 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.11, per 1000 atoms: 0.23 Number of scatterers: 22286 At special positions: 0 Unit cell: (139.308, 155.194, 129.532, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 67 16.00 P 18 15.00 Mg 6 11.99 O 4361 8.00 N 3842 7.00 C 13992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 928.1 milliseconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5256 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 17 sheets defined 41.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.561A pdb=" N LEU A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 242' Processing helix chain 'A' and resid 258 through 274 removed outlier: 4.198A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.718A pdb=" N TYR A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 335 through 338 removed outlier: 3.744A pdb=" N LEU A 338 " --> pdb=" O PRO A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.948A pdb=" N ILE A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 404 removed outlier: 4.535A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 460 through 467 removed outlier: 3.811A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 487 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 511 through 514 Processing helix chain 'A' and resid 515 through 537 Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.868A pdb=" N LEU A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 4.340A pdb=" N THR A 564 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 259 through 274 Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 298 through 318 Processing helix chain 'B' and resid 333 through 338 removed outlier: 4.221A pdb=" N LEU B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.639A pdb=" N GLN B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 460 through 467 removed outlier: 3.594A pdb=" N PHE B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 488 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 511 through 514 removed outlier: 3.727A pdb=" N ASN B 514 " --> pdb=" O LYS B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 514' Processing helix chain 'B' and resid 515 through 537 Processing helix chain 'B' and resid 543 through 559 Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'C' and resid 236 through 242 removed outlier: 4.008A pdb=" N ASP C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 266 removed outlier: 3.535A pdb=" N ASP C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 removed outlier: 3.635A pdb=" N HIS C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 343 through 361 Processing helix chain 'C' and resid 388 through 391 Processing helix chain 'C' and resid 392 through 401 removed outlier: 3.838A pdb=" N LEU C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'C' and resid 470 through 487 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 511 through 514 removed outlier: 3.943A pdb=" N ASN C 514 " --> pdb=" O LYS C 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 514' Processing helix chain 'C' and resid 515 through 538 Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.753A pdb=" N LEU C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 566 through 578 removed outlier: 3.914A pdb=" N TRP C 570 " --> pdb=" O ASN C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 268 through 274 removed outlier: 3.886A pdb=" N PHE D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 281 Processing helix chain 'D' and resid 300 through 315 removed outlier: 4.040A pdb=" N ALA D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.663A pdb=" N LEU D 338 " --> pdb=" O GLY D 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 338' Processing helix chain 'D' and resid 339 through 342 removed outlier: 3.950A pdb=" N VAL D 342 " --> pdb=" O ASN D 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 339 through 342' Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.905A pdb=" N ARG D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 376 Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 441 through 453 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.921A pdb=" N GLU D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 487 Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.685A pdb=" N ARG D 494 " --> pdb=" O ASP D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 537 Processing helix chain 'D' and resid 543 through 559 removed outlier: 3.530A pdb=" N LEU D 547 " --> pdb=" O ARG D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 578 Processing helix chain 'E' and resid 131 through 135 removed outlier: 3.514A pdb=" N SER E 134 " --> pdb=" O ASP E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 193 Processing helix chain 'E' and resid 236 through 243 removed outlier: 4.099A pdb=" N ASP E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 258 through 274 removed outlier: 4.187A pdb=" N LEU E 270 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 274 through 281 removed outlier: 3.551A pdb=" N TYR E 278 " --> pdb=" O HIS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 318 removed outlier: 3.695A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 327 removed outlier: 3.596A pdb=" N ALA E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 338 removed outlier: 4.073A pdb=" N LEU E 337 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.561A pdb=" N ARG E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 360 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 376 removed outlier: 3.608A pdb=" N ILE E 376 " --> pdb=" O MET E 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 373 through 376' Processing helix chain 'E' and resid 387 through 401 removed outlier: 4.001A pdb=" N THR E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) Proline residue: E 394 - end of helix Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 460 through 467 removed outlier: 4.082A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE E 467 " --> pdb=" O ASP E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 487 Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 515 through 538 Processing helix chain 'E' and resid 543 through 558 removed outlier: 3.722A pdb=" N LEU E 547 " --> pdb=" O ARG E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 578 removed outlier: 4.094A pdb=" N ILE E 573 " --> pdb=" O ASP E 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 193 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 257 through 274 removed outlier: 4.183A pdb=" N LEU F 270 " --> pdb=" O ASP F 266 " (cutoff:3.500A) Proline residue: F 271 - end of helix Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.977A pdb=" N TYR F 278 " --> pdb=" O HIS F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 316 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.722A pdb=" N TYR F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 338 Processing helix chain 'F' and resid 344 through 360 Processing helix chain 'F' and resid 388 through 400 Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 422 through 427 removed outlier: 3.591A pdb=" N LEU F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG F 427 " --> pdb=" O PRO F 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 422 through 427' Processing helix chain 'F' and resid 441 through 453 Processing helix chain 'F' and resid 460 through 466 removed outlier: 4.388A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 487 Processing helix chain 'F' and resid 511 through 514 removed outlier: 3.503A pdb=" N ASN F 514 " --> pdb=" O LYS F 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 511 through 514' Processing helix chain 'F' and resid 515 through 537 Processing helix chain 'F' and resid 543 through 558 Processing helix chain 'F' and resid 569 through 578 removed outlier: 4.424A pdb=" N GLY F 575 " --> pdb=" O ALA F 571 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 125 removed outlier: 7.116A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 151 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 167 removed outlier: 6.824A pdb=" N LEU A 175 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE A 167 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG A 173 " --> pdb=" O ILE A 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 188 current: chain 'A' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 228 through 232 current: chain 'B' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 183 through 188 current: chain 'B' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 228 through 232 current: chain 'C' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 183 through 188 current: chain 'C' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 228 through 233 current: chain 'D' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 183 through 188 current: chain 'D' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 228 through 233 current: chain 'E' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 183 through 188 current: chain 'E' and resid 228 through 231 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 228 through 231 current: chain 'F' and resid 173 through 176 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 184 through 188 current: chain 'F' and resid 228 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 333 removed outlier: 3.581A pdb=" N ALA A 414 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 289 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER A 415 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 291 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY A 288 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A 435 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 290 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.015A pdb=" N GLU A 506 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU A 497 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N MET A 508 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE A 495 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 586 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU A 497 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 584 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 499 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 107 removed outlier: 6.648A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR B 107 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR B 112 " --> pdb=" O THR B 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 120 through 125 current: chain 'E' and resid 112 through 117 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 120 through 125 current: chain 'E' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 332 removed outlier: 6.193A pdb=" N LEU B 330 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP B 371 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 332 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 506 through 509 Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 107 removed outlier: 6.825A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 120 through 125 current: chain 'C' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 152 current: chain 'F' and resid 112 through 117 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 120 through 125 current: chain 'F' and resid 151 through 152 Processing sheet with id=AA9, first strand: chain 'C' and resid 328 through 332 removed outlier: 6.602A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 366 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE C 412 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 368 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA C 414 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE C 370 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY C 288 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE C 435 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU C 290 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 506 through 509 removed outlier: 4.029A pdb=" N TYR C 583 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 125 removed outlier: 6.598A pdb=" N ASP D 114 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 151 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 328 through 333 removed outlier: 7.172A pdb=" N TYR D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE D 369 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU D 330 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP D 371 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE D 332 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D 366 " --> pdb=" O ILE D 410 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE D 412 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL D 368 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA D 414 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE D 370 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 289 " --> pdb=" O GLY D 413 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N SER D 415 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU D 291 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY D 288 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE D 435 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU D 290 " --> pdb=" O ILE D 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 505 through 508 removed outlier: 3.827A pdb=" N THR D 499 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR D 583 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 329 through 331 removed outlier: 6.678A pdb=" N LEU E 330 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP E 371 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 433 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 506 through 509 removed outlier: 5.956A pdb=" N GLU E 506 " --> pdb=" O GLU E 497 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU E 497 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET E 508 " --> pdb=" O PHE E 495 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG E 585 " --> pdb=" O GLU E 497 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR E 583 " --> pdb=" O THR E 499 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 330 through 333 removed outlier: 6.230A pdb=" N LEU F 290 " --> pdb=" O ILE F 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 505 through 509 861 hydrogen bonds defined for protein. 2469 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: 3.92 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5988 1.33 - 1.45: 3482 1.45 - 1.57: 13039 1.57 - 1.69: 30 1.69 - 1.81: 116 Bond restraints: 22655 Sorted by residual: bond pdb=" C4 ATP F 701 " pdb=" C5 ATP F 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 ATP C 701 " pdb=" C5 ATP C 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP D 701 " pdb=" C5 ATP D 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.76e+01 ... (remaining 22650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 30573 4.51 - 9.02: 96 9.02 - 13.54: 0 13.54 - 18.05: 4 18.05 - 22.56: 8 Bond angle restraints: 30681 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 117.31 22.56 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 117.65 22.22 1.00e+00 1.00e+00 4.94e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 117.85 22.02 1.00e+00 1.00e+00 4.85e+02 angle pdb=" PB ATP E 701 " pdb=" O3B ATP E 701 " pdb=" PG ATP E 701 " ideal model delta sigma weight residual 139.87 117.94 21.93 1.00e+00 1.00e+00 4.81e+02 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 119.41 20.46 1.00e+00 1.00e+00 4.19e+02 ... (remaining 30676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13286 18.00 - 35.99: 523 35.99 - 53.99: 121 53.99 - 71.99: 29 71.99 - 89.99: 36 Dihedral angle restraints: 13995 sinusoidal: 5851 harmonic: 8144 Sorted by residual: dihedral pdb=" CA LEU B 561 " pdb=" C LEU B 561 " pdb=" N PRO B 562 " pdb=" CA PRO B 562 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU D 557 " pdb=" CG GLU D 557 " pdb=" CD GLU D 557 " pdb=" OE1 GLU D 557 " ideal model delta sinusoidal sigma weight residual 0.00 88.63 -88.63 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 183 " pdb=" CG GLU B 183 " pdb=" CD GLU B 183 " pdb=" OE1 GLU B 183 " ideal model delta sinusoidal sigma weight residual 0.00 -86.76 86.76 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 13992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2641 0.043 - 0.086: 571 0.086 - 0.128: 268 0.128 - 0.171: 4 0.171 - 0.214: 5 Chirality restraints: 3489 Sorted by residual: chirality pdb=" CA ILE C 435 " pdb=" N ILE C 435 " pdb=" C ILE C 435 " pdb=" CB ILE C 435 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE C 437 " pdb=" N ILE C 437 " pdb=" C ILE C 437 " pdb=" CB ILE C 437 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU E 221 " pdb=" N LEU E 221 " pdb=" C LEU E 221 " pdb=" CB LEU E 221 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 3486 not shown) Planarity restraints: 3988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 229 " 0.029 2.00e-02 2.50e+03 5.91e-02 3.49e+01 pdb=" C ALA E 229 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA E 229 " 0.040 2.00e-02 2.50e+03 pdb=" N PHE E 230 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 334 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO B 335 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 334 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO E 335 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 335 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 335 " 0.022 5.00e-02 4.00e+02 ... (remaining 3985 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 221 2.60 - 3.17: 19373 3.17 - 3.75: 34706 3.75 - 4.32: 46756 4.32 - 4.90: 77190 Nonbonded interactions: 178246 Sorted by model distance: nonbonded pdb=" O1G ATP E 701 " pdb="MG MG E 702 " model vdw 2.022 2.170 nonbonded pdb=" O1B ATP D 701 " pdb="MG MG D 702 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR A 300 " pdb="MG MG A 702 " model vdw 2.133 2.170 nonbonded pdb=" OG1 THR E 300 " pdb="MG MG E 702 " model vdw 2.144 2.170 nonbonded pdb=" O1B ATP A 701 " pdb="MG MG A 702 " model vdw 2.145 2.170 ... (remaining 178241 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 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 701 through 702)) selection = (chain 'B' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 701 through 702)) selection = (chain 'C' and (resid 97 through 377 or resid 390 through 702)) selection = chain 'D' selection = (chain 'E' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 701 through 702)) selection = (chain 'F' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.330 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.004 0.083 22655 Z= 0.304 Angle : 0.734 22.561 30681 Z= 0.563 Chirality : 0.042 0.214 3489 Planarity : 0.003 0.059 3988 Dihedral : 11.582 89.987 8739 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 2.05 % Allowed : 5.27 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2792 helix: 2.09 (0.18), residues: 945 sheet: 0.23 (0.22), residues: 502 loop : 0.08 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 350 TYR 0.008 0.001 TYR B 449 PHE 0.008 0.001 PHE F 341 TRP 0.007 0.001 TRP F 187 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00393 (22655) covalent geometry : angle 0.73432 (30681) hydrogen bonds : bond 0.13601 ( 861) hydrogen bonds : angle 5.28295 ( 2469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7264 (m) cc_final: 0.6972 (t) REVERT: A 396 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 408 ASN cc_start: 0.6529 (OUTLIER) cc_final: 0.5392 (m110) REVERT: B 137 LYS cc_start: 0.6457 (ttmt) cc_final: 0.5855 (tptp) REVERT: B 384 VAL cc_start: 0.8206 (m) cc_final: 0.7672 (t) REVERT: C 314 MET cc_start: 0.6615 (tpt) cc_final: 0.6356 (tpt) REVERT: C 373 MET cc_start: 0.8430 (mmt) cc_final: 0.8207 (mpp) REVERT: C 420 MET cc_start: 0.7588 (mmm) cc_final: 0.7051 (mtm) REVERT: C 495 PHE cc_start: 0.5343 (t80) cc_final: 0.4023 (t80) REVERT: D 420 MET cc_start: 0.6935 (mtt) cc_final: 0.6560 (tpt) REVERT: D 524 ASP cc_start: 0.7654 (m-30) cc_final: 0.7381 (m-30) REVERT: E 122 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7192 (tpp) REVERT: E 124 LEU cc_start: 0.7571 (mp) cc_final: 0.6990 (mp) REVERT: E 389 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8598 (pp20) REVERT: F 316 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6742 (pm20) REVERT: F 373 MET cc_start: 0.8463 (tpp) cc_final: 0.8093 (tpp) outliers start: 49 outliers final: 14 residues processed: 316 average time/residue: 0.1620 time to fit residues: 78.1096 Evaluate side-chains 158 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 234 PRO Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 316 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 529 ASN A 539 GLN B 263 GLN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 GLN B 546 HIS C 172 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS D 172 HIS D 348 HIS D 416 ASN D 446 GLN D 520 GLN E 108 HIS E 408 ASN ** F 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 HIS F 348 HIS F 354 GLN F 395 GLN F 520 GLN F 546 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.062247 restraints weight = 104541.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063717 restraints weight = 62004.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064702 restraints weight = 43087.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.065313 restraints weight = 33603.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065755 restraints weight = 28541.212| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 22655 Z= 0.269 Angle : 0.701 8.577 30681 Z= 0.368 Chirality : 0.046 0.174 3489 Planarity : 0.006 0.054 3988 Dihedral : 9.005 89.869 3315 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.34 % Allowed : 9.61 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.49 (0.16), residues: 2792 helix: 1.30 (0.17), residues: 971 sheet: -0.01 (0.22), residues: 521 loop : -0.18 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 184 TYR 0.016 0.002 TYR C 328 PHE 0.022 0.002 PHE C 495 TRP 0.011 0.002 TRP F 570 HIS 0.007 0.001 HIS D 460 Details of bonding type rmsd covalent geometry : bond 0.00619 (22655) covalent geometry : angle 0.70092 (30681) hydrogen bonds : bond 0.04415 ( 861) hydrogen bonds : angle 4.86264 ( 2469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5837 (pm20) cc_final: 0.5621 (pm20) REVERT: A 243 LEU cc_start: 0.7270 (mt) cc_final: 0.6977 (pp) REVERT: A 396 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7618 (tt) REVERT: B 137 LYS cc_start: 0.6697 (ttmt) cc_final: 0.5967 (tptp) REVERT: C 420 MET cc_start: 0.7566 (mmm) cc_final: 0.6806 (mtm) REVERT: C 551 ILE cc_start: 0.5840 (OUTLIER) cc_final: 0.5637 (tt) REVERT: D 269 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6985 (mp0) REVERT: D 524 ASP cc_start: 0.7811 (m-30) cc_final: 0.7505 (m-30) REVERT: D 536 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7300 (mt-10) REVERT: E 122 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7260 (tpp) REVERT: E 124 LEU cc_start: 0.7781 (mp) cc_final: 0.6912 (mt) REVERT: E 273 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8700 (mm) REVERT: E 389 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8558 (pp20) REVERT: F 316 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: F 373 MET cc_start: 0.8689 (tpp) cc_final: 0.8375 (tpp) REVERT: G 1 MET cc_start: 0.6660 (pmm) cc_final: 0.5482 (mtt) outliers start: 56 outliers final: 33 residues processed: 186 average time/residue: 0.1500 time to fit residues: 45.0922 Evaluate side-chains 156 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 570 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 69 optimal weight: 0.9990 chunk 230 optimal weight: 0.0770 chunk 148 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 135 optimal weight: 0.0970 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 HIS B 460 HIS C 339 ASN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS E 274 HIS E 520 GLN F 108 HIS ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.078798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.064516 restraints weight = 103561.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065482 restraints weight = 60893.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066215 restraints weight = 42064.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066476 restraints weight = 36481.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066527 restraints weight = 34014.777| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 22655 Z= 0.109 Angle : 0.527 7.563 30681 Z= 0.273 Chirality : 0.042 0.162 3489 Planarity : 0.004 0.048 3988 Dihedral : 8.453 88.604 3309 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.13 % Allowed : 11.03 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.77 (0.16), residues: 2792 helix: 1.71 (0.17), residues: 956 sheet: -0.07 (0.22), residues: 516 loop : -0.05 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 378 TYR 0.011 0.001 TYR F 228 PHE 0.023 0.001 PHE B 155 TRP 0.018 0.002 TRP B 570 HIS 0.003 0.001 HIS D 460 Details of bonding type rmsd covalent geometry : bond 0.00246 (22655) covalent geometry : angle 0.52721 (30681) hydrogen bonds : bond 0.03323 ( 861) hydrogen bonds : angle 4.33570 ( 2469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.6001 (pm20) cc_final: 0.5646 (pm20) REVERT: A 396 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7604 (tt) REVERT: B 109 ASP cc_start: 0.8459 (p0) cc_final: 0.8055 (p0) REVERT: B 137 LYS cc_start: 0.6594 (ttmt) cc_final: 0.5697 (tptp) REVERT: B 384 VAL cc_start: 0.8588 (m) cc_final: 0.8016 (t) REVERT: C 486 MET cc_start: 0.8407 (ttp) cc_final: 0.7929 (ttp) REVERT: D 269 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7276 (mp0) REVERT: D 524 ASP cc_start: 0.7791 (m-30) cc_final: 0.7497 (m-30) REVERT: D 536 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7360 (mt-10) REVERT: E 122 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7166 (tpp) REVERT: E 124 LEU cc_start: 0.7802 (mp) cc_final: 0.7012 (mt) REVERT: E 233 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7785 (tp) REVERT: E 389 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8683 (pp20) REVERT: F 122 MET cc_start: 0.7203 (mmm) cc_final: 0.6880 (mmm) REVERT: F 316 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: F 333 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7626 (tptp) REVERT: F 373 MET cc_start: 0.8717 (tpp) cc_final: 0.8349 (tpp) REVERT: G 1 MET cc_start: 0.6450 (pmm) cc_final: 0.5610 (mtt) outliers start: 51 outliers final: 26 residues processed: 184 average time/residue: 0.1421 time to fit residues: 43.1286 Evaluate side-chains 152 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 570 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 124 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 chunk 155 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS D 348 HIS ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.076955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062595 restraints weight = 104602.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063762 restraints weight = 66812.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.064112 restraints weight = 45092.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064509 restraints weight = 39447.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.064570 restraints weight = 36836.585| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 22655 Z= 0.179 Angle : 0.590 9.822 30681 Z= 0.305 Chirality : 0.043 0.187 3489 Planarity : 0.005 0.049 3988 Dihedral : 8.633 88.249 3309 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.76 % Allowed : 11.78 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.53 (0.16), residues: 2792 helix: 1.43 (0.17), residues: 974 sheet: -0.11 (0.22), residues: 506 loop : -0.19 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 378 TYR 0.016 0.002 TYR F 228 PHE 0.016 0.002 PHE B 272 TRP 0.030 0.002 TRP B 570 HIS 0.005 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00417 (22655) covalent geometry : angle 0.59003 (30681) hydrogen bonds : bond 0.03679 ( 861) hydrogen bonds : angle 4.44136 ( 2469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5789 (pm20) cc_final: 0.5525 (pm20) REVERT: A 396 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7747 (tt) REVERT: B 137 LYS cc_start: 0.6705 (ttmt) cc_final: 0.5986 (tptt) REVERT: B 384 VAL cc_start: 0.8696 (m) cc_final: 0.8229 (t) REVERT: C 420 MET cc_start: 0.7864 (mmm) cc_final: 0.7038 (mtm) REVERT: D 269 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7135 (mp0) REVERT: D 524 ASP cc_start: 0.7699 (m-30) cc_final: 0.7409 (m-30) REVERT: E 122 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7286 (tpp) REVERT: E 124 LEU cc_start: 0.7989 (mp) cc_final: 0.7140 (mt) REVERT: E 233 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7948 (tp) REVERT: E 273 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8616 (mm) REVERT: E 389 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: F 122 MET cc_start: 0.7198 (mmm) cc_final: 0.6992 (mmm) REVERT: F 316 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: F 333 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7622 (tptp) REVERT: F 371 ASP cc_start: 0.7657 (t0) cc_final: 0.6352 (p0) REVERT: G 1 MET cc_start: 0.6535 (pmm) cc_final: 0.5699 (mtt) REVERT: G 3 GLN cc_start: 0.7865 (mp10) cc_final: 0.7654 (mp10) outliers start: 66 outliers final: 42 residues processed: 183 average time/residue: 0.1312 time to fit residues: 40.0821 Evaluate side-chains 163 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 570 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 272 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 215 optimal weight: 0.0170 chunk 140 optimal weight: 9.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 HIS D 172 HIS D 348 HIS ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.076268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.061593 restraints weight = 103688.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063021 restraints weight = 62604.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063970 restraints weight = 43868.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064588 restraints weight = 34369.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064992 restraints weight = 29249.498| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22655 Z= 0.183 Angle : 0.592 8.095 30681 Z= 0.309 Chirality : 0.043 0.164 3489 Planarity : 0.005 0.058 3988 Dihedral : 8.725 89.137 3309 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.63 % Allowed : 13.16 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.35 (0.16), residues: 2792 helix: 1.34 (0.17), residues: 972 sheet: -0.33 (0.22), residues: 505 loop : -0.29 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 543 TYR 0.024 0.002 TYR F 228 PHE 0.017 0.002 PHE B 272 TRP 0.024 0.002 TRP B 570 HIS 0.004 0.001 HIS D 460 Details of bonding type rmsd covalent geometry : bond 0.00425 (22655) covalent geometry : angle 0.59248 (30681) hydrogen bonds : bond 0.03621 ( 861) hydrogen bonds : angle 4.44588 ( 2469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 117 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7766 (tt) REVERT: B 137 LYS cc_start: 0.6768 (ttmt) cc_final: 0.5934 (tptt) REVERT: C 232 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7006 (tpt-90) REVERT: C 420 MET cc_start: 0.7831 (mmm) cc_final: 0.7384 (mmm) REVERT: D 524 ASP cc_start: 0.7703 (m-30) cc_final: 0.7430 (m-30) REVERT: D 555 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.5000 (m-80) REVERT: E 122 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7324 (tpp) REVERT: E 233 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8128 (tp) REVERT: E 273 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8503 (mm) REVERT: E 389 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8628 (pp20) REVERT: E 518 MET cc_start: 0.7236 (ttm) cc_final: 0.6818 (ttm) REVERT: F 316 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: F 371 ASP cc_start: 0.7724 (t0) cc_final: 0.7509 (t0) REVERT: G 1 MET cc_start: 0.6683 (pmm) cc_final: 0.5652 (mtt) REVERT: G 3 GLN cc_start: 0.8084 (mp10) cc_final: 0.7863 (mp10) outliers start: 63 outliers final: 44 residues processed: 172 average time/residue: 0.1321 time to fit residues: 38.0703 Evaluate side-chains 161 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 570 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 148 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 156 optimal weight: 0.5980 chunk 212 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 348 HIS E 408 ASN F 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.077150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.062351 restraints weight = 103533.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063839 restraints weight = 61087.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064838 restraints weight = 42284.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065449 restraints weight = 32857.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.065901 restraints weight = 27859.616| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22655 Z= 0.117 Angle : 0.534 8.388 30681 Z= 0.275 Chirality : 0.042 0.146 3489 Planarity : 0.004 0.063 3988 Dihedral : 8.413 89.841 3309 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.38 % Allowed : 14.75 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.52 (0.16), residues: 2792 helix: 1.55 (0.17), residues: 965 sheet: -0.29 (0.23), residues: 501 loop : -0.21 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 265 TYR 0.016 0.001 TYR F 228 PHE 0.029 0.001 PHE B 155 TRP 0.013 0.001 TRP A 187 HIS 0.003 0.000 HIS D 460 Details of bonding type rmsd covalent geometry : bond 0.00269 (22655) covalent geometry : angle 0.53409 (30681) hydrogen bonds : bond 0.03118 ( 861) hydrogen bonds : angle 4.18588 ( 2469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5451 (pm20) cc_final: 0.5175 (pm20) REVERT: B 137 LYS cc_start: 0.6761 (ttmt) cc_final: 0.5868 (tptt) REVERT: B 384 VAL cc_start: 0.8552 (m) cc_final: 0.8070 (t) REVERT: C 232 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6990 (tpt-90) REVERT: C 420 MET cc_start: 0.7822 (mmm) cc_final: 0.7377 (mmm) REVERT: D 269 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6803 (mp0) REVERT: D 524 ASP cc_start: 0.7707 (m-30) cc_final: 0.7455 (m-30) REVERT: D 555 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5112 (m-80) REVERT: E 182 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5790 (pm20) REVERT: E 233 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8244 (tp) REVERT: E 389 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8627 (pp20) REVERT: G 1 MET cc_start: 0.6589 (pmm) cc_final: 0.5762 (mtt) outliers start: 57 outliers final: 34 residues processed: 172 average time/residue: 0.1305 time to fit residues: 37.8765 Evaluate side-chains 152 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 570 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 100 optimal weight: 0.8980 chunk 269 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS F 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.076124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061819 restraints weight = 104202.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.062599 restraints weight = 69926.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.063104 restraints weight = 52332.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.063254 restraints weight = 47024.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.063374 restraints weight = 40939.132| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22655 Z= 0.166 Angle : 0.572 8.406 30681 Z= 0.296 Chirality : 0.043 0.262 3489 Planarity : 0.004 0.065 3988 Dihedral : 8.431 89.569 3301 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.38 % Allowed : 14.79 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.35 (0.16), residues: 2792 helix: 1.40 (0.17), residues: 977 sheet: -0.47 (0.22), residues: 512 loop : -0.28 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 142 TYR 0.016 0.002 TYR F 228 PHE 0.018 0.002 PHE E 353 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS D 460 Details of bonding type rmsd covalent geometry : bond 0.00387 (22655) covalent geometry : angle 0.57181 (30681) hydrogen bonds : bond 0.03471 ( 861) hydrogen bonds : angle 4.29979 ( 2469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 118 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5518 (pm20) cc_final: 0.5302 (pm20) REVERT: B 137 LYS cc_start: 0.6775 (ttmt) cc_final: 0.5896 (tptt) REVERT: B 384 VAL cc_start: 0.8604 (m) cc_final: 0.8137 (t) REVERT: B 502 ASN cc_start: 0.6364 (t0) cc_final: 0.5864 (m-40) REVERT: C 232 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6967 (tpt-90) REVERT: C 420 MET cc_start: 0.7790 (mmm) cc_final: 0.7244 (mmm) REVERT: D 182 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5510 (pm20) REVERT: D 213 LYS cc_start: 0.5988 (tttt) cc_final: 0.5586 (mtmm) REVERT: D 269 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6974 (mp0) REVERT: D 430 ARG cc_start: 0.3870 (OUTLIER) cc_final: 0.3530 (mpp-170) REVERT: D 524 ASP cc_start: 0.7638 (m-30) cc_final: 0.7396 (m-30) REVERT: D 555 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.5130 (m-80) REVERT: E 182 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5744 (pm20) REVERT: E 273 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8485 (mm) REVERT: E 389 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8664 (pp20) REVERT: F 122 MET cc_start: 0.6789 (mmm) cc_final: 0.6540 (mmm) REVERT: G 1 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.5979 (mtt) outliers start: 57 outliers final: 37 residues processed: 169 average time/residue: 0.1389 time to fit residues: 38.7597 Evaluate side-chains 160 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 167 optimal weight: 0.0770 chunk 153 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 231 optimal weight: 2.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.076108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062035 restraints weight = 102448.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.063036 restraints weight = 69396.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.063392 restraints weight = 45868.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.063571 restraints weight = 44326.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.063671 restraints weight = 40153.631| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22655 Z= 0.158 Angle : 0.570 9.320 30681 Z= 0.294 Chirality : 0.043 0.176 3489 Planarity : 0.004 0.063 3988 Dihedral : 8.437 89.032 3299 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.76 % Allowed : 14.54 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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 (0.16), residues: 2792 helix: 1.36 (0.17), residues: 976 sheet: -0.50 (0.23), residues: 495 loop : -0.35 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 120 TYR 0.017 0.001 TYR F 228 PHE 0.030 0.002 PHE B 155 TRP 0.015 0.001 TRP A 187 HIS 0.004 0.001 HIS B 546 Details of bonding type rmsd covalent geometry : bond 0.00368 (22655) covalent geometry : angle 0.57020 (30681) hydrogen bonds : bond 0.03358 ( 861) hydrogen bonds : angle 4.30660 ( 2469) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 116 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5619 (pm20) cc_final: 0.5332 (pm20) REVERT: A 243 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6765 (mt) REVERT: B 137 LYS cc_start: 0.6814 (ttmt) cc_final: 0.5587 (tptt) REVERT: B 384 VAL cc_start: 0.8589 (m) cc_final: 0.8162 (t) REVERT: B 502 ASN cc_start: 0.6494 (t0) cc_final: 0.5919 (m-40) REVERT: C 232 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6979 (tpt-90) REVERT: C 420 MET cc_start: 0.7824 (mmm) cc_final: 0.7265 (mmm) REVERT: D 182 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5747 (pm20) REVERT: D 269 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7020 (mp0) REVERT: D 420 MET cc_start: 0.6541 (mtt) cc_final: 0.6310 (mpp) REVERT: D 524 ASP cc_start: 0.7629 (m-30) cc_final: 0.7387 (m-30) REVERT: D 555 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.4984 (m-80) REVERT: E 182 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5711 (pm20) REVERT: E 273 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8380 (mm) REVERT: E 389 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8647 (pp20) REVERT: G 1 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.5965 (mtt) outliers start: 66 outliers final: 42 residues processed: 175 average time/residue: 0.1325 time to fit residues: 38.8876 Evaluate side-chains 161 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 185 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 153 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 HIS C 274 HIS D 144 ASN D 348 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 521 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.076028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062156 restraints weight = 103877.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.063042 restraints weight = 63028.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063777 restraints weight = 42981.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063992 restraints weight = 37861.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064012 restraints weight = 33540.198| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22655 Z= 0.154 Angle : 0.575 9.272 30681 Z= 0.295 Chirality : 0.042 0.145 3489 Planarity : 0.004 0.068 3988 Dihedral : 8.438 86.996 3299 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.42 % Allowed : 14.67 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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 (0.16), residues: 2792 helix: 1.36 (0.17), residues: 975 sheet: -0.57 (0.23), residues: 506 loop : -0.34 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 120 TYR 0.016 0.001 TYR F 228 PHE 0.028 0.002 PHE B 155 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS D 460 Details of bonding type rmsd covalent geometry : bond 0.00360 (22655) covalent geometry : angle 0.57491 (30681) hydrogen bonds : bond 0.03380 ( 861) hydrogen bonds : angle 4.28534 ( 2469) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 113 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8060 (t0) cc_final: 0.7777 (m-30) REVERT: A 243 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6709 (mt) REVERT: B 137 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6136 (tptt) REVERT: B 384 VAL cc_start: 0.8577 (m) cc_final: 0.8154 (t) REVERT: B 502 ASN cc_start: 0.6349 (t0) cc_final: 0.5910 (m-40) REVERT: C 232 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7004 (tpt-90) REVERT: C 420 MET cc_start: 0.7802 (mmm) cc_final: 0.7245 (mmm) REVERT: D 182 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5958 (pm20) REVERT: D 269 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6993 (mp0) REVERT: D 277 LEU cc_start: 0.8584 (mt) cc_final: 0.8203 (tp) REVERT: D 420 MET cc_start: 0.6410 (mtt) cc_final: 0.6143 (mpp) REVERT: D 524 ASP cc_start: 0.7643 (m-30) cc_final: 0.7402 (m-30) REVERT: D 555 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.4851 (m-80) REVERT: E 182 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5771 (pm20) REVERT: E 273 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8399 (mm) REVERT: E 389 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8593 (pp20) REVERT: G 1 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6112 (mtt) outliers start: 58 outliers final: 39 residues processed: 163 average time/residue: 0.1345 time to fit residues: 36.4262 Evaluate side-chains 157 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 242 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 546 HIS C 274 HIS D 348 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.076293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.062219 restraints weight = 103414.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.063218 restraints weight = 66337.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063819 restraints weight = 44169.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.063935 restraints weight = 43015.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064005 restraints weight = 37433.318| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22655 Z= 0.131 Angle : 0.565 9.978 30681 Z= 0.289 Chirality : 0.042 0.154 3489 Planarity : 0.004 0.064 3988 Dihedral : 8.357 88.847 3299 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.13 % Allowed : 15.00 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.31 (0.16), residues: 2792 helix: 1.41 (0.17), residues: 975 sheet: -0.54 (0.23), residues: 485 loop : -0.33 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 120 TYR 0.014 0.001 TYR F 228 PHE 0.036 0.002 PHE B 155 TRP 0.015 0.001 TRP A 187 HIS 0.010 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00306 (22655) covalent geometry : angle 0.56508 (30681) hydrogen bonds : bond 0.03223 ( 861) hydrogen bonds : angle 4.20710 ( 2469) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6865 (mt) REVERT: A 373 MET cc_start: 0.7928 (mmt) cc_final: 0.7477 (mmt) REVERT: B 137 LYS cc_start: 0.7057 (ttmt) cc_final: 0.6474 (tptt) REVERT: B 384 VAL cc_start: 0.8537 (m) cc_final: 0.8094 (t) REVERT: B 502 ASN cc_start: 0.6433 (t0) cc_final: 0.6041 (m-40) REVERT: B 518 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7921 (ttp) REVERT: C 420 MET cc_start: 0.7790 (mmm) cc_final: 0.7209 (mmm) REVERT: D 182 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5967 (pm20) REVERT: D 269 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6958 (mp0) REVERT: D 277 LEU cc_start: 0.8557 (mt) cc_final: 0.8219 (tt) REVERT: D 420 MET cc_start: 0.6407 (mtt) cc_final: 0.6163 (mpp) REVERT: D 524 ASP cc_start: 0.7601 (m-30) cc_final: 0.7370 (m-30) REVERT: D 555 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.4901 (m-80) REVERT: E 182 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5742 (pm20) REVERT: E 273 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8354 (mm) REVERT: E 389 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8616 (pp20) REVERT: G 1 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6124 (mtt) outliers start: 51 outliers final: 40 residues processed: 156 average time/residue: 0.1209 time to fit residues: 32.0370 Evaluate side-chains 155 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 570 TRP Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 174 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 HIS C 274 HIS D 348 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.076509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.062924 restraints weight = 102771.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063562 restraints weight = 59574.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.064115 restraints weight = 42293.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.064236 restraints weight = 41707.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.064247 restraints weight = 35846.209| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22655 Z= 0.123 Angle : 0.560 10.228 30681 Z= 0.287 Chirality : 0.042 0.148 3489 Planarity : 0.004 0.063 3988 Dihedral : 8.280 89.508 3299 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.26 % Allowed : 15.00 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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 (0.16), residues: 2792 helix: 1.45 (0.17), residues: 975 sheet: -0.57 (0.23), residues: 501 loop : -0.29 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 120 TYR 0.020 0.001 TYR C 583 PHE 0.037 0.001 PHE B 155 TRP 0.015 0.001 TRP A 187 HIS 0.015 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00284 (22655) covalent geometry : angle 0.56035 (30681) hydrogen bonds : bond 0.03094 ( 861) hydrogen bonds : angle 4.15638 ( 2469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.57 seconds wall clock time: 54 minutes 12.38 seconds (3252.38 seconds total)