Starting phenix.real_space_refine on Sat Sep 12 02:00:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n7v_0364/09_2026/6n7v_0364.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7v_0364/09_2026/6n7v_0364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6n7v_0364/09_2026/6n7v_0364.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n7v_0364/09_2026/6n7v_0364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n7v_0364/09_2026/6n7v_0364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7v_0364/09_2026/6n7v_0364.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7v_0364/09_2026/6n7v_0364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7v_0364/09_2026/6n7v_0364.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 31 5.49 5 Mg 5 5.21 5 S 78 5.16 5 C 7963 2.51 5 N 2258 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12861 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: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2003 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1971 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 320 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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: "F" 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} Time building chain proxies: 3.11, per 1000 atoms: 0.24 Number of scatterers: 12861 At special positions: 0 Unit cell: (77.4, 125.56, 135.88, 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 78 16.00 P 31 15.00 Mg 5 11.99 O 2526 8.00 N 2258 7.00 C 7963 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: 0.82 Conformation dependent library (CDL) restraints added in 655.3 milliseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2862 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 37.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 273 through 280 removed outlier: 4.071A pdb=" N SER A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 300 removed outlier: 4.556A pdb=" N ASN A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.574A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.546A pdb=" N THR A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.766A 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: 3.599A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 387 removed outlier: 3.971A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.705A pdb=" N ALA A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.673A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 4.210A 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: 3.915A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.544A pdb=" N PHE B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.513A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.830A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.704A pdb=" N ILE C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.503A pdb=" N LYS C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.585A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.586A pdb=" N ALA C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 358 removed outlier: 3.854A pdb=" N ILE C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.907A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 3.964A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 removed outlier: 3.969A pdb=" N LEU C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 removed outlier: 3.669A pdb=" N VAL C 430 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 removed outlier: 4.016A pdb=" N MET C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.990A pdb=" N GLY C 478 " --> pdb=" O HIS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.996A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.631A pdb=" N ILE D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.501A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 332 " --> pdb=" O GLN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.687A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.628A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.919A 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 375 removed outlier: 3.730A pdb=" N GLU D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 4.104A 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 440 through 456 removed outlier: 3.684A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.522A pdb=" N GLU D 477 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 495 removed outlier: 3.863A pdb=" N GLN D 494 " --> pdb=" O GLY D 490 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 490 through 495' Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 317 through 329 Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.756A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.685A pdb=" N LYS E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 387 removed outlier: 3.837A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 415 Processing helix chain 'E' and resid 440 through 457 removed outlier: 3.921A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.594A pdb=" N GLY E 478 " --> pdb=" O HIS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 494 removed outlier: 3.732A pdb=" N ARG E 493 " --> pdb=" O GLY E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 329 Processing helix chain 'F' and resid 347 through 358 Processing helix chain 'F' and resid 365 through 372 removed outlier: 3.985A pdb=" N LYS F 369 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 387 removed outlier: 3.583A pdb=" N GLU F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 415 Processing helix chain 'F' and resid 440 through 457 Processing helix chain 'F' and resid 474 through 478 removed outlier: 3.941A pdb=" N GLY F 478 " --> pdb=" O HIS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 494 removed outlier: 3.702A pdb=" N ARG F 493 " --> pdb=" O GLY F 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.889A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU B 306 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 462 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 308 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 307 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE B 500 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET B 309 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU B 502 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 311 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.069A 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: 7.253A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET A 309 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 502 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 311 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG A 504 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 308 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 393 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL F 266 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.437A pdb=" N VAL C 337 " --> pdb=" O HIS C 392 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N TYR C 394 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 339 " --> pdb=" O TYR C 394 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY C 338 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP C 424 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA C 340 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE C 308 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE C 529 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 265 through 267 removed outlier: 6.446A pdb=" N ILE D 421 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE D 463 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU D 423 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL D 307 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ILE D 500 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET D 309 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU D 502 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR D 311 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 516 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY D 531 " --> pdb=" O VAL D 516 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE D 518 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE D 529 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 265 through 267 removed outlier: 6.621A pdb=" N VAL E 337 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TYR E 394 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE E 421 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE E 463 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU E 423 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N HIS E 465 " --> pdb=" O LEU E 423 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE E 308 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS E 464 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL E 310 " --> pdb=" O CYS E 464 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR E 498 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 502 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 265 through 267 removed outlier: 3.738A pdb=" N TYR F 394 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS F 336 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS F 464 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER F 312 " --> pdb=" O CYS F 464 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL F 307 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE F 500 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET F 309 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N LEU F 502 " --> pdb=" O MET F 309 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR F 311 " --> pdb=" O LEU F 502 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.19 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: 2149 1.31 - 1.44: 3211 1.44 - 1.57: 7489 1.57 - 1.69: 56 1.69 - 1.82: 132 Bond restraints: 13037 Sorted by residual: bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C6 TTP F 700 " pdb=" N1 TTP F 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.423 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.422 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 13032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 17200 2.45 - 4.90: 299 4.90 - 7.35: 65 7.35 - 9.81: 16 9.81 - 12.26: 8 Bond angle restraints: 17588 Sorted by residual: angle pdb=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT T 14 " pdb=" C4 DT T 14 " pdb=" O4 DT T 14 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT T 6 " pdb=" C4 DT T 6 " pdb=" O4 DT T 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 17583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 7641 35.22 - 70.45: 118 70.45 - 105.67: 12 105.67 - 140.89: 6 140.89 - 176.12: 8 Dihedral angle restraints: 7785 sinusoidal: 3315 harmonic: 4470 Sorted by residual: 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 -3.88 -176.12 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 -58.32 114.54 -172.85 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2 TTP E 700 " pdb=" C1' TTP E 700 " pdb=" N1 TTP E 700 " pdb=" O4' TTP E 700 " ideal model delta sinusoidal sigma weight residual 301.68 134.33 167.36 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 7782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1449 0.051 - 0.103: 417 0.103 - 0.154: 122 0.154 - 0.205: 6 0.205 - 0.257: 9 Chirality restraints: 2003 Sorted by residual: 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 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3' TTP B 700 " pdb=" C2' TTP B 700 " pdb=" C4' TTP B 700 " pdb=" O3' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.64e+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 -2.76 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2000 not shown) Planarity restraints: 2165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 412 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C MET E 412 " 0.031 2.00e-02 2.50e+03 pdb=" O MET E 412 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG E 413 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO D 511 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET F 412 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C MET F 412 " 0.031 2.00e-02 2.50e+03 pdb=" O MET F 412 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG F 413 " -0.010 2.00e-02 2.50e+03 ... (remaining 2162 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 192 2.68 - 3.23: 10953 3.23 - 3.79: 18851 3.79 - 4.34: 25755 4.34 - 4.90: 42571 Nonbonded interactions: 98322 Sorted by model distance: nonbonded pdb=" OE1 GLN E 343 " pdb="MG MG E 701 " model vdw 2.119 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.144 2.170 nonbonded pdb=" O2G TTP F 700 " pdb="MG MG F 701 " model vdw 2.145 2.170 nonbonded pdb=" OE1 GLN F 343 " pdb="MG MG F 701 " model vdw 2.198 2.170 nonbonded pdb=" O1B TTP C 700 " pdb="MG MG C 701 " model vdw 2.206 2.170 ... (remaining 98317 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 264 through 277 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 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 throu \ gh 545)) selection = (chain 'B' and (resid 264 through 277 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 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 throu \ gh 545)) selection = (chain 'C' and (resid 264 through 277 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 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 264 through 277 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or resid 439 through 506 or resid 510 through 5 \ 45)) selection = (chain 'E' and (resid 264 through 277 or resid 285 through 506 or resid 510 thro \ ugh 545)) selection = (chain 'F' and (resid 264 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.790 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 0.090 13037 Z= 0.289 Angle : 0.896 12.258 17588 Z= 0.496 Chirality : 0.053 0.257 2003 Planarity : 0.004 0.045 2165 Dihedral : 14.423 176.116 4923 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.15 % Allowed : 3.11 % Favored : 96.74 % 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: -3.41 (0.18), residues: 1554 helix: -2.69 (0.16), residues: 523 sheet: -0.74 (0.29), residues: 311 loop : -2.57 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 359 TYR 0.012 0.001 TYR B 535 PHE 0.017 0.002 PHE A 523 TRP 0.016 0.002 TRP A 541 HIS 0.012 0.002 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.29 (13037) covalent geometry : angle 0.89608 / 0.50 (17588) hydrogen bonds : bond 0.18294 / 12.19 ( 429) hydrogen bonds : angle 7.71980 / 5.48 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.7033 (mm110) cc_final: 0.6610 (tm-30) REVERT: A 329 TRP cc_start: 0.7059 (m-10) cc_final: 0.6550 (m-10) REVERT: A 341 MET cc_start: 0.5231 (mmt) cc_final: 0.4997 (mmm) REVERT: A 356 LEU cc_start: 0.8364 (tp) cc_final: 0.8097 (mt) REVERT: A 411 TYR cc_start: 0.6837 (t80) cc_final: 0.6374 (t80) REVERT: A 412 MET cc_start: 0.8601 (ttm) cc_final: 0.7746 (tmm) REVERT: A 418 CYS cc_start: 0.6168 (p) cc_final: 0.4840 (m) REVERT: A 419 ASP cc_start: 0.7546 (m-30) cc_final: 0.7272 (m-30) REVERT: A 448 LYS cc_start: 0.8818 (mttt) cc_final: 0.8539 (mttp) REVERT: A 506 GLN cc_start: 0.7896 (pt0) cc_final: 0.7691 (pt0) REVERT: A 510 MET cc_start: 0.6260 (mtp) cc_final: 0.5918 (mpp) REVERT: B 445 LEU cc_start: 0.8701 (tp) cc_final: 0.8454 (mm) REVERT: B 446 MET cc_start: 0.8265 (tpt) cc_final: 0.8022 (tmm) REVERT: B 494 GLN cc_start: 0.8832 (mt0) cc_final: 0.8548 (mt0) REVERT: B 533 MET cc_start: 0.7256 (mtm) cc_final: 0.6908 (mtm) REVERT: C 316 MET cc_start: 0.7829 (mmm) cc_final: 0.7498 (mmt) REVERT: C 328 GLN cc_start: 0.8164 (mm110) cc_final: 0.7926 (mm-40) REVERT: C 408 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7203 (mmtt) REVERT: D 307 VAL cc_start: 0.7904 (t) cc_final: 0.7479 (t) REVERT: D 323 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7687 (mmp80) REVERT: D 341 MET cc_start: 0.8393 (mmp) cc_final: 0.8142 (mmt) REVERT: D 537 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7517 (mmtm) REVERT: E 266 VAL cc_start: 0.8039 (t) cc_final: 0.7839 (p) REVERT: E 278 HIS cc_start: 0.8299 (t70) cc_final: 0.7821 (t-90) REVERT: E 306 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6636 (mt-10) REVERT: F 298 LYS cc_start: 0.7403 (ttmm) cc_final: 0.7039 (mmtp) REVERT: F 476 GLU cc_start: 0.7268 (mp0) cc_final: 0.6862 (mp0) outliers start: 2 outliers final: 1 residues processed: 381 average time/residue: 0.1288 time to fit residues: 68.1313 Evaluate side-chains 190 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 504 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 0.0270 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 444 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 475 HIS E 358 ASN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN F 392 HIS ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.123981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103114 restraints weight = 30736.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105807 restraints weight = 18334.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107600 restraints weight = 12502.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.108973 restraints weight = 9488.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109804 restraints weight = 7694.898| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13037 Z= 0.122 Angle : 0.631 8.342 17588 Z= 0.306 Chirality : 0.043 0.168 2003 Planarity : 0.004 0.072 2165 Dihedral : 16.417 175.438 1942 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.78 % Allowed : 12.08 % Favored : 86.14 % 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: -2.06 (0.20), residues: 1554 helix: -0.92 (0.21), residues: 521 sheet: -0.26 (0.30), residues: 320 loop : -2.24 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.010 0.001 TYR A 535 PHE 0.018 0.001 PHE E 321 TRP 0.008 0.001 TRP F 541 HIS 0.007 0.001 HIS F 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13037) covalent geometry : angle 0.63145 / 0.31 (17588) hydrogen bonds : bond 0.03277 / 2.16 ( 429) hydrogen bonds : angle 5.21357 / 3.76 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6983 (mm110) cc_final: 0.6669 (tm-30) REVERT: A 380 GLN cc_start: 0.8182 (mp10) cc_final: 0.7870 (pp30) REVERT: A 411 TYR cc_start: 0.6703 (t80) cc_final: 0.6444 (t80) REVERT: A 510 MET cc_start: 0.6330 (mtp) cc_final: 0.6051 (mpp) REVERT: B 533 MET cc_start: 0.7640 (mtm) cc_final: 0.7427 (mtm) REVERT: D 323 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7635 (mmp80) REVERT: D 341 MET cc_start: 0.8091 (mmp) cc_final: 0.7491 (tpp) REVERT: D 352 ASP cc_start: 0.6755 (t0) cc_final: 0.6420 (t70) REVERT: D 537 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7783 (mmtm) REVERT: E 306 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6702 (mt-10) REVERT: E 309 MET cc_start: 0.7609 (mmt) cc_final: 0.7007 (mmt) REVERT: E 445 LEU cc_start: 0.8739 (tp) cc_final: 0.8511 (tp) REVERT: F 341 MET cc_start: 0.5264 (mmt) cc_final: 0.5008 (mmm) REVERT: F 538 GLU cc_start: 0.7920 (mp0) cc_final: 0.7614 (pm20) outliers start: 24 outliers final: 14 residues processed: 224 average time/residue: 0.1079 time to fit residues: 35.6585 Evaluate side-chains 186 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 538 GLU Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 121 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 364 GLN ** F 465 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 = 0.3965 r_free = 0.3965 target = 0.118757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.097691 restraints weight = 31070.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.100316 restraints weight = 18766.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.102126 restraints weight = 12803.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.103254 restraints weight = 9696.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104186 restraints weight = 8006.188| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13037 Z= 0.138 Angle : 0.617 8.502 17588 Z= 0.298 Chirality : 0.043 0.162 2003 Planarity : 0.004 0.102 2165 Dihedral : 15.836 167.551 1938 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.00 % Allowed : 14.08 % Favored : 83.91 % 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: -1.53 (0.21), residues: 1554 helix: -0.14 (0.23), residues: 519 sheet: -0.21 (0.30), residues: 325 loop : -2.09 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 504 TYR 0.016 0.001 TYR A 547 PHE 0.016 0.001 PHE C 452 TRP 0.008 0.001 TRP B 541 HIS 0.008 0.001 HIS E 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (13037) covalent geometry : angle 0.61652 / 0.30 (17588) hydrogen bonds : bond 0.03122 / 2.08 ( 429) hydrogen bonds : angle 4.81561 / 3.46 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 TYR cc_start: 0.6596 (t80) cc_final: 0.6279 (t80) REVERT: A 510 MET cc_start: 0.6307 (mtp) cc_final: 0.6053 (mpp) REVERT: C 316 MET cc_start: 0.7823 (mmt) cc_final: 0.7587 (tpp) REVERT: C 333 MET cc_start: 0.8502 (mmt) cc_final: 0.8123 (mmp) REVERT: D 470 ASP cc_start: 0.8993 (p0) cc_final: 0.8764 (p0) REVERT: E 306 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6525 (mt-10) REVERT: E 445 LEU cc_start: 0.8828 (tp) cc_final: 0.8613 (tp) REVERT: E 446 MET cc_start: 0.8727 (mmm) cc_final: 0.8439 (mmm) REVERT: F 341 MET cc_start: 0.5144 (mmt) cc_final: 0.4898 (mmm) outliers start: 27 outliers final: 19 residues processed: 199 average time/residue: 0.1030 time to fit residues: 30.8246 Evaluate side-chains 180 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 114 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 91 optimal weight: 0.0050 chunk 128 optimal weight: 0.0770 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 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 = 0.3976 r_free = 0.3976 target = 0.118512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.098556 restraints weight = 31693.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.101073 restraints weight = 19338.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102762 restraints weight = 13378.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.103939 restraints weight = 10282.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.104815 restraints weight = 8491.756| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13037 Z= 0.201 Angle : 0.679 8.202 17588 Z= 0.333 Chirality : 0.046 0.159 2003 Planarity : 0.004 0.069 2165 Dihedral : 15.662 161.913 1938 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.41 % Allowed : 13.94 % Favored : 82.65 % 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: -1.35 (0.21), residues: 1554 helix: 0.21 (0.23), residues: 539 sheet: -0.48 (0.30), residues: 323 loop : -2.00 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 276 TYR 0.014 0.002 TYR F 535 PHE 0.017 0.002 PHE E 321 TRP 0.012 0.002 TRP B 329 HIS 0.008 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (13037) covalent geometry : angle 0.67905 / 0.33 (17588) hydrogen bonds : bond 0.03640 / 2.38 ( 429) hydrogen bonds : angle 4.87528 / 3.48 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.7322 (tp40) cc_final: 0.7030 (tp40) REVERT: A 380 GLN cc_start: 0.8305 (mp10) cc_final: 0.8018 (mp10) REVERT: A 411 TYR cc_start: 0.6666 (t80) cc_final: 0.6302 (t80) REVERT: A 507 GLN cc_start: 0.8204 (mp10) cc_final: 0.7943 (pm20) REVERT: B 309 MET cc_start: 0.7740 (mmm) cc_final: 0.7170 (mmm) REVERT: B 316 MET cc_start: 0.7877 (tpp) cc_final: 0.7417 (mmp) REVERT: D 311 THR cc_start: 0.8805 (p) cc_final: 0.8430 (p) REVERT: D 316 MET cc_start: 0.8047 (mmp) cc_final: 0.7660 (mmp) REVERT: D 470 ASP cc_start: 0.8873 (p0) cc_final: 0.8623 (p0) REVERT: D 532 TYR cc_start: 0.8463 (m-80) cc_final: 0.8238 (m-10) REVERT: E 306 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6788 (mt-10) REVERT: E 441 MET cc_start: 0.6573 (tmm) cc_final: 0.6260 (tmm) REVERT: E 445 LEU cc_start: 0.9017 (tp) cc_final: 0.8774 (tp) REVERT: E 495 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8873 (mp) REVERT: F 316 MET cc_start: 0.5744 (mmm) cc_final: 0.4376 (mtp) outliers start: 46 outliers final: 31 residues processed: 213 average time/residue: 0.0944 time to fit residues: 31.0122 Evaluate side-chains 192 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 538 GLU Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 412 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 118 optimal weight: 0.0030 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 105 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.5890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.116082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095002 restraints weight = 31400.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.097569 restraints weight = 19046.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099277 restraints weight = 13163.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.100555 restraints weight = 10079.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101440 restraints weight = 8278.739| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13037 Z= 0.107 Angle : 0.589 10.459 17588 Z= 0.285 Chirality : 0.043 0.163 2003 Planarity : 0.003 0.067 2165 Dihedral : 15.355 159.057 1938 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.15 % Allowed : 15.27 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1554 helix: 0.59 (0.24), residues: 529 sheet: -0.33 (0.30), residues: 323 loop : -1.88 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 439 TYR 0.008 0.001 TYR E 535 PHE 0.018 0.001 PHE C 452 TRP 0.007 0.001 TRP B 541 HIS 0.007 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (13037) covalent geometry : angle 0.58939 / 0.29 (17588) hydrogen bonds : bond 0.02809 / 1.84 ( 429) hydrogen bonds : angle 4.58918 / 3.28 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.7303 (tp40) cc_final: 0.6951 (tp40) REVERT: A 380 GLN cc_start: 0.8359 (mp10) cc_final: 0.8067 (mp10) REVERT: A 411 TYR cc_start: 0.6848 (t80) cc_final: 0.6502 (t80) REVERT: B 309 MET cc_start: 0.7995 (mmm) cc_final: 0.7694 (mmm) REVERT: B 477 GLU cc_start: 0.6691 (mp0) cc_final: 0.6437 (mp0) REVERT: D 311 THR cc_start: 0.8739 (p) cc_final: 0.8308 (p) REVERT: E 306 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6617 (mt-10) REVERT: E 445 LEU cc_start: 0.8933 (tp) cc_final: 0.8657 (tp) REVERT: E 495 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8833 (mp) REVERT: F 316 MET cc_start: 0.5677 (mmm) cc_final: 0.4213 (mtt) REVERT: F 510 MET cc_start: 0.6291 (tpp) cc_final: 0.5884 (ttp) outliers start: 29 outliers final: 23 residues processed: 194 average time/residue: 0.0941 time to fit residues: 27.9898 Evaluate side-chains 180 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 154 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 324 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.113994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093778 restraints weight = 32065.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096273 restraints weight = 19586.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.097916 restraints weight = 13558.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099085 restraints weight = 10434.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099903 restraints weight = 8645.531| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13037 Z= 0.308 Angle : 0.806 9.760 17588 Z= 0.397 Chirality : 0.050 0.182 2003 Planarity : 0.005 0.074 2165 Dihedral : 15.840 155.238 1938 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.19 % Allowed : 15.05 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.21), residues: 1554 helix: 0.02 (0.22), residues: 550 sheet: -0.85 (0.30), residues: 318 loop : -2.00 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 276 TYR 0.019 0.002 TYR A 535 PHE 0.019 0.003 PHE E 523 TRP 0.016 0.003 TRP B 329 HIS 0.012 0.002 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.31 (13037) covalent geometry : angle 0.80587 / 0.40 (17588) hydrogen bonds : bond 0.04474 / 2.92 ( 429) hydrogen bonds : angle 5.23018 / 3.72 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 333 MET cc_start: 0.8542 (mtt) cc_final: 0.8127 (mpp) REVERT: A 380 GLN cc_start: 0.8372 (mp10) cc_final: 0.8069 (mp10) REVERT: A 411 TYR cc_start: 0.6861 (t80) cc_final: 0.6436 (t80) REVERT: A 428 ILE cc_start: 0.7191 (mt) cc_final: 0.6898 (mp) REVERT: B 477 GLU cc_start: 0.6946 (mp0) cc_final: 0.6710 (mp0) REVERT: D 311 THR cc_start: 0.9200 (p) cc_final: 0.8857 (p) REVERT: D 470 ASP cc_start: 0.8945 (p0) cc_final: 0.8742 (p0) REVERT: E 510 MET cc_start: 0.8438 (mmm) cc_final: 0.7756 (mpp) REVERT: F 316 MET cc_start: 0.6421 (mmm) cc_final: 0.5569 (mtt) REVERT: F 454 LYS cc_start: 0.6079 (mmpt) cc_final: 0.5836 (mmpt) REVERT: F 492 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7799 (mt) outliers start: 43 outliers final: 35 residues processed: 192 average time/residue: 0.0866 time to fit residues: 25.8948 Evaluate side-chains 189 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 104 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.116725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096719 restraints weight = 31430.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099237 restraints weight = 19256.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.100943 restraints weight = 13260.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.102148 restraints weight = 10140.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.102709 restraints weight = 8348.615| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13037 Z= 0.147 Angle : 0.635 8.965 17588 Z= 0.311 Chirality : 0.044 0.177 2003 Planarity : 0.003 0.074 2165 Dihedral : 15.551 155.353 1938 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.45 % Allowed : 16.09 % Favored : 81.47 % 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: -1.29 (0.21), residues: 1554 helix: 0.31 (0.23), residues: 557 sheet: -0.74 (0.30), residues: 322 loop : -1.89 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 323 TYR 0.020 0.002 TYR D 532 PHE 0.017 0.001 PHE E 321 TRP 0.009 0.001 TRP F 381 HIS 0.009 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (13037) covalent geometry : angle 0.63533 / 0.31 (17588) hydrogen bonds : bond 0.03279 / 2.14 ( 429) hydrogen bonds : angle 4.87311 / 3.46 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.7070 (tp40) cc_final: 0.6557 (tp40) REVERT: A 411 TYR cc_start: 0.6761 (t80) cc_final: 0.6273 (t80) REVERT: D 311 THR cc_start: 0.8874 (p) cc_final: 0.8492 (p) REVERT: D 470 ASP cc_start: 0.8798 (p0) cc_final: 0.8591 (p0) REVERT: E 306 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6858 (mt-10) REVERT: E 441 MET cc_start: 0.6681 (tmm) cc_final: 0.6350 (tmm) REVERT: E 510 MET cc_start: 0.8445 (mmm) cc_final: 0.7755 (mpp) REVERT: F 316 MET cc_start: 0.6323 (mmm) cc_final: 0.5488 (mtp) REVERT: F 492 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7759 (mt) outliers start: 33 outliers final: 26 residues processed: 185 average time/residue: 0.0973 time to fit residues: 27.5447 Evaluate side-chains 180 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 111 optimal weight: 0.0040 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.114490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093622 restraints weight = 31409.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.096042 restraints weight = 19681.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.097724 restraints weight = 13795.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.098901 restraints weight = 10632.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.099713 restraints weight = 8854.028| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13037 Z= 0.104 Angle : 0.607 10.790 17588 Z= 0.292 Chirality : 0.043 0.189 2003 Planarity : 0.003 0.070 2165 Dihedral : 15.097 158.002 1938 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.37 % Allowed : 16.83 % Favored : 80.80 % 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 (0.22), residues: 1554 helix: 0.67 (0.23), residues: 544 sheet: -0.39 (0.31), residues: 308 loop : -1.72 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 323 TYR 0.023 0.001 TYR A 547 PHE 0.013 0.001 PHE E 321 TRP 0.014 0.001 TRP A 381 HIS 0.005 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (13037) covalent geometry : angle 0.60716 / 0.29 (17588) hydrogen bonds : bond 0.02624 / 1.72 ( 429) hydrogen bonds : angle 4.61710 / 3.30 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6786 (tp40) cc_final: 0.6363 (tp40) REVERT: A 341 MET cc_start: 0.6551 (mmm) cc_final: 0.6321 (mmm) REVERT: A 380 GLN cc_start: 0.8494 (mp10) cc_final: 0.8226 (pm20) REVERT: A 411 TYR cc_start: 0.6918 (t80) cc_final: 0.6431 (t80) REVERT: A 533 MET cc_start: 0.7123 (mtp) cc_final: 0.6454 (ttm) REVERT: B 425 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6457 (m-70) REVERT: B 445 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7995 (tp) REVERT: D 311 THR cc_start: 0.8897 (p) cc_final: 0.8533 (p) REVERT: D 341 MET cc_start: 0.7561 (mmt) cc_final: 0.6973 (mmp) REVERT: D 470 ASP cc_start: 0.8900 (p0) cc_final: 0.8665 (p0) REVERT: E 306 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6572 (mt-10) REVERT: E 510 MET cc_start: 0.8467 (mmm) cc_final: 0.7758 (mpp) REVERT: F 316 MET cc_start: 0.6279 (mmm) cc_final: 0.5272 (mtp) REVERT: F 492 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7808 (mt) REVERT: F 510 MET cc_start: 0.5892 (tpp) cc_final: 0.5604 (ttp) outliers start: 32 outliers final: 24 residues processed: 182 average time/residue: 0.0945 time to fit residues: 26.3221 Evaluate side-chains 182 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 0.0000 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 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 = 0.3893 r_free = 0.3893 target = 0.113635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092900 restraints weight = 31749.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.095279 restraints weight = 19750.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.096972 restraints weight = 13893.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098064 restraints weight = 10700.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098909 restraints weight = 8901.373| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13037 Z= 0.124 Angle : 0.621 11.103 17588 Z= 0.298 Chirality : 0.043 0.178 2003 Planarity : 0.003 0.072 2165 Dihedral : 14.995 156.796 1938 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.08 % Allowed : 17.20 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.22), residues: 1554 helix: 0.66 (0.23), residues: 549 sheet: -0.39 (0.30), residues: 321 loop : -1.67 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 323 TYR 0.014 0.001 TYR D 547 PHE 0.014 0.001 PHE E 321 TRP 0.012 0.001 TRP A 381 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (13037) covalent geometry : angle 0.62140 / 0.30 (17588) hydrogen bonds : bond 0.02807 / 1.81 ( 429) hydrogen bonds : angle 4.55747 / 3.25 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 341 MET cc_start: 0.6551 (mmm) cc_final: 0.6269 (mmm) REVERT: A 411 TYR cc_start: 0.6781 (t80) cc_final: 0.6243 (t80) REVERT: B 425 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6640 (m-70) REVERT: B 445 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8246 (tp) REVERT: D 311 THR cc_start: 0.8977 (p) cc_final: 0.8591 (p) REVERT: D 470 ASP cc_start: 0.8921 (p0) cc_final: 0.8640 (p0) REVERT: E 306 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6607 (mt-10) REVERT: E 510 MET cc_start: 0.8450 (mmm) cc_final: 0.7706 (mpp) REVERT: F 316 MET cc_start: 0.6316 (mmm) cc_final: 0.5283 (mtp) REVERT: F 492 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7989 (mt) outliers start: 28 outliers final: 21 residues processed: 176 average time/residue: 0.0957 time to fit residues: 25.5811 Evaluate side-chains 177 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.115605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095802 restraints weight = 31676.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098204 restraints weight = 19351.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099886 restraints weight = 13561.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.100976 restraints weight = 10394.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.101597 restraints weight = 8658.446| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13037 Z= 0.209 Angle : 0.710 10.294 17588 Z= 0.343 Chirality : 0.046 0.172 2003 Planarity : 0.004 0.078 2165 Dihedral : 15.146 159.218 1938 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.78 % Allowed : 17.57 % Favored : 80.65 % 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: -1.20 (0.22), residues: 1554 helix: 0.33 (0.23), residues: 564 sheet: -0.72 (0.30), residues: 315 loop : -1.79 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 323 TYR 0.017 0.002 TYR D 547 PHE 0.015 0.002 PHE E 321 TRP 0.012 0.002 TRP A 541 HIS 0.006 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (13037) covalent geometry : angle 0.70976 / 0.34 (17588) hydrogen bonds : bond 0.03497 / 2.26 ( 429) hydrogen bonds : angle 4.77678 / 3.41 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 341 MET cc_start: 0.6740 (mmm) cc_final: 0.6512 (mmm) REVERT: A 411 TYR cc_start: 0.6847 (t80) cc_final: 0.6256 (t80) REVERT: B 425 HIS cc_start: 0.6724 (t-90) cc_final: 0.6471 (m-70) REVERT: B 445 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8385 (tp) REVERT: D 311 THR cc_start: 0.9062 (p) cc_final: 0.8743 (p) REVERT: D 341 MET cc_start: 0.7546 (mmt) cc_final: 0.7313 (mmp) REVERT: D 470 ASP cc_start: 0.8906 (p0) cc_final: 0.8650 (p0) REVERT: E 510 MET cc_start: 0.8506 (mmm) cc_final: 0.7783 (mpp) REVERT: F 316 MET cc_start: 0.6318 (mmm) cc_final: 0.5895 (mtp) REVERT: F 344 GLU cc_start: 0.7750 (mp0) cc_final: 0.7405 (mp0) REVERT: F 492 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7905 (mt) outliers start: 24 outliers final: 22 residues processed: 168 average time/residue: 0.0943 time to fit residues: 24.5084 Evaluate side-chains 175 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 113 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 104 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 144 optimal weight: 0.0270 chunk 149 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098208 restraints weight = 31314.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.100727 restraints weight = 19275.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.102472 restraints weight = 13309.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.103705 restraints weight = 10112.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.104362 restraints weight = 8294.724| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13037 Z= 0.116 Angle : 0.628 9.670 17588 Z= 0.302 Chirality : 0.044 0.175 2003 Planarity : 0.003 0.075 2165 Dihedral : 14.946 161.861 1938 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.78 % Allowed : 17.79 % Favored : 80.43 % 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: -0.96 (0.22), residues: 1554 helix: 0.56 (0.23), residues: 563 sheet: -0.52 (0.30), residues: 314 loop : -1.70 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 323 TYR 0.018 0.001 TYR D 547 PHE 0.015 0.001 PHE E 321 TRP 0.011 0.001 TRP F 381 HIS 0.004 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13037) covalent geometry : angle 0.62829 / 0.30 (17588) hydrogen bonds : bond 0.02776 / 1.80 ( 429) hydrogen bonds : angle 4.58269 / 3.28 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.00 seconds wall clock time: 35 minutes 35.06 seconds (2135.06 seconds total)