Starting phenix.real_space_refine on Fri Sep 11 18:39:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7i_0357/09_2026/6n7i_0357_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7i_0357/09_2026/6n7i_0357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n7i_0357/09_2026/6n7i_0357_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7i_0357/09_2026/6n7i_0357_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n7i_0357/09_2026/6n7i_0357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7i_0357/09_2026/6n7i_0357.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 27 5.49 5 Mg 4 5.21 5 S 65 5.16 5 C 6701 2.51 5 N 1899 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10833 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2111 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 4, 'TRANS': 269} Chain breaks: 3 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2127 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1861 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.92, per 1000 atoms: 0.27 Number of scatterers: 10833 At special positions: 0 Unit cell: (80.25, 120.91, 135.89, 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 65 16.00 P 27 15.00 Mg 4 11.99 O 2137 8.00 N 1899 7.00 C 6701 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: 0.92 Conformation dependent library (CDL) restraints added in 396.8 milliseconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 38.6% alpha, 15.3% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 273 through 280 removed outlier: 3.687A pdb=" N SER A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.495A pdb=" N ASN A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 298' Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.807A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.785A pdb=" N THR A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 4.121A pdb=" N GLN A 364 " --> pdb=" O ARG A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.898A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.529A pdb=" N PHE A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.583A pdb=" N TYR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.356A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.574A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.575A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 4.460A pdb=" N ASN B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 298' Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.533A pdb=" N ALA B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.881A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 373 removed outlier: 3.539A pdb=" N LYS B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.764A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 removed outlier: 3.523A pdb=" N ALA B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.639A pdb=" N GLY B 478 " --> pdb=" O HIS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.976A pdb=" N LEU B 486 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 292 through 300 removed outlier: 4.376A pdb=" N ASN C 296 " --> pdb=" O CYS C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.671A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.583A pdb=" N ALA C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.700A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.739A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 4.068A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 removed outlier: 3.988A pdb=" N LEU C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.606A pdb=" N VAL C 430 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 removed outlier: 3.767A pdb=" N MET C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 removed outlier: 4.113A pdb=" N GLY C 478 " --> pdb=" O HIS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.760A pdb=" N ASP C 485 " --> pdb=" O SER C 482 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 486' Processing helix chain 'C' and resid 490 through 495 removed outlier: 3.635A pdb=" N GLN C 494 " --> pdb=" O GLY C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 318 through 331 removed outlier: 3.649A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.567A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.639A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 370' Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.785A pdb=" N GLU D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.559A pdb=" N ASP D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 417 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 440 through 457 removed outlier: 3.544A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.832A pdb=" N GLY D 478 " --> pdb=" O HIS D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.763A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.544A pdb=" N LYS E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.663A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 414 Processing helix chain 'E' and resid 440 through 457 removed outlier: 3.836A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 Processing helix chain 'F' and resid 273 through 280 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.743A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU B 306 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 462 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE B 308 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N CYS B 464 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 310 " --> pdb=" O CYS B 464 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 307 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 500 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET B 309 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU B 502 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 311 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 544 removed outlier: 7.050A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 307 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE A 500 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET A 309 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU A 502 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR A 311 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ARG A 504 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 421 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 463 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 423 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.622A pdb=" N VAL C 337 " --> pdb=" O HIS C 392 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR C 394 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 339 " --> pdb=" O TYR C 394 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 308 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL C 307 " --> pdb=" O THR C 498 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE C 500 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N MET C 309 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 502 " --> pdb=" O MET C 309 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR C 311 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 516 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 529 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 265 through 267 removed outlier: 7.043A pdb=" N VAL E 337 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N TYR E 394 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU E 339 " --> pdb=" O TYR E 394 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE E 421 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE E 463 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU E 423 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE E 308 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N CYS E 464 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL E 310 " --> pdb=" O CYS E 464 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL E 307 " --> pdb=" O THR E 498 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE E 500 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET E 309 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU E 502 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR E 311 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR E 532 " --> pdb=" O SER E 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 391 through 392 removed outlier: 6.466A pdb=" N VAL D 337 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 421 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE D 463 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU D 423 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU D 306 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL D 462 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N CYS D 464 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL D 310 " --> pdb=" O CYS D 464 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1810 1.31 - 1.43: 2714 1.43 - 1.56: 6301 1.56 - 1.69: 49 1.69 - 1.81: 110 Bond restraints: 10984 Sorted by residual: bond pdb=" O3B TTP B 700 " pdb=" PG TTP B 700 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " ideal model delta sigma weight residual 1.748 1.596 0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 1.748 1.596 0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C2 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.377 1.485 -0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 10979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 14483 2.72 - 5.44: 254 5.44 - 8.16: 51 8.16 - 10.88: 20 10.88 - 13.60: 17 Bond angle restraints: 14825 Sorted by residual: angle pdb=" N LYS D 318 " pdb=" CA LYS D 318 " pdb=" C LYS D 318 " ideal model delta sigma weight residual 112.68 103.19 9.49 1.33e+00 5.65e-01 5.09e+01 angle pdb=" O5' DT T 10 " pdb=" C5' DT T 10 " pdb=" C4' DT T 10 " ideal model delta sigma weight residual 109.40 113.40 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU A 288 " pdb=" CA LEU A 288 " pdb=" CB LEU A 288 " ideal model delta sigma weight residual 109.84 101.69 8.15 1.63e+00 3.76e-01 2.50e+01 angle pdb=" C2 TTP C 700 " pdb=" N3 TTP C 700 " pdb=" C4 TTP C 700 " ideal model delta sigma weight residual 128.28 114.68 13.60 3.00e+00 1.11e-01 2.06e+01 angle pdb=" N3 DT T 11 " pdb=" C4 DT T 11 " pdb=" O4 DT T 11 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 14820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.29: 6385 28.29 - 56.58: 223 56.58 - 84.86: 40 84.86 - 113.15: 1 113.15 - 141.44: 1 Dihedral angle restraints: 6650 sinusoidal: 2891 harmonic: 3759 Sorted by residual: dihedral pdb=" CD ARG D 413 " pdb=" NE ARG D 413 " pdb=" CZ ARG D 413 " pdb=" NH1 ARG D 413 " ideal model delta sinusoidal sigma weight residual 0.00 57.24 -57.24 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CD ARG A 504 " pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " pdb=" NH1 ARG A 504 " ideal model delta sinusoidal sigma weight residual 0.00 -49.43 49.43 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" CD ARG A 276 " pdb=" NE ARG A 276 " pdb=" CZ ARG A 276 " pdb=" NH1 ARG A 276 " ideal model delta sinusoidal sigma weight residual 0.00 42.67 -42.67 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 6647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1400 0.071 - 0.142: 260 0.142 - 0.214: 23 0.214 - 0.285: 4 0.285 - 0.356: 1 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CA ASN B 388 " pdb=" N ASN B 388 " pdb=" C ASN B 388 " pdb=" CB ASN B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C4' TTP D 700 " pdb=" C3' TTP D 700 " pdb=" C5' TTP D 700 " pdb=" O4' TTP D 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.74 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C4' TTP B 700 " pdb=" C3' TTP B 700 " pdb=" C5' TTP B 700 " pdb=" O4' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.70 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1685 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 413 " 0.918 9.50e-02 1.11e+02 4.12e-01 1.03e+02 pdb=" NE ARG D 413 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG D 413 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 413 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 413 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 504 " 0.828 9.50e-02 1.11e+02 3.71e-01 8.37e+01 pdb=" NE ARG A 504 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 504 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 504 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 504 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 276 " -0.736 9.50e-02 1.11e+02 3.30e-01 6.63e+01 pdb=" NE ARG A 276 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 276 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 276 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 276 " -0.022 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 252 2.71 - 3.25: 9516 3.25 - 3.80: 16307 3.80 - 4.35: 21738 4.35 - 4.90: 36488 Nonbonded interactions: 84301 Sorted by model distance: nonbonded pdb=" NE2 GLN C 343 " pdb="MG MG C 701 " model vdw 2.157 2.250 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 2.185 2.170 nonbonded pdb=" O1G TTP B 700 " pdb="MG MG B 701 " model vdw 2.200 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.223 2.170 nonbonded pdb=" O2B TTP E 700 " pdb="MG MG E 701 " model vdw 2.223 2.170 ... (remaining 84296 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 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'B' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'C' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 285 through 506 or resid 510 through 545)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.006 0.153 10984 Z= 0.351 Angle : 1.041 13.604 14825 Z= 0.550 Chirality : 0.056 0.356 1688 Planarity : 0.017 0.412 1822 Dihedral : 13.988 141.440 4244 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.53 % Allowed : 4.58 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.19), residues: 1308 helix: -2.86 (0.17), residues: 432 sheet: -0.33 (0.35), residues: 254 loop : -2.71 (0.20), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 479 TYR 0.007 0.001 TYR A 547 PHE 0.011 0.002 PHE D 523 TRP 0.016 0.002 TRP C 381 HIS 0.009 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.35 (10984) covalent geometry : angle 1.04095 / 0.55 (14825) hydrogen bonds : bond 0.15509 / 10.94 ( 350) hydrogen bonds : angle 7.84658 / 5.66 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 319 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 341 MET cc_start: 0.7360 (mmt) cc_final: 0.7120 (mmt) REVERT: A 388 ASN cc_start: 0.6762 (m-40) cc_final: 0.6182 (t0) REVERT: A 487 ARG cc_start: 0.7228 (ptm160) cc_final: 0.6669 (ptp90) REVERT: A 513 LEU cc_start: 0.7069 (tp) cc_final: 0.6773 (tp) REVERT: B 408 LYS cc_start: 0.7905 (mttp) cc_final: 0.7684 (mmmt) REVERT: E 470 ASP cc_start: 0.5859 (p0) cc_final: 0.5582 (m-30) REVERT: E 532 TYR cc_start: 0.7350 (m-80) cc_final: 0.7147 (m-80) outliers start: 6 outliers final: 0 residues processed: 321 average time/residue: 0.1338 time to fit residues: 57.2805 Evaluate side-chains 144 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 ASN A 465 HIS A 512 ASN B 357 HIS C 465 HIS D 325 GLN D 425 HIS E 358 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.167858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142909 restraints weight = 14438.165| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.69 r_work: 0.3745 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10984 Z= 0.139 Angle : 0.589 8.727 14825 Z= 0.294 Chirality : 0.044 0.170 1688 Planarity : 0.004 0.049 1822 Dihedral : 13.640 132.518 1738 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.94 % Allowed : 9.96 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.22), residues: 1308 helix: -0.89 (0.23), residues: 436 sheet: -0.04 (0.35), residues: 252 loop : -2.09 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 517 TYR 0.019 0.001 TYR D 411 PHE 0.021 0.002 PHE D 452 TRP 0.013 0.001 TRP A 541 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10984) covalent geometry : angle 0.58878 / 0.29 (14825) hydrogen bonds : bond 0.03378 / 2.30 ( 350) hydrogen bonds : angle 5.24169 / 3.80 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 GLN cc_start: 0.6821 (mt0) cc_final: 0.6579 (mt0) REVERT: A 388 ASN cc_start: 0.6538 (m-40) cc_final: 0.6053 (t0) REVERT: A 487 ARG cc_start: 0.7292 (ptm160) cc_final: 0.6657 (ptp90) REVERT: A 538 GLU cc_start: 0.7242 (tp30) cc_final: 0.6921 (tp30) REVERT: B 273 GLU cc_start: 0.8323 (tp30) cc_final: 0.8069 (mp0) REVERT: B 359 ARG cc_start: 0.8140 (mpt180) cc_final: 0.7862 (mmt90) REVERT: B 408 LYS cc_start: 0.8064 (mttp) cc_final: 0.7677 (mmmt) REVERT: E 470 ASP cc_start: 0.5979 (p0) cc_final: 0.5716 (m-30) REVERT: E 532 TYR cc_start: 0.7417 (m-80) cc_final: 0.7195 (m-80) outliers start: 22 outliers final: 14 residues processed: 176 average time/residue: 0.1180 time to fit residues: 28.9260 Evaluate side-chains 146 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 489 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 27 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 ASN A 465 HIS C 324 GLN ** E 425 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 = 0.4088 r_free = 0.4088 target = 0.163913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139903 restraints weight = 14572.003| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.64 r_work: 0.3703 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10984 Z= 0.160 Angle : 0.582 8.863 14825 Z= 0.292 Chirality : 0.045 0.165 1688 Planarity : 0.004 0.050 1822 Dihedral : 12.822 132.958 1738 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.00 % Allowed : 10.93 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.23), residues: 1308 helix: -0.17 (0.24), residues: 438 sheet: -0.00 (0.34), residues: 252 loop : -1.86 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 276 TYR 0.017 0.001 TYR D 411 PHE 0.018 0.002 PHE E 523 TRP 0.010 0.002 TRP A 541 HIS 0.008 0.001 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (10984) covalent geometry : angle 0.58191 / 0.29 (14825) hydrogen bonds : bond 0.03443 / 2.37 ( 350) hydrogen bonds : angle 4.86410 / 3.52 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 380 GLN cc_start: 0.6914 (mt0) cc_final: 0.6628 (mt0) REVERT: A 388 ASN cc_start: 0.6557 (m-40) cc_final: 0.6088 (t0) REVERT: B 359 ARG cc_start: 0.8145 (mpt180) cc_final: 0.7815 (mmt90) REVERT: B 408 LYS cc_start: 0.8051 (mttp) cc_final: 0.7715 (mmmt) REVERT: E 532 TYR cc_start: 0.7275 (m-80) cc_final: 0.7038 (m-80) outliers start: 34 outliers final: 20 residues processed: 163 average time/residue: 0.1050 time to fit residues: 24.6619 Evaluate side-chains 137 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.0070 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131864 restraints weight = 14773.540| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.74 r_work: 0.3593 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10984 Z= 0.189 Angle : 0.606 9.171 14825 Z= 0.305 Chirality : 0.046 0.164 1688 Planarity : 0.004 0.039 1822 Dihedral : 12.850 133.230 1738 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.52 % Allowed : 11.89 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.23), residues: 1308 helix: 0.03 (0.24), residues: 441 sheet: -0.08 (0.34), residues: 254 loop : -1.72 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 303 TYR 0.017 0.001 TYR D 411 PHE 0.022 0.002 PHE E 523 TRP 0.009 0.002 TRP D 381 HIS 0.008 0.001 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (10984) covalent geometry : angle 0.60637 / 0.31 (14825) hydrogen bonds : bond 0.03608 / 2.49 ( 350) hydrogen bonds : angle 4.78856 / 3.46 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.420 Fit side-chains REVERT: A 380 GLN cc_start: 0.7002 (mt0) cc_final: 0.6662 (mt0) REVERT: A 388 ASN cc_start: 0.6438 (m-40) cc_final: 0.6098 (t0) REVERT: A 538 GLU cc_start: 0.7140 (tp30) cc_final: 0.6891 (tp30) REVERT: B 408 LYS cc_start: 0.7928 (mttp) cc_final: 0.7593 (mmmt) REVERT: D 319 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8341 (m) REVERT: E 385 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6971 (tp) REVERT: E 532 TYR cc_start: 0.7376 (m-80) cc_final: 0.7120 (m-80) outliers start: 40 outliers final: 28 residues processed: 157 average time/residue: 0.1046 time to fit residues: 23.9131 Evaluate side-chains 146 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS B 465 HIS D 375 ASN D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.163606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139913 restraints weight = 14530.470| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.63 r_work: 0.3703 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10984 Z= 0.108 Angle : 0.522 8.517 14825 Z= 0.265 Chirality : 0.043 0.163 1688 Planarity : 0.003 0.039 1822 Dihedral : 12.308 132.705 1738 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.29 % Allowed : 14.27 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.24), residues: 1308 helix: 0.39 (0.25), residues: 441 sheet: 0.06 (0.34), residues: 257 loop : -1.52 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 276 TYR 0.010 0.001 TYR E 411 PHE 0.013 0.001 PHE C 321 TRP 0.004 0.001 TRP A 541 HIS 0.004 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (10984) covalent geometry : angle 0.52165 / 0.27 (14825) hydrogen bonds : bond 0.02928 / 1.99 ( 350) hydrogen bonds : angle 4.52673 / 3.26 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.417 Fit side-chains REVERT: A 380 GLN cc_start: 0.6920 (mt0) cc_final: 0.6567 (mt0) REVERT: A 386 PHE cc_start: 0.6656 (m-80) cc_final: 0.6429 (t80) REVERT: A 388 ASN cc_start: 0.6549 (m-40) cc_final: 0.6133 (t0) REVERT: A 460 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7887 (tt) REVERT: A 538 GLU cc_start: 0.7218 (tp30) cc_final: 0.6977 (tp30) REVERT: B 408 LYS cc_start: 0.7814 (mttp) cc_final: 0.7552 (mmmt) REVERT: C 412 MET cc_start: 0.8056 (mtt) cc_final: 0.7854 (ttt) REVERT: D 319 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8107 (m) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.1089 time to fit residues: 23.2329 Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 489 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 0.0050 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.162915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138989 restraints weight = 14607.182| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.65 r_work: 0.3690 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10984 Z= 0.123 Angle : 0.522 8.763 14825 Z= 0.265 Chirality : 0.043 0.163 1688 Planarity : 0.003 0.037 1822 Dihedral : 12.289 132.946 1738 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.08 % Allowed : 14.19 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1308 helix: 0.56 (0.25), residues: 440 sheet: 0.10 (0.34), residues: 257 loop : -1.39 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 404 TYR 0.013 0.001 TYR D 411 PHE 0.015 0.001 PHE C 321 TRP 0.004 0.001 TRP D 541 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10984) covalent geometry : angle 0.52208 / 0.27 (14825) hydrogen bonds : bond 0.02936 / 2.00 ( 350) hydrogen bonds : angle 4.46980 / 3.23 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.437 Fit side-chains REVERT: A 316 MET cc_start: 0.7434 (mmm) cc_final: 0.7097 (mmm) REVERT: A 380 GLN cc_start: 0.6872 (mt0) cc_final: 0.6547 (mt0) REVERT: A 386 PHE cc_start: 0.6649 (m-80) cc_final: 0.6344 (t80) REVERT: A 388 ASN cc_start: 0.6533 (m-40) cc_final: 0.6161 (t0) REVERT: A 460 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7920 (tt) REVERT: B 408 LYS cc_start: 0.7825 (mttp) cc_final: 0.7604 (mmmt) REVERT: C 412 MET cc_start: 0.8096 (mtt) cc_final: 0.7882 (ttt) REVERT: D 319 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8123 (m) outliers start: 35 outliers final: 27 residues processed: 149 average time/residue: 0.1009 time to fit residues: 22.0223 Evaluate side-chains 146 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 30 optimal weight: 5.9990 chunk 79 optimal weight: 0.0470 chunk 7 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.163940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140328 restraints weight = 14457.264| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.62 r_work: 0.3711 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10984 Z= 0.104 Angle : 0.521 12.019 14825 Z= 0.261 Chirality : 0.042 0.164 1688 Planarity : 0.002 0.038 1822 Dihedral : 12.137 132.730 1738 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 14.63 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1308 helix: 0.67 (0.25), residues: 441 sheet: 0.17 (0.34), residues: 257 loop : -1.31 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 276 TYR 0.013 0.001 TYR D 411 PHE 0.014 0.001 PHE C 321 TRP 0.003 0.001 TRP C 381 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (10984) covalent geometry : angle 0.52055 / 0.26 (14825) hydrogen bonds : bond 0.02727 / 1.85 ( 350) hydrogen bonds : angle 4.37537 / 3.16 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.434 Fit side-chains REVERT: A 388 ASN cc_start: 0.6532 (m-40) cc_final: 0.6161 (t0) REVERT: A 460 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 408 LYS cc_start: 0.7799 (mttp) cc_final: 0.7539 (mmmt) REVERT: D 468 ASN cc_start: 0.8006 (t0) cc_final: 0.7739 (t0) REVERT: D 509 ASP cc_start: 0.6644 (p0) cc_final: 0.6420 (p0) REVERT: E 510 MET cc_start: 0.7226 (ptp) cc_final: 0.6621 (mtp) outliers start: 34 outliers final: 28 residues processed: 151 average time/residue: 0.0985 time to fit residues: 21.8854 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139835 restraints weight = 14610.256| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.65 r_work: 0.3704 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10984 Z= 0.113 Angle : 0.524 10.439 14825 Z= 0.264 Chirality : 0.043 0.164 1688 Planarity : 0.003 0.045 1822 Dihedral : 12.111 133.010 1738 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.91 % Allowed : 14.89 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1308 helix: 0.82 (0.25), residues: 441 sheet: 0.26 (0.34), residues: 255 loop : -1.22 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 276 TYR 0.014 0.001 TYR D 411 PHE 0.015 0.001 PHE C 321 TRP 0.004 0.001 TRP A 329 HIS 0.005 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (10984) covalent geometry : angle 0.52360 / 0.26 (14825) hydrogen bonds : bond 0.02812 / 1.91 ( 350) hydrogen bonds : angle 4.31438 / 3.12 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.526 Fit side-chains REVERT: A 388 ASN cc_start: 0.6519 (m-40) cc_final: 0.6112 (t0) REVERT: A 460 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7938 (tt) REVERT: B 408 LYS cc_start: 0.7823 (mttp) cc_final: 0.7598 (mmmt) REVERT: C 412 MET cc_start: 0.8138 (mtt) cc_final: 0.7808 (ttt) REVERT: D 452 PHE cc_start: 0.8648 (t80) cc_final: 0.8432 (t80) REVERT: E 446 MET cc_start: 0.6490 (mmt) cc_final: 0.5627 (mmt) outliers start: 33 outliers final: 29 residues processed: 144 average time/residue: 0.0958 time to fit residues: 20.3457 Evaluate side-chains 144 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 HIS D 296 ASN D 468 ASN ** E 425 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 = 0.4074 r_free = 0.4074 target = 0.162504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138667 restraints weight = 14540.240| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.64 r_work: 0.3692 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10984 Z= 0.130 Angle : 0.544 10.153 14825 Z= 0.272 Chirality : 0.043 0.178 1688 Planarity : 0.003 0.036 1822 Dihedral : 12.200 133.070 1738 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.08 % Allowed : 15.15 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1308 helix: 0.80 (0.25), residues: 443 sheet: 0.27 (0.34), residues: 255 loop : -1.26 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 276 TYR 0.014 0.001 TYR D 411 PHE 0.016 0.002 PHE A 386 TRP 0.005 0.001 TRP A 329 HIS 0.005 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10984) covalent geometry : angle 0.54373 / 0.27 (14825) hydrogen bonds : bond 0.02959 / 2.02 ( 350) hydrogen bonds : angle 4.33794 / 3.14 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.389 Fit side-chains REVERT: A 388 ASN cc_start: 0.6531 (m-40) cc_final: 0.6172 (t0) REVERT: A 460 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7961 (tt) REVERT: B 408 LYS cc_start: 0.7810 (mttp) cc_final: 0.7525 (mmmt) REVERT: C 412 MET cc_start: 0.8120 (mtt) cc_final: 0.7811 (ttt) REVERT: E 446 MET cc_start: 0.6537 (mmt) cc_final: 0.5681 (mmt) outliers start: 35 outliers final: 31 residues processed: 140 average time/residue: 0.0941 time to fit residues: 19.2602 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.163110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139404 restraints weight = 14485.441| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.63 r_work: 0.3699 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10984 Z= 0.118 Angle : 0.530 9.978 14825 Z= 0.267 Chirality : 0.043 0.177 1688 Planarity : 0.003 0.036 1822 Dihedral : 12.108 133.090 1738 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.00 % Allowed : 15.15 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1308 helix: 0.89 (0.25), residues: 443 sheet: 0.30 (0.34), residues: 256 loop : -1.21 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 276 TYR 0.013 0.001 TYR D 411 PHE 0.016 0.001 PHE A 378 TRP 0.005 0.001 TRP A 381 HIS 0.005 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10984) covalent geometry : angle 0.53035 / 0.27 (14825) hydrogen bonds : bond 0.02845 / 1.94 ( 350) hydrogen bonds : angle 4.28287 / 3.10 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.438 Fit side-chains REVERT: A 316 MET cc_start: 0.7049 (mmm) cc_final: 0.6659 (mmm) REVERT: A 388 ASN cc_start: 0.6694 (m-40) cc_final: 0.6173 (t0) REVERT: A 460 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7924 (tt) REVERT: B 408 LYS cc_start: 0.7800 (mttp) cc_final: 0.7583 (mmmt) REVERT: C 380 GLN cc_start: 0.8186 (mp10) cc_final: 0.7970 (mm-40) REVERT: C 412 MET cc_start: 0.8112 (mtt) cc_final: 0.7816 (ttt) REVERT: E 446 MET cc_start: 0.6540 (mmt) cc_final: 0.5692 (mmt) REVERT: E 510 MET cc_start: 0.7253 (ptp) cc_final: 0.6734 (mtp) outliers start: 34 outliers final: 31 residues processed: 137 average time/residue: 0.1047 time to fit residues: 20.8761 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 489 SER Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 74 optimal weight: 0.0470 chunk 80 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.164371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140841 restraints weight = 14537.148| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.63 r_work: 0.3718 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10984 Z= 0.101 Angle : 0.513 9.924 14825 Z= 0.258 Chirality : 0.042 0.163 1688 Planarity : 0.002 0.036 1822 Dihedral : 11.963 133.055 1738 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 15.07 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1308 helix: 1.05 (0.26), residues: 439 sheet: 0.30 (0.33), residues: 272 loop : -1.21 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 276 TYR 0.013 0.001 TYR D 411 PHE 0.016 0.001 PHE A 378 TRP 0.004 0.001 TRP A 381 HIS 0.005 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (10984) covalent geometry : angle 0.51347 / 0.26 (14825) hydrogen bonds : bond 0.02614 / 1.77 ( 350) hydrogen bonds : angle 4.19805 / 3.04 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.77 seconds wall clock time: 50 minutes 46.54 seconds (3046.54 seconds total)