Starting phenix.real_space_refine on Wed Mar 4 04:49:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7i_0357/03_2026/6n7i_0357_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7i_0357/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7i_0357/03_2026/6n7i_0357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7i_0357/03_2026/6n7i_0357.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7i_0357/03_2026/6n7i_0357_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7i_0357/03_2026/6n7i_0357_neut.cif" } 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-dev-5986/lib/python3.9/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: 2.76, per 1000 atoms: 0.25 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: 0.60 Conformation dependent library (CDL) restraints added in 601.7 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: 1.28 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: 1.44 Time building geometry restraints manager: 0.82 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=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.430 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.429 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C2 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.410 1.485 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 10979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 14531 2.64 - 5.27: 234 5.27 - 7.91: 43 7.91 - 10.55: 11 10.55 - 13.19: 6 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=" 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=" PA TTP D 700 " pdb=" O3A TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sigma weight residual 120.50 133.69 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" PA TTP B 700 " pdb=" O3A TTP B 700 " pdb=" PB TTP B 700 " ideal model delta sigma weight residual 120.50 133.20 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" PA TTP E 700 " pdb=" O3A TTP E 700 " pdb=" PB TTP E 700 " ideal model delta sigma weight residual 120.50 132.39 -11.89 3.00e+00 1.11e-01 1.57e+01 ... (remaining 14820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 6410 35.51 - 71.03: 125 71.03 - 106.54: 10 106.54 - 142.06: 3 142.06 - 177.57: 6 Dihedral angle restraints: 6554 sinusoidal: 2795 harmonic: 3759 Sorted by residual: dihedral pdb=" O2G TTP D 700 " pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.43 -177.57 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G TTP E 700 " pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " pdb=" PB TTP E 700 " ideal model delta sinusoidal sigma weight residual -180.00 -6.25 -173.75 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2 TTP C 700 " pdb=" C1' TTP C 700 " pdb=" N1 TTP C 700 " pdb=" O4' TTP C 700 " ideal model delta sinusoidal sigma weight residual -58.32 101.51 -159.82 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 6551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1401 0.071 - 0.142: 260 0.142 - 0.214: 22 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=" C3' TTP E 700 " pdb=" C2' TTP E 700 " pdb=" C4' TTP E 700 " pdb=" O3' TTP E 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3' TTP D 700 " pdb=" C2' TTP D 700 " pdb=" C4' TTP D 700 " pdb=" O3' TTP D 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.57e+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: 1.860 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.005 0.093 10984 Z= 0.300 Angle : 0.911 13.186 14825 Z= 0.488 Chirality : 0.055 0.356 1688 Planarity : 0.017 0.412 1822 Dihedral : 14.815 177.571 4148 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 covalent geometry : bond 0.00527 (10984) covalent geometry : angle 0.91098 (14825) hydrogen bonds : bond 0.15509 ( 350) hydrogen bonds : angle 7.84658 ( 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 : 0.371 Fit side-chains revert: symmetry clash REVERT: A 341 MET cc_start: 0.7360 (mmt) cc_final: 0.7121 (mmt) REVERT: A 388 ASN cc_start: 0.6762 (m-40) cc_final: 0.6183 (t0) 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: 0.5575 (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: 0.1302 time to fit residues: 55.1077 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 : 0.303 ------------------------------------------------------------------------------- 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: 3.9990 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: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 465 HIS A 512 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 325 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.165773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141103 restraints weight = 14450.717| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.67 r_work: 0.3716 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10984 Z= 0.153 Angle : 0.615 8.993 14825 Z= 0.300 Chirality : 0.044 0.160 1688 Planarity : 0.004 0.043 1822 Dihedral : 15.974 164.711 1642 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.11 % Allowed : 9.69 % Favored : 88.19 % 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: -1.98 (0.22), residues: 1308 helix: -0.99 (0.22), residues: 451 sheet: -0.07 (0.34), residues: 252 loop : -2.10 (0.23), residues: 605 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 0.014 0.002 TRP A 541 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00362 (10984) covalent geometry : angle 0.61549 (14825) hydrogen bonds : bond 0.03531 ( 350) hydrogen bonds : angle 5.16193 ( 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 173 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 380 GLN cc_start: 0.6923 (mt0) cc_final: 0.6625 (mt0) REVERT: A 388 ASN cc_start: 0.6610 (m-40) cc_final: 0.6086 (t0) REVERT: B 273 GLU cc_start: 0.8335 (tp30) cc_final: 0.8075 (mp0) REVERT: B 359 ARG cc_start: 0.8224 (mpt180) cc_final: 0.7892 (mmt90) REVERT: B 408 LYS cc_start: 0.8069 (mttp) cc_final: 0.7682 (mmmt) REVERT: E 316 MET cc_start: 0.8125 (mmm) cc_final: 0.7783 (mmt) REVERT: E 470 ASP cc_start: 0.6037 (p0) cc_final: 0.5804 (m-30) REVERT: E 532 TYR cc_start: 0.7422 (m-80) cc_final: 0.7205 (m-80) outliers start: 24 outliers final: 15 residues processed: 169 average time/residue: 0.1087 time to fit residues: 25.5018 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 LEU 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 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 389 ASP Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 482 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: 2.9990 chunk 96 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 475 HIS C 324 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4064 r_free = 0.4064 target = 0.161842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137955 restraints weight = 14585.610| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.64 r_work: 0.3674 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10984 Z= 0.168 Angle : 0.608 8.471 14825 Z= 0.300 Chirality : 0.044 0.167 1688 Planarity : 0.004 0.070 1822 Dihedral : 15.705 160.600 1642 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.52 % Allowed : 11.10 % Favored : 85.37 % 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: -0.28 (0.24), residues: 453 sheet: -0.01 (0.34), residues: 254 loop : -1.80 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 276 TYR 0.016 0.001 TYR D 411 PHE 0.020 0.002 PHE E 523 TRP 0.008 0.002 TRP C 381 HIS 0.007 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00400 (10984) covalent geometry : angle 0.60813 (14825) hydrogen bonds : bond 0.03566 ( 350) hydrogen bonds : angle 4.78768 ( 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 180 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.330 Fit side-chains REVERT: A 316 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7157 (mpp) REVERT: A 380 GLN cc_start: 0.6949 (mt0) cc_final: 0.6246 (mt0) REVERT: A 388 ASN cc_start: 0.6651 (m-40) cc_final: 0.6106 (t0) REVERT: B 359 ARG cc_start: 0.8151 (mpt180) cc_final: 0.7784 (mmt90) REVERT: B 408 LYS cc_start: 0.7975 (mttp) cc_final: 0.7659 (mmmt) outliers start: 40 outliers final: 25 residues processed: 170 average time/residue: 0.0999 time to fit residues: 24.3707 Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 LEU 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 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 320 THR 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 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: 3.9990 chunk 81 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 468 ASN E 296 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 = 0.4045 r_free = 0.4045 target = 0.161093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137056 restraints weight = 14686.002| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.67 r_work: 0.3655 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10984 Z= 0.103 Angle : 0.525 7.826 14825 Z= 0.261 Chirality : 0.042 0.150 1688 Planarity : 0.002 0.040 1822 Dihedral : 15.280 159.326 1642 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.29 % Allowed : 12.69 % Favored : 85.02 % 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: -0.90 (0.23), residues: 1308 helix: 0.15 (0.25), residues: 453 sheet: 0.22 (0.34), residues: 256 loop : -1.54 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 276 TYR 0.015 0.001 TYR D 411 PHE 0.012 0.001 PHE C 321 TRP 0.004 0.001 TRP C 381 HIS 0.005 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00235 (10984) covalent geometry : angle 0.52490 (14825) hydrogen bonds : bond 0.02754 ( 350) hydrogen bonds : angle 4.44421 ( 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 168 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.397 Fit side-chains REVERT: A 316 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7358 (mpp) REVERT: A 388 ASN cc_start: 0.6453 (m-40) cc_final: 0.6076 (t0) REVERT: B 408 LYS cc_start: 0.7893 (mttp) cc_final: 0.7550 (mmmt) REVERT: C 412 MET cc_start: 0.8107 (mtt) cc_final: 0.7744 (ttt) REVERT: D 375 ASN cc_start: 0.7665 (OUTLIER) cc_final: 0.7433 (t0) REVERT: D 452 PHE cc_start: 0.8672 (t80) cc_final: 0.8427 (t80) REVERT: E 510 MET cc_start: 0.7237 (ptp) cc_final: 0.6742 (mtp) outliers start: 26 outliers final: 18 residues processed: 161 average time/residue: 0.1000 time to fit residues: 23.0390 Evaluate side-chains 144 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 516 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 515 LEU Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.0870 chunk 88 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 507 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.165846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.142309 restraints weight = 14464.444| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.64 r_work: 0.3735 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10984 Z= 0.099 Angle : 0.510 7.983 14825 Z= 0.254 Chirality : 0.041 0.132 1688 Planarity : 0.002 0.038 1822 Dihedral : 15.068 159.697 1642 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.47 % Allowed : 12.78 % Favored : 84.76 % 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: -0.60 (0.24), residues: 1308 helix: 0.43 (0.25), residues: 454 sheet: 0.35 (0.34), residues: 256 loop : -1.37 (0.25), residues: 598 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 0.011 0.001 PHE C 321 TRP 0.004 0.001 TRP C 381 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00224 (10984) covalent geometry : angle 0.51031 (14825) hydrogen bonds : bond 0.02645 ( 350) hydrogen bonds : angle 4.32209 ( 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 160 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.388 Fit side-chains REVERT: A 386 PHE cc_start: 0.6859 (m-80) cc_final: 0.6634 (t80) REVERT: A 388 ASN cc_start: 0.6581 (m-40) cc_final: 0.6218 (t0) REVERT: B 408 LYS cc_start: 0.7817 (mttp) cc_final: 0.7603 (mmmt) REVERT: D 452 PHE cc_start: 0.8644 (t80) cc_final: 0.8425 (t80) REVERT: E 510 MET cc_start: 0.7290 (ptp) cc_final: 0.6883 (mtp) outliers start: 28 outliers final: 21 residues processed: 153 average time/residue: 0.0932 time to fit residues: 20.7813 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 : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 542 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 516 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 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 LEU 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 482 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: 7.9990 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN D 375 ASN D 468 ASN E 296 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.163814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140190 restraints weight = 14560.834| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.64 r_work: 0.3713 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10984 Z= 0.125 Angle : 0.554 10.447 14825 Z= 0.270 Chirality : 0.042 0.143 1688 Planarity : 0.003 0.038 1822 Dihedral : 15.054 159.884 1642 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.08 % Allowed : 12.95 % Favored : 83.96 % 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: -0.56 (0.24), residues: 1308 helix: 0.49 (0.25), residues: 456 sheet: 0.31 (0.34), residues: 263 loop : -1.37 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 276 TYR 0.014 0.001 TYR D 411 PHE 0.013 0.001 PHE C 321 TRP 0.007 0.001 TRP A 381 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00292 (10984) covalent geometry : angle 0.55410 (14825) hydrogen bonds : bond 0.02890 ( 350) hydrogen bonds : angle 4.32725 ( 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 163 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.402 Fit side-chains REVERT: A 386 PHE cc_start: 0.6671 (m-80) cc_final: 0.6417 (t80) REVERT: A 388 ASN cc_start: 0.6602 (m-40) cc_final: 0.6091 (t0) REVERT: B 408 LYS cc_start: 0.7800 (mttp) cc_final: 0.7569 (mmmt) REVERT: B 428 ILE cc_start: 0.7491 (mt) cc_final: 0.7219 (mt) REVERT: E 510 MET cc_start: 0.7203 (ptp) cc_final: 0.6840 (mtp) outliers start: 35 outliers final: 31 residues processed: 152 average time/residue: 0.0886 time to fit residues: 19.7133 Evaluate side-chains 150 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 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 482 SER 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 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 342 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 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 516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 30 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139448 restraints weight = 14462.515| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.63 r_work: 0.3703 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10984 Z= 0.133 Angle : 0.563 9.556 14825 Z= 0.275 Chirality : 0.043 0.146 1688 Planarity : 0.003 0.037 1822 Dihedral : 15.035 159.665 1642 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.08 % Allowed : 14.27 % Favored : 82.64 % 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: -0.48 (0.24), residues: 1308 helix: 0.52 (0.25), residues: 459 sheet: 0.22 (0.33), residues: 267 loop : -1.23 (0.26), residues: 582 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 0.013 0.001 PHE C 321 TRP 0.006 0.001 TRP A 381 HIS 0.004 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00312 (10984) covalent geometry : angle 0.56267 (14825) hydrogen bonds : bond 0.02931 ( 350) hydrogen bonds : angle 4.34295 ( 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 158 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.244 Fit side-chains REVERT: A 316 MET cc_start: 0.7345 (mmm) cc_final: 0.7070 (mmm) REVERT: B 408 LYS cc_start: 0.7782 (mttp) cc_final: 0.7566 (mmmt) REVERT: B 428 ILE cc_start: 0.7504 (mt) cc_final: 0.7232 (mt) REVERT: E 446 MET cc_start: 0.6540 (mmt) cc_final: 0.5678 (mmt) REVERT: E 510 MET cc_start: 0.7264 (ptp) cc_final: 0.6780 (mtp) outliers start: 35 outliers final: 34 residues processed: 148 average time/residue: 0.0898 time to fit residues: 19.6651 Evaluate side-chains 150 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU 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 A residue 541 TRP Chi-restraints excluded: chain A residue 542 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 482 SER 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 388 ASN 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 416 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 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 513 LEU 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: 0.4980 chunk 90 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.163556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140009 restraints weight = 14543.967| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.64 r_work: 0.3710 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3846 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= 0.115 Angle : 0.545 9.167 14825 Z= 0.267 Chirality : 0.042 0.148 1688 Planarity : 0.002 0.036 1822 Dihedral : 14.912 159.158 1642 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.82 % Allowed : 14.80 % 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: -0.36 (0.24), residues: 1308 helix: 0.70 (0.25), residues: 451 sheet: 0.28 (0.34), residues: 268 loop : -1.22 (0.26), residues: 589 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 0.013 0.001 PHE C 321 TRP 0.005 0.001 TRP A 329 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00268 (10984) covalent geometry : angle 0.54549 (14825) hydrogen bonds : bond 0.02772 ( 350) hydrogen bonds : angle 4.29671 ( 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 156 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.363 Fit side-chains REVERT: A 316 MET cc_start: 0.7268 (mmm) cc_final: 0.6962 (mmm) REVERT: A 388 ASN cc_start: 0.6736 (m-40) cc_final: 0.6064 (t0) REVERT: B 408 LYS cc_start: 0.7772 (mttp) cc_final: 0.7538 (mmmt) REVERT: B 428 ILE cc_start: 0.7518 (mt) cc_final: 0.7250 (mt) REVERT: D 341 MET cc_start: 0.7812 (mmt) cc_final: 0.7512 (mmt) REVERT: E 446 MET cc_start: 0.6536 (mmt) cc_final: 0.5661 (mmt) REVERT: E 510 MET cc_start: 0.7261 (ptp) cc_final: 0.6803 (mtp) outliers start: 32 outliers final: 30 residues processed: 148 average time/residue: 0.0892 time to fit residues: 19.1488 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 : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP 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 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 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 416 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 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 465 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 = 0.4097 r_free = 0.4097 target = 0.164413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140933 restraints weight = 14413.131| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.63 r_work: 0.3722 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10984 Z= 0.104 Angle : 0.533 9.652 14825 Z= 0.261 Chirality : 0.042 0.147 1688 Planarity : 0.002 0.038 1822 Dihedral : 14.742 159.425 1642 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.08 % Allowed : 14.63 % Favored : 82.29 % 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: -0.25 (0.24), residues: 1308 helix: 0.87 (0.26), residues: 447 sheet: 0.38 (0.34), residues: 268 loop : -1.23 (0.26), residues: 593 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 0.018 0.001 PHE A 378 TRP 0.004 0.001 TRP A 329 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00241 (10984) covalent geometry : angle 0.53335 (14825) hydrogen bonds : bond 0.02623 ( 350) hydrogen bonds : angle 4.20861 ( 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 157 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.421 Fit side-chains REVERT: A 316 MET cc_start: 0.7161 (mmm) cc_final: 0.6891 (mmm) REVERT: A 388 ASN cc_start: 0.6325 (m-40) cc_final: 0.5866 (t0) REVERT: B 408 LYS cc_start: 0.7743 (mttp) cc_final: 0.7522 (mmmt) REVERT: B 428 ILE cc_start: 0.7515 (mt) cc_final: 0.7246 (mt) REVERT: D 341 MET cc_start: 0.7708 (mmt) cc_final: 0.7252 (mmp) REVERT: D 452 PHE cc_start: 0.8620 (t80) cc_final: 0.8345 (t80) REVERT: E 316 MET cc_start: 0.8108 (mmm) cc_final: 0.7856 (mmm) REVERT: E 446 MET cc_start: 0.6523 (mmt) cc_final: 0.5617 (mmt) REVERT: E 510 MET cc_start: 0.7163 (ptp) cc_final: 0.6818 (mtp) outliers start: 35 outliers final: 31 residues processed: 145 average time/residue: 0.0924 time to fit residues: 19.4956 Evaluate side-chains 151 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 A residue 541 TRP Chi-restraints excluded: chain A residue 542 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 468 ASN Chi-restraints excluded: chain D residue 516 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 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: 0.4980 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 465 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 = 0.4098 r_free = 0.4098 target = 0.164532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141121 restraints weight = 14418.239| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.63 r_work: 0.3724 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10984 Z= 0.104 Angle : 0.537 10.368 14825 Z= 0.262 Chirality : 0.042 0.146 1688 Planarity : 0.002 0.036 1822 Dihedral : 14.667 159.853 1642 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.82 % Allowed : 14.71 % Favored : 82.47 % 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: -0.15 (0.24), residues: 1308 helix: 0.92 (0.26), residues: 447 sheet: 0.45 (0.34), residues: 268 loop : -1.15 (0.26), residues: 593 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 0.017 0.001 PHE A 378 TRP 0.004 0.001 TRP A 381 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00241 (10984) covalent geometry : angle 0.53688 (14825) hydrogen bonds : bond 0.02619 ( 350) hydrogen bonds : angle 4.19138 ( 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 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.396 Fit side-chains REVERT: A 316 MET cc_start: 0.7271 (mmm) cc_final: 0.6967 (mmm) REVERT: A 388 ASN cc_start: 0.6289 (m-40) cc_final: 0.5816 (t0) REVERT: B 408 LYS cc_start: 0.7738 (mttp) cc_final: 0.7516 (mmmt) REVERT: B 428 ILE cc_start: 0.7525 (mt) cc_final: 0.7258 (mt) REVERT: D 341 MET cc_start: 0.7729 (mmt) cc_final: 0.7183 (mmp) REVERT: D 452 PHE cc_start: 0.8621 (t80) cc_final: 0.8403 (t80) REVERT: E 316 MET cc_start: 0.8099 (mmm) cc_final: 0.7847 (mmm) REVERT: E 446 MET cc_start: 0.6347 (mmt) cc_final: 0.5443 (mmt) REVERT: E 510 MET cc_start: 0.7182 (ptp) cc_final: 0.6881 (mtp) outliers start: 32 outliers final: 29 residues processed: 143 average time/residue: 0.0966 time to fit residues: 20.0074 Evaluate side-chains 148 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP 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 416 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 477 GLU 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: 0.6980 chunk 80 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 465 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 = 0.4073 r_free = 0.4073 target = 0.162181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138642 restraints weight = 14574.048| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.63 r_work: 0.3692 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4056 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= 0.134 Angle : 0.569 9.992 14825 Z= 0.277 Chirality : 0.043 0.146 1688 Planarity : 0.003 0.036 1822 Dihedral : 14.781 159.932 1642 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.00 % Allowed : 14.71 % Favored : 82.29 % 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: 0.84 (0.25), residues: 446 sheet: 0.45 (0.34), residues: 262 loop : -1.11 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 276 TYR 0.008 0.001 TYR D 411 PHE 0.015 0.001 PHE A 378 TRP 0.006 0.001 TRP A 381 HIS 0.004 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00317 (10984) covalent geometry : angle 0.56874 (14825) hydrogen bonds : bond 0.02958 ( 350) hydrogen bonds : angle 4.29184 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.67 seconds wall clock time: 45 minutes 41.77 seconds (2741.77 seconds total)