Starting phenix.real_space_refine on Thu Jun 19 12:39:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pxb_13696/06_2025/7pxb_13696_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pxb_13696/06_2025/7pxb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pxb_13696/06_2025/7pxb_13696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pxb_13696/06_2025/7pxb_13696.map" model { file = "/net/cci-nas-00/data/ceres_data/7pxb_13696/06_2025/7pxb_13696_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pxb_13696/06_2025/7pxb_13696_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.45, per 1000 atoms: 0.69 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: 6.28 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.85 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: 6.79 Time building geometry restraints manager: 7.33 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 587 or resid 701 throu \ gh 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 53.470 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (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 TRP 0.007 0.001 TRP F 187 HIS 0.002 0.000 HIS B 323 PHE 0.008 0.001 PHE F 341 TYR 0.008 0.001 TYR B 449 ARG 0.002 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.13601 ( 861) hydrogen bonds : angle 5.28295 ( 2469) covalent geometry : bond 0.00393 (22655) covalent geometry : angle 0.73432 (30681) *********************** 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 : 2.581 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: 0.6971 (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: 0.3753 time to fit residues: 178.7674 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 : 3.076 ------------------------------------------------------------------------------- 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 235 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 253 optimal weight: 0.9980 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 460 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.077753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062865 restraints weight = 104054.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.064338 restraints weight = 61040.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.065316 restraints weight = 42252.785| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 22655 Z= 0.254 Angle : 0.664 8.424 30681 Z= 0.348 Chirality : 0.045 0.187 3489 Planarity : 0.005 0.052 3988 Dihedral : 8.928 86.542 3315 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.26 % Allowed : 9.49 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2792 helix: 1.49 (0.17), residues: 969 sheet: 0.01 (0.21), residues: 538 loop : -0.09 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 570 HIS 0.006 0.001 HIS D 460 PHE 0.019 0.002 PHE C 510 TYR 0.014 0.002 TYR B 292 ARG 0.008 0.001 ARG C 165 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 861) hydrogen bonds : angle 4.78037 ( 2469) covalent geometry : bond 0.00589 (22655) covalent geometry : angle 0.66357 (30681) *********************** 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 196 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5832 (pm20) cc_final: 0.5616 (pm20) REVERT: A 243 LEU cc_start: 0.7178 (mt) cc_final: 0.6908 (pp) REVERT: A 396 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7619 (tt) REVERT: B 137 LYS cc_start: 0.6672 (ttmt) cc_final: 0.5908 (tptp) REVERT: B 384 VAL cc_start: 0.8545 (m) cc_final: 0.8099 (t) REVERT: C 314 MET cc_start: 0.7000 (tpt) cc_final: 0.6726 (tpt) REVERT: C 420 MET cc_start: 0.7551 (mmm) cc_final: 0.6787 (mtm) REVERT: C 495 PHE cc_start: 0.4169 (t80) cc_final: 0.3943 (t80) REVERT: D 225 LYS cc_start: 0.9229 (mmmt) cc_final: 0.9026 (mmmt) REVERT: D 269 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7026 (mp0) REVERT: D 480 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7928 (tp30) REVERT: D 524 ASP cc_start: 0.7886 (m-30) cc_final: 0.7589 (m-30) REVERT: D 536 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7374 (mt-10) REVERT: E 122 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7257 (tpp) REVERT: E 124 LEU cc_start: 0.7797 (mp) cc_final: 0.6926 (mt) REVERT: E 273 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8598 (mm) REVERT: E 389 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8618 (pp20) REVERT: F 316 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: F 333 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7661 (tptp) REVERT: F 371 ASP cc_start: 0.7901 (t0) cc_final: 0.6609 (p0) REVERT: F 373 MET cc_start: 0.8606 (tpp) cc_final: 0.8291 (tpp) REVERT: G 1 MET cc_start: 0.6600 (pmm) cc_final: 0.5527 (mtt) outliers start: 54 outliers final: 34 residues processed: 186 average time/residue: 0.3223 time to fit residues: 96.3375 Evaluate side-chains 158 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 342 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 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 79 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 243 optimal weight: 0.0870 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.079176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064401 restraints weight = 102257.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.065893 restraints weight = 60077.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066895 restraints weight = 41702.226| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 22655 Z= 0.107 Angle : 0.527 8.899 30681 Z= 0.271 Chirality : 0.042 0.143 3489 Planarity : 0.004 0.054 3988 Dihedral : 8.435 86.660 3309 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.92 % Allowed : 10.99 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 2792 helix: 1.77 (0.17), residues: 956 sheet: -0.04 (0.22), residues: 523 loop : -0.00 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 570 HIS 0.003 0.000 HIS D 460 PHE 0.023 0.001 PHE B 155 TYR 0.011 0.001 TYR C 328 ARG 0.009 0.000 ARG F 378 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 861) hydrogen bonds : angle 4.32361 ( 2469) covalent geometry : bond 0.00232 (22655) covalent geometry : angle 0.52748 (30681) *********************** 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 187 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 2.633 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: 0.5857 (pm20) cc_final: 0.5573 (pm20) REVERT: A 396 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7539 (tt) REVERT: B 109 ASP cc_start: 0.8395 (p0) cc_final: 0.7986 (p0) REVERT: B 137 LYS cc_start: 0.6555 (ttmt) cc_final: 0.5707 (tptp) REVERT: B 384 VAL cc_start: 0.8406 (m) cc_final: 0.7913 (t) REVERT: C 314 MET cc_start: 0.7028 (tpt) cc_final: 0.6709 (tpp) REVERT: D 269 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7206 (mp0) REVERT: D 314 MET cc_start: 0.6230 (ptt) cc_final: 0.4391 (tpt) REVERT: D 524 ASP cc_start: 0.7780 (m-30) cc_final: 0.7486 (m-30) REVERT: D 536 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7333 (mt-10) REVERT: E 122 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7230 (tpp) REVERT: E 124 LEU cc_start: 0.7696 (mp) cc_final: 0.6877 (mt) REVERT: E 233 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7649 (tp) REVERT: E 389 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8679 (pp20) REVERT: F 122 MET cc_start: 0.7118 (mmm) cc_final: 0.6769 (mmm) REVERT: F 316 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: F 333 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7657 (tptp) REVERT: F 373 MET cc_start: 0.8663 (tpp) cc_final: 0.8297 (tpp) REVERT: G 1 MET cc_start: 0.6462 (pmm) cc_final: 0.5559 (mtt) outliers start: 46 outliers final: 28 residues processed: 183 average time/residue: 0.3085 time to fit residues: 93.1236 Evaluate side-chains 155 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 2.570 ------------------------------------------------------------------------------- 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 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 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 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 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 277 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 HIS F 354 GLN ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.075868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061839 restraints weight = 105497.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.062636 restraints weight = 63819.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063193 restraints weight = 44223.089| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 22655 Z= 0.246 Angle : 0.677 10.009 30681 Z= 0.351 Chirality : 0.045 0.198 3489 Planarity : 0.005 0.055 3988 Dihedral : 9.049 89.869 3309 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.76 % Allowed : 12.04 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2792 helix: 1.12 (0.17), residues: 973 sheet: -0.19 (0.22), residues: 496 loop : -0.33 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 570 HIS 0.008 0.001 HIS C 274 PHE 0.021 0.002 PHE B 155 TYR 0.023 0.002 TYR F 228 ARG 0.007 0.001 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 861) hydrogen bonds : angle 4.77310 ( 2469) covalent geometry : bond 0.00569 (22655) covalent geometry : angle 0.67745 (30681) *********************** 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 183 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 117 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7769 (tt) REVERT: B 161 ILE cc_start: 0.8362 (mm) cc_final: 0.8147 (mm) REVERT: C 314 MET cc_start: 0.7422 (tpt) cc_final: 0.7099 (tpp) REVERT: C 420 MET cc_start: 0.7869 (mmm) cc_final: 0.7023 (mtm) REVERT: D 524 ASP cc_start: 0.7753 (m-30) cc_final: 0.7476 (m-30) REVERT: E 122 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7294 (tpp) REVERT: E 233 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7988 (tp) REVERT: E 273 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8635 (mm) REVERT: E 389 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: F 316 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: F 373 MET cc_start: 0.8796 (tpp) cc_final: 0.8301 (ttt) REVERT: G 1 MET cc_start: 0.6698 (pmm) cc_final: 0.5731 (mtt) REVERT: G 4 GLU cc_start: 0.8279 (pm20) cc_final: 0.8073 (pm20) outliers start: 66 outliers final: 40 residues processed: 176 average time/residue: 0.3045 time to fit residues: 89.1829 Evaluate side-chains 155 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 2.548 ------------------------------------------------------------------------------- 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 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 238 VAL 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 268 VAL 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 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 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 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 99 optimal weight: 1.9990 chunk 136 optimal weight: 0.0770 chunk 209 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 208 optimal weight: 0.5980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3675 r_free = 0.3675 target = 0.077823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.063430 restraints weight = 103480.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064960 restraints weight = 62295.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.065511 restraints weight = 38720.347| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22655 Z= 0.103 Angle : 0.534 10.684 30681 Z= 0.273 Chirality : 0.042 0.171 3489 Planarity : 0.004 0.050 3988 Dihedral : 8.388 87.639 3309 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 13.50 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2792 helix: 1.62 (0.17), residues: 954 sheet: -0.21 (0.22), residues: 505 loop : -0.11 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 187 HIS 0.002 0.000 HIS D 460 PHE 0.033 0.001 PHE B 155 TYR 0.015 0.001 TYR F 228 ARG 0.007 0.000 ARG F 123 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 861) hydrogen bonds : angle 4.21879 ( 2469) covalent geometry : bond 0.00226 (22655) covalent geometry : angle 0.53351 (30681) *********************** 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 167 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5435 (pm20) cc_final: 0.5223 (pm20) REVERT: A 243 LEU cc_start: 0.7098 (pp) cc_final: 0.6575 (pp) REVERT: A 396 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7613 (tt) REVERT: B 384 VAL cc_start: 0.8520 (m) cc_final: 0.8038 (t) REVERT: C 314 MET cc_start: 0.7330 (tpt) cc_final: 0.7074 (tpp) REVERT: C 373 MET cc_start: 0.8902 (mmp) cc_final: 0.8678 (mmp) REVERT: C 420 MET cc_start: 0.7830 (mmm) cc_final: 0.7343 (mmm) REVERT: C 559 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6749 (mm-30) REVERT: D 269 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6857 (mp0) REVERT: D 524 ASP cc_start: 0.7740 (m-30) cc_final: 0.7482 (m-30) REVERT: E 122 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7266 (tpp) REVERT: E 233 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7934 (tp) REVERT: E 273 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8370 (mm) REVERT: E 389 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8629 (pp20) REVERT: F 316 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: F 333 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7645 (tptp) REVERT: F 371 ASP cc_start: 0.7666 (t0) cc_final: 0.6387 (p0) REVERT: F 373 MET cc_start: 0.8789 (tpp) cc_final: 0.8389 (tpp) REVERT: G 1 MET cc_start: 0.6472 (pmm) cc_final: 0.5777 (mtt) REVERT: G 4 GLU cc_start: 0.8224 (pm20) cc_final: 0.7934 (pm20) outliers start: 43 outliers final: 30 residues processed: 161 average time/residue: 0.2978 time to fit residues: 79.8924 Evaluate side-chains 150 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 584 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 268 VAL 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 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 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 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 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 145 optimal weight: 0.0870 chunk 163 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 241 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 60 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.1258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 514 ASN ** 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 = 0.3671 r_free = 0.3671 target = 0.077605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.062886 restraints weight = 103405.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064359 restraints weight = 60956.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.065335 restraints weight = 42280.994| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3044 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= 0.113 Angle : 0.526 9.708 30681 Z= 0.269 Chirality : 0.041 0.148 3489 Planarity : 0.004 0.042 3988 Dihedral : 8.254 87.829 3309 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.34 % Allowed : 14.38 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2792 helix: 1.73 (0.17), residues: 965 sheet: -0.25 (0.22), residues: 507 loop : -0.10 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.003 0.000 HIS D 460 PHE 0.017 0.001 PHE E 353 TYR 0.013 0.001 TYR F 228 ARG 0.004 0.000 ARG A 543 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 861) hydrogen bonds : angle 4.11385 ( 2469) covalent geometry : bond 0.00258 (22655) covalent geometry : angle 0.52577 (30681) *********************** 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 174 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5534 (pm20) cc_final: 0.5260 (pm20) REVERT: A 243 LEU cc_start: 0.6784 (pp) cc_final: 0.6288 (mt) REVERT: B 384 VAL cc_start: 0.8542 (m) cc_final: 0.8068 (t) REVERT: C 314 MET cc_start: 0.7454 (tpt) cc_final: 0.7170 (tpp) REVERT: C 420 MET cc_start: 0.7812 (mmm) cc_final: 0.7338 (mmm) REVERT: D 269 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6976 (mp0) REVERT: D 524 ASP cc_start: 0.7746 (m-30) cc_final: 0.7475 (m-30) REVERT: D 555 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.5193 (m-80) REVERT: E 182 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5665 (pm20) REVERT: E 233 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8118 (tp) REVERT: E 273 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8401 (mm) REVERT: E 389 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8719 (pp20) REVERT: F 316 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: F 373 MET cc_start: 0.8860 (tpp) cc_final: 0.8342 (ttt) REVERT: G 1 MET cc_start: 0.6500 (pmm) cc_final: 0.5761 (mtt) outliers start: 56 outliers final: 33 residues processed: 169 average time/residue: 0.2978 time to fit residues: 85.4687 Evaluate side-chains 153 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 188 LEU Chi-restraints excluded: chain B residue 331 ASN 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 268 VAL 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 125 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 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 570 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 0.0870 chunk 265 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 514 ASN ** 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 = 0.3687 r_free = 0.3687 target = 0.078261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.063567 restraints weight = 102785.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065075 restraints weight = 60438.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.066053 restraints weight = 41685.889| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22655 Z= 0.096 Angle : 0.511 9.795 30681 Z= 0.259 Chirality : 0.041 0.146 3489 Planarity : 0.004 0.040 3988 Dihedral : 7.922 89.226 3304 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.13 % Allowed : 14.46 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2792 helix: 1.84 (0.17), residues: 965 sheet: -0.30 (0.22), residues: 520 loop : -0.02 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 187 HIS 0.002 0.000 HIS D 460 PHE 0.012 0.001 PHE D 353 TYR 0.012 0.001 TYR A 251 ARG 0.004 0.000 ARG A 543 Details of bonding type rmsd hydrogen bonds : bond 0.02700 ( 861) hydrogen bonds : angle 3.96449 ( 2469) covalent geometry : bond 0.00214 (22655) covalent geometry : angle 0.51118 (30681) *********************** 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 177 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 2.750 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: 0.5577 (pm20) cc_final: 0.5245 (pm20) REVERT: A 243 LEU cc_start: 0.7112 (pp) cc_final: 0.6746 (mt) REVERT: A 408 ASN cc_start: 0.6563 (OUTLIER) cc_final: 0.5703 (p0) REVERT: A 508 MET cc_start: 0.7782 (mmm) cc_final: 0.7508 (mmp) REVERT: B 244 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: B 384 VAL cc_start: 0.8445 (m) cc_final: 0.7881 (t) REVERT: B 518 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7993 (ttp) REVERT: C 420 MET cc_start: 0.7801 (mmm) cc_final: 0.7351 (mmm) REVERT: D 269 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6950 (mp0) REVERT: D 524 ASP cc_start: 0.7768 (m-30) cc_final: 0.7491 (m-30) REVERT: E 181 ASP cc_start: 0.6871 (t0) cc_final: 0.6516 (t0) REVERT: E 182 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5311 (pm20) REVERT: E 273 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8382 (mm) REVERT: E 389 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8725 (pm20) REVERT: F 316 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: G 1 MET cc_start: 0.6609 (pmm) cc_final: 0.5814 (mtt) outliers start: 51 outliers final: 30 residues processed: 174 average time/residue: 0.3066 time to fit residues: 90.5248 Evaluate side-chains 150 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 408 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 GLU 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 268 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain D residue 228 TYR 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 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 389 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 570 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 182 optimal weight: 0.0170 chunk 35 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.077229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.062518 restraints weight = 103692.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063981 restraints weight = 61126.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064968 restraints weight = 42517.049| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22655 Z= 0.139 Angle : 0.547 9.039 30681 Z= 0.279 Chirality : 0.042 0.221 3489 Planarity : 0.004 0.041 3988 Dihedral : 8.019 89.705 3301 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.09 % Allowed : 14.83 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2792 helix: 1.77 (0.17), residues: 970 sheet: -0.34 (0.22), residues: 514 loop : -0.09 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.003 0.001 HIS D 460 PHE 0.024 0.001 PHE B 155 TYR 0.017 0.001 TYR C 583 ARG 0.005 0.000 ARG C 585 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 861) hydrogen bonds : angle 4.05621 ( 2469) covalent geometry : bond 0.00323 (22655) covalent geometry : angle 0.54744 (30681) *********************** 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 168 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5764 (pm20) cc_final: 0.5517 (pm20) REVERT: A 508 MET cc_start: 0.7840 (mmm) cc_final: 0.7563 (mmp) REVERT: B 384 VAL cc_start: 0.8571 (m) cc_final: 0.8105 (t) REVERT: B 518 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8037 (ttp) REVERT: C 420 MET cc_start: 0.7820 (mmm) cc_final: 0.7284 (mmm) REVERT: D 269 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7033 (mp0) REVERT: D 524 ASP cc_start: 0.7738 (m-30) cc_final: 0.7452 (m-30) REVERT: D 555 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.5006 (m-80) REVERT: E 273 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8458 (mm) REVERT: E 389 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.8692 (pp20) REVERT: G 1 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5785 (mtt) outliers start: 50 outliers final: 34 residues processed: 163 average time/residue: 0.2838 time to fit residues: 78.5986 Evaluate side-chains 154 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 268 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 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 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 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 F residue 188 LEU Chi-restraints excluded: chain F residue 389 GLU 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 6 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 247 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 HIS F 354 GLN F 546 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.076256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062934 restraints weight = 104145.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.063091 restraints weight = 68633.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.063626 restraints weight = 48497.620| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3623 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= 0.169 Angle : 0.587 9.257 30681 Z= 0.303 Chirality : 0.043 0.226 3489 Planarity : 0.004 0.054 3988 Dihedral : 8.290 88.153 3298 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.13 % Allowed : 14.92 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2792 helix: 1.49 (0.17), residues: 970 sheet: -0.45 (0.22), residues: 514 loop : -0.25 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 187 HIS 0.004 0.001 HIS D 460 PHE 0.026 0.002 PHE B 155 TYR 0.019 0.002 TYR F 228 ARG 0.007 0.001 ARG F 318 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 861) hydrogen bonds : angle 4.26556 ( 2469) covalent geometry : bond 0.00393 (22655) covalent geometry : angle 0.58700 (30681) *********************** 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: 51 poor density : 120 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.5738 (pm20) cc_final: 0.5482 (pm20) REVERT: A 508 MET cc_start: 0.7949 (mmm) cc_final: 0.7624 (mmp) REVERT: B 373 MET cc_start: 0.8193 (tpp) cc_final: 0.7515 (ttt) REVERT: B 384 VAL cc_start: 0.8696 (m) cc_final: 0.8235 (t) REVERT: B 502 ASN cc_start: 0.6295 (t0) cc_final: 0.5763 (m-40) REVERT: B 518 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8081 (ttp) REVERT: C 420 MET cc_start: 0.7789 (mmm) cc_final: 0.7244 (mmm) REVERT: D 182 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5487 (pm20) REVERT: D 213 LYS cc_start: 0.5997 (tttt) cc_final: 0.5705 (mtmm) REVERT: D 269 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7034 (mp0) REVERT: D 420 MET cc_start: 0.6394 (mtt) cc_final: 0.6166 (mpp) REVERT: D 524 ASP cc_start: 0.7602 (m-30) cc_final: 0.7377 (m-30) REVERT: D 555 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.4961 (m-80) REVERT: E 182 GLU cc_start: 0.6163 (OUTLIER) cc_final: 0.5733 (pm20) REVERT: E 273 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8483 (mm) REVERT: E 389 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8615 (pp20) REVERT: G 1 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.5957 (mtt) outliers start: 51 outliers final: 36 residues processed: 165 average time/residue: 0.3046 time to fit residues: 83.9419 Evaluate side-chains 158 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 113 VAL 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 268 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 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 182 GLU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 358 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 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 351 LEU Chi-restraints excluded: chain F residue 522 VAL 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 201 optimal weight: 0.4980 chunk 210 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 chunk 260 optimal weight: 0.1980 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 246 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 144 ASN D 348 HIS F 354 GLN ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.077529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.062954 restraints weight = 103146.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064459 restraints weight = 60557.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.065465 restraints weight = 41737.524| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22655 Z= 0.101 Angle : 0.546 10.359 30681 Z= 0.276 Chirality : 0.042 0.220 3489 Planarity : 0.004 0.046 3988 Dihedral : 7.983 86.817 3298 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 15.25 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2792 helix: 1.71 (0.17), residues: 965 sheet: -0.43 (0.23), residues: 517 loop : -0.12 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 187 HIS 0.003 0.000 HIS F 546 PHE 0.035 0.001 PHE B 155 TYR 0.012 0.001 TYR F 228 ARG 0.006 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.02845 ( 861) hydrogen bonds : angle 4.00931 ( 2469) covalent geometry : bond 0.00227 (22655) covalent geometry : angle 0.54570 (30681) ********************** 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: 43 poor density : 120 time to evaluate : 2.804 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: 0.5765 (pm20) cc_final: 0.5477 (pm20) REVERT: A 243 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7004 (mt) REVERT: A 508 MET cc_start: 0.7782 (mmm) cc_final: 0.7518 (mmp) REVERT: B 384 VAL cc_start: 0.8578 (m) cc_final: 0.8080 (t) REVERT: B 502 ASN cc_start: 0.5837 (t0) cc_final: 0.5496 (m-40) REVERT: B 518 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7900 (ttp) REVERT: C 245 GLU cc_start: 0.4332 (OUTLIER) cc_final: 0.4044 (mp0) REVERT: C 420 MET cc_start: 0.7731 (mmm) cc_final: 0.7222 (mmm) REVERT: D 269 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7077 (mp0) REVERT: D 420 MET cc_start: 0.6276 (mtt) cc_final: 0.6036 (mpp) REVERT: D 524 ASP cc_start: 0.7707 (m-30) cc_final: 0.7423 (m-30) REVERT: D 555 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.4887 (m-80) REVERT: E 182 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5425 (pm20) REVERT: E 273 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8322 (mm) REVERT: E 389 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8666 (pp20) REVERT: G 1 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.5882 (mtt) outliers start: 43 outliers final: 31 residues processed: 157 average time/residue: 0.2943 time to fit residues: 77.8677 Evaluate side-chains 151 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 113 VAL 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 245 GLU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 228 TYR 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 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 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 165 optimal weight: 0.3980 chunk 145 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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** C 263 GLN F 354 GLN ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.075016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061688 restraints weight = 104460.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062050 restraints weight = 59868.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.062371 restraints weight = 46993.314| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 22655 Z= 0.254 Angle : 0.679 9.808 30681 Z= 0.352 Chirality : 0.045 0.203 3489 Planarity : 0.005 0.061 3988 Dihedral : 8.628 88.355 3298 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.80 % Allowed : 15.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2792 helix: 1.15 (0.17), residues: 970 sheet: -0.67 (0.22), residues: 524 loop : -0.43 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 570 HIS 0.006 0.001 HIS D 460 PHE 0.028 0.002 PHE B 155 TYR 0.024 0.002 TYR F 228 ARG 0.007 0.001 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 861) hydrogen bonds : angle 4.56930 ( 2469) covalent geometry : bond 0.00586 (22655) covalent geometry : angle 0.67898 (30681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6505.66 seconds wall clock time: 114 minutes 8.40 seconds (6848.40 seconds total)