Starting phenix.real_space_refine on Thu Jul 31 02:06:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7v_0364/07_2025/6n7v_0364.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7v_0364/07_2025/6n7v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7v_0364/07_2025/6n7v_0364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7v_0364/07_2025/6n7v_0364.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7v_0364/07_2025/6n7v_0364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7v_0364/07_2025/6n7v_0364.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.53, per 1000 atoms: 0.66 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: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.61 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: 3.67 Time building geometry restraints manager: 3.63 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: 17215 2.45 - 4.90: 284 4.90 - 7.35: 65 7.35 - 9.81: 16 9.81 - 12.26: 8 Bond angle restraints: 17588 Sorted by residual: angle pdb=" PA TTP E 700 " pdb=" O3A TTP E 700 " pdb=" PB TTP E 700 " ideal model delta sigma weight residual 120.50 132.76 -12.26 3.00e+00 1.11e-01 1.67e+01 angle pdb=" PB TTP E 700 " pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " ideal model delta sigma weight residual 120.50 132.75 -12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" PA TTP F 700 " pdb=" O3A TTP F 700 " pdb=" PB TTP F 700 " ideal model delta sigma weight residual 120.50 132.68 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PB TTP F 700 " pdb=" O3B TTP F 700 " pdb=" PG TTP F 700 " ideal model delta sigma weight residual 120.50 132.68 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PB TTP B 700 " pdb=" O3B TTP B 700 " pdb=" PG TTP B 700 " ideal model delta sigma weight residual 120.50 132.65 -12.15 3.00e+00 1.11e-01 1.64e+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: 1462 0.051 - 0.103: 407 0.103 - 0.154: 120 0.154 - 0.205: 5 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: 0.950 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: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.190 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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= 0.274 Angle : 0.892 12.258 17588 Z= 0.471 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 : 3.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP A 541 HIS 0.012 0.002 HIS C 425 PHE 0.017 0.002 PHE A 523 TYR 0.012 0.001 TYR B 535 ARG 0.006 0.001 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.18294 ( 429) hydrogen bonds : angle 7.71980 ( 1224) covalent geometry : bond 0.00501 (13037) covalent geometry : angle 0.89181 (17588) *********************** 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 : 1.477 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: 0.6611 (tm-30) REVERT: A 329 TRP cc_start: 0.7059 (m-10) cc_final: 0.6551 (m-10) REVERT: A 341 MET cc_start: 0.5231 (mmt) cc_final: 0.5000 (mmm) REVERT: A 356 LEU cc_start: 0.8364 (tp) cc_final: 0.8096 (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: 0.7745 (tmm) REVERT: A 418 CYS cc_start: 0.6168 (p) cc_final: 0.4839 (m) REVERT: A 419 ASP cc_start: 0.7546 (m-30) cc_final: 0.7268 (m-30) REVERT: A 448 LYS cc_start: 0.8818 (mttt) cc_final: 0.8536 (mttp) REVERT: A 506 GLN cc_start: 0.7896 (pt0) cc_final: 0.7692 (pt0) REVERT: A 510 MET cc_start: 0.6259 (mtp) cc_final: 0.5920 (mpp) REVERT: B 445 LEU cc_start: 0.8701 (tp) cc_final: 0.8458 (mm) REVERT: B 494 GLN cc_start: 0.8832 (mt0) cc_final: 0.8555 (mt0) REVERT: B 533 MET cc_start: 0.7255 (mtm) cc_final: 0.6911 (mtm) REVERT: C 316 MET cc_start: 0.7829 (mmm) cc_final: 0.7499 (mmt) REVERT: C 328 GLN cc_start: 0.8164 (mm110) cc_final: 0.7925 (mm-40) REVERT: C 408 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7205 (mmtt) REVERT: D 307 VAL cc_start: 0.7904 (t) cc_final: 0.7480 (t) REVERT: D 323 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7686 (mmp80) REVERT: D 341 MET cc_start: 0.8393 (mmp) cc_final: 0.8141 (mmt) REVERT: D 537 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7517 (mmtm) 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: 0.6640 (mt-10) REVERT: F 298 LYS cc_start: 0.7403 (ttmm) cc_final: 0.7038 (mmtp) REVERT: F 476 GLU cc_start: 0.7268 (mp0) cc_final: 0.6864 (mp0) outliers start: 2 outliers final: 1 residues processed: 381 average time/residue: 0.2866 time to fit residues: 149.3782 Evaluate side-chains 191 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 134 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN D 278 HIS ** 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 343 GLN F 364 GLN F 392 HIS ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.116205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095378 restraints weight = 30903.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097840 restraints weight = 18622.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099576 restraints weight = 12929.358| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13037 Z= 0.191 Angle : 0.683 9.613 17588 Z= 0.333 Chirality : 0.045 0.154 2003 Planarity : 0.004 0.062 2165 Dihedral : 16.113 165.512 1942 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.45 % Allowed : 11.71 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.20), residues: 1554 helix: -0.75 (0.21), residues: 519 sheet: -0.50 (0.30), residues: 316 loop : -2.19 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 329 HIS 0.007 0.001 HIS B 357 PHE 0.024 0.002 PHE E 321 TYR 0.013 0.002 TYR A 535 ARG 0.005 0.001 ARG F 361 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 429) hydrogen bonds : angle 5.22677 ( 1224) covalent geometry : bond 0.00433 (13037) covalent geometry : angle 0.68314 (17588) *********************** 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 240 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 1.275 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 356 LEU cc_start: 0.8401 (tp) cc_final: 0.8193 (mt) REVERT: A 411 TYR cc_start: 0.6736 (t80) cc_final: 0.6331 (t80) REVERT: A 510 MET cc_start: 0.6176 (mtp) cc_final: 0.5922 (mpp) REVERT: B 341 MET cc_start: 0.8702 (mmt) cc_final: 0.8379 (tpp) REVERT: B 477 GLU cc_start: 0.6378 (mp0) cc_final: 0.6103 (mp0) REVERT: C 333 MET cc_start: 0.8174 (mpp) cc_final: 0.7935 (mmp) REVERT: C 438 GLU cc_start: 0.8447 (pt0) cc_final: 0.8163 (pt0) REVERT: D 323 ARG cc_start: 0.7803 (ttm110) cc_final: 0.7576 (mmp80) REVERT: D 352 ASP cc_start: 0.7138 (t0) cc_final: 0.6749 (t70) REVERT: D 537 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7931 (mmtp) REVERT: E 306 GLU cc_start: 0.7715 (mt-10) cc_final: 0.6922 (mt-10) REVERT: E 514 VAL cc_start: 0.8887 (m) cc_final: 0.8617 (p) REVERT: E 533 MET cc_start: 0.8173 (mpp) cc_final: 0.7937 (mpp) REVERT: F 298 LYS cc_start: 0.8020 (ttmm) cc_final: 0.7393 (mmtp) REVERT: F 538 GLU cc_start: 0.8031 (mp0) cc_final: 0.7821 (pm20) REVERT: F 539 THR cc_start: 0.6341 (p) cc_final: 0.6106 (t) outliers start: 33 outliers final: 20 residues processed: 234 average time/residue: 0.2431 time to fit residues: 82.7835 Evaluate side-chains 196 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 297 ASP 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 484 THR Chi-restraints excluded: chain F residue 310 VAL 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 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** 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 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.116964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.096026 restraints weight = 31241.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.098635 restraints weight = 18726.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.100434 restraints weight = 12846.345| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13037 Z= 0.120 Angle : 0.586 7.108 17588 Z= 0.283 Chirality : 0.043 0.164 2003 Planarity : 0.003 0.062 2165 Dihedral : 15.419 161.527 1938 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.08 % Allowed : 13.86 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.21), residues: 1554 helix: -0.01 (0.23), residues: 533 sheet: -0.34 (0.30), residues: 322 loop : -2.06 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 541 HIS 0.006 0.001 HIS B 425 PHE 0.016 0.001 PHE E 321 TYR 0.020 0.001 TYR A 547 ARG 0.004 0.000 ARG C 303 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 429) hydrogen bonds : angle 4.72329 ( 1224) covalent geometry : bond 0.00272 (13037) covalent geometry : angle 0.58618 (17588) *********************** 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 219 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8531 (tp) cc_final: 0.8247 (mt) REVERT: A 411 TYR cc_start: 0.6897 (t80) cc_final: 0.6548 (t80) REVERT: A 510 MET cc_start: 0.6301 (mtp) cc_final: 0.6031 (mpp) REVERT: B 341 MET cc_start: 0.8666 (mmt) cc_final: 0.8332 (tpp) REVERT: B 445 LEU cc_start: 0.8881 (tp) cc_final: 0.8478 (tp) REVERT: D 316 MET cc_start: 0.8446 (mmp) cc_final: 0.7934 (mmp) REVERT: D 323 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7424 (mtm110) REVERT: D 341 MET cc_start: 0.8129 (mmt) cc_final: 0.7921 (mmt) REVERT: D 352 ASP cc_start: 0.6898 (t0) cc_final: 0.5676 (t70) REVERT: D 470 ASP cc_start: 0.9112 (p0) cc_final: 0.8805 (p0) REVERT: D 537 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7927 (mmtp) REVERT: E 306 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6599 (mt-10) REVERT: E 446 MET cc_start: 0.8775 (mmm) cc_final: 0.8490 (mmm) REVERT: E 533 MET cc_start: 0.8122 (mpp) cc_final: 0.7891 (mpp) REVERT: F 298 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7223 (mmtp) outliers start: 28 outliers final: 22 residues processed: 214 average time/residue: 0.2387 time to fit residues: 75.3234 Evaluate side-chains 191 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 496 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 449 LEU 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 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 E residue 538 GLU Chi-restraints excluded: chain F residue 321 PHE 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 34 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 69 optimal weight: 0.1980 chunk 133 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 325 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN E 278 HIS ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN F 444 ASN ** 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 = 0.3924 r_free = 0.3924 target = 0.116345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095165 restraints weight = 31347.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097750 restraints weight = 18965.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099542 restraints weight = 13046.581| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13037 Z= 0.126 Angle : 0.581 9.724 17588 Z= 0.282 Chirality : 0.043 0.162 2003 Planarity : 0.003 0.062 2165 Dihedral : 15.048 159.261 1938 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.74 % Allowed : 13.71 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.21), residues: 1554 helix: 0.39 (0.23), residues: 537 sheet: -0.23 (0.31), residues: 310 loop : -1.97 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 541 HIS 0.008 0.001 HIS E 278 PHE 0.015 0.001 PHE E 321 TYR 0.023 0.001 TYR A 547 ARG 0.004 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 429) hydrogen bonds : angle 4.61042 ( 1224) covalent geometry : bond 0.00287 (13037) covalent geometry : angle 0.58141 (17588) *********************** 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 221 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8519 (tp) cc_final: 0.8102 (mt) REVERT: A 411 TYR cc_start: 0.7226 (t80) cc_final: 0.6755 (t80) REVERT: A 510 MET cc_start: 0.6294 (mtp) cc_final: 0.6092 (mpp) REVERT: B 441 MET cc_start: 0.6423 (ttt) cc_final: 0.6067 (ttt) REVERT: B 445 LEU cc_start: 0.8815 (tp) cc_final: 0.8559 (tp) REVERT: D 311 THR cc_start: 0.8806 (p) cc_final: 0.8328 (p) REVERT: D 352 ASP cc_start: 0.6870 (t0) cc_final: 0.5809 (t0) REVERT: D 470 ASP cc_start: 0.9003 (p0) cc_final: 0.8723 (p0) REVERT: D 537 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7983 (mmtp) REVERT: E 306 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6599 (mt-10) REVERT: E 446 MET cc_start: 0.8787 (mmm) cc_final: 0.8516 (mmm) REVERT: E 533 MET cc_start: 0.8147 (mpp) cc_final: 0.7878 (mpp) REVERT: F 298 LYS cc_start: 0.7380 (ttmm) cc_final: 0.6989 (mmtp) REVERT: F 341 MET cc_start: 0.5590 (mmt) cc_final: 0.5352 (mmm) REVERT: F 492 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7918 (mt) outliers start: 37 outliers final: 27 residues processed: 212 average time/residue: 0.2227 time to fit residues: 70.7560 Evaluate side-chains 196 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 496 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU 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 C residue 412 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 449 LEU 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 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 456 THR Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 538 GLU Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 380 GLN ** 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 ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** F 465 HIS ** 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 = 0.3965 r_free = 0.3965 target = 0.117857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.098073 restraints weight = 31782.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.100638 restraints weight = 19405.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102406 restraints weight = 13262.238| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13037 Z= 0.171 Angle : 0.625 7.913 17588 Z= 0.306 Chirality : 0.044 0.154 2003 Planarity : 0.004 0.064 2165 Dihedral : 15.004 155.656 1938 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.04 % Allowed : 14.08 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.21), residues: 1554 helix: 0.39 (0.23), residues: 548 sheet: -0.36 (0.30), residues: 310 loop : -1.88 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 541 HIS 0.007 0.001 HIS B 465 PHE 0.016 0.002 PHE E 321 TYR 0.024 0.002 TYR A 547 ARG 0.008 0.001 ARG D 323 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 429) hydrogen bonds : angle 4.68089 ( 1224) covalent geometry : bond 0.00391 (13037) covalent geometry : angle 0.62521 (17588) *********************** 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 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8497 (tp) cc_final: 0.8111 (mt) REVERT: A 380 GLN cc_start: 0.8092 (mp10) cc_final: 0.7739 (mp10) REVERT: A 411 TYR cc_start: 0.6993 (t80) cc_final: 0.6413 (t80) REVERT: B 341 MET cc_start: 0.8779 (mmt) cc_final: 0.8444 (tpp) REVERT: B 441 MET cc_start: 0.6264 (ttt) cc_final: 0.5926 (ttt) REVERT: B 445 LEU cc_start: 0.8965 (tp) cc_final: 0.8698 (tp) REVERT: D 311 THR cc_start: 0.8854 (p) cc_final: 0.8440 (p) REVERT: D 316 MET cc_start: 0.8085 (mmp) cc_final: 0.7563 (mmp) REVERT: D 323 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7510 (mmp80) REVERT: D 352 ASP cc_start: 0.7031 (t0) cc_final: 0.6795 (t70) REVERT: D 470 ASP cc_start: 0.8967 (p0) cc_final: 0.8711 (p0) REVERT: D 537 LYS cc_start: 0.8213 (mmmt) cc_final: 0.8013 (mmtp) REVERT: E 306 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6722 (mt-10) REVERT: E 441 MET cc_start: 0.6882 (tmm) cc_final: 0.6635 (tmt) REVERT: E 495 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8982 (mp) REVERT: E 533 MET cc_start: 0.8218 (mpp) cc_final: 0.7880 (mpp) REVERT: F 298 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7247 (mmtp) REVERT: F 499 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (mm) outliers start: 41 outliers final: 31 residues processed: 205 average time/residue: 0.2384 time to fit residues: 72.2253 Evaluate side-chains 199 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 423 LEU Chi-restraints excluded: chain A residue 496 SER 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 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 412 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 468 ASN 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 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 456 THR Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 495 LEU 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 357 HIS Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 499 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 157 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN F 465 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.114657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095407 restraints weight = 31377.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096753 restraints weight = 19841.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098039 restraints weight = 14139.460| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13037 Z= 0.116 Angle : 0.574 7.912 17588 Z= 0.278 Chirality : 0.042 0.160 2003 Planarity : 0.003 0.065 2165 Dihedral : 14.742 157.848 1938 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.52 % Allowed : 14.68 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1554 helix: 0.63 (0.23), residues: 546 sheet: -0.32 (0.31), residues: 311 loop : -1.73 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 541 HIS 0.007 0.001 HIS B 465 PHE 0.013 0.001 PHE E 321 TYR 0.019 0.001 TYR A 547 ARG 0.005 0.000 ARG D 323 Details of bonding type rmsd hydrogen bonds : bond 0.02727 ( 429) hydrogen bonds : angle 4.50059 ( 1224) covalent geometry : bond 0.00262 (13037) covalent geometry : angle 0.57377 (17588) *********************** 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 213 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8428 (tp) cc_final: 0.8066 (mt) REVERT: A 380 GLN cc_start: 0.8545 (mp10) cc_final: 0.8246 (mp10) REVERT: A 411 TYR cc_start: 0.6954 (t80) cc_final: 0.6431 (t80) REVERT: A 533 MET cc_start: 0.7130 (mtp) cc_final: 0.6835 (ttm) REVERT: B 341 MET cc_start: 0.8716 (mmt) cc_final: 0.8391 (tpp) REVERT: B 441 MET cc_start: 0.6412 (ttt) cc_final: 0.6092 (ttt) REVERT: B 445 LEU cc_start: 0.8886 (tp) cc_final: 0.8646 (tp) REVERT: D 311 THR cc_start: 0.8940 (p) cc_final: 0.8552 (p) REVERT: D 323 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7408 (mmp80) REVERT: D 352 ASP cc_start: 0.6910 (t0) cc_final: 0.6659 (t70) REVERT: D 412 MET cc_start: 0.7321 (mtt) cc_final: 0.7072 (mtm) REVERT: D 470 ASP cc_start: 0.8957 (p0) cc_final: 0.8706 (p0) REVERT: E 306 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6583 (mt-10) REVERT: E 510 MET cc_start: 0.8518 (mmm) cc_final: 0.8057 (mpp) REVERT: F 298 LYS cc_start: 0.7460 (ttmm) cc_final: 0.7119 (mmtp) outliers start: 34 outliers final: 29 residues processed: 203 average time/residue: 0.2342 time to fit residues: 71.0721 Evaluate side-chains 194 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 458 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 542 LEU 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 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 412 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 449 LEU 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 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 310 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 73 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 91 optimal weight: 0.0020 chunk 148 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN F 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.115220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094659 restraints weight = 31491.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097180 restraints weight = 19374.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.098847 restraints weight = 13350.741| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13037 Z= 0.105 Angle : 0.569 9.250 17588 Z= 0.273 Chirality : 0.042 0.159 2003 Planarity : 0.003 0.070 2165 Dihedral : 14.539 159.564 1938 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.37 % Allowed : 15.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1554 helix: 0.79 (0.23), residues: 545 sheet: -0.26 (0.31), residues: 309 loop : -1.60 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 381 HIS 0.011 0.001 HIS B 465 PHE 0.013 0.001 PHE E 321 TYR 0.011 0.001 TYR D 532 ARG 0.004 0.000 ARG D 323 Details of bonding type rmsd hydrogen bonds : bond 0.02532 ( 429) hydrogen bonds : angle 4.38984 ( 1224) covalent geometry : bond 0.00241 (13037) covalent geometry : angle 0.56895 (17588) *********************** 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 206 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8527 (tp) cc_final: 0.8104 (mt) REVERT: A 380 GLN cc_start: 0.8570 (mp10) cc_final: 0.8263 (mp10) REVERT: A 411 TYR cc_start: 0.6777 (t80) cc_final: 0.6213 (t80) REVERT: A 438 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6612 (pp20) REVERT: A 510 MET cc_start: 0.6370 (mpp) cc_final: 0.5613 (mpp) REVERT: B 445 LEU cc_start: 0.8851 (tp) cc_final: 0.8622 (tp) REVERT: D 311 THR cc_start: 0.8903 (p) cc_final: 0.8514 (p) REVERT: D 323 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7361 (mmp80) REVERT: D 470 ASP cc_start: 0.8917 (p0) cc_final: 0.8655 (p0) REVERT: E 306 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6673 (mt-10) REVERT: E 510 MET cc_start: 0.8524 (mmm) cc_final: 0.8063 (mpp) REVERT: F 298 LYS cc_start: 0.7412 (ttmm) cc_final: 0.7048 (mmtp) outliers start: 32 outliers final: 23 residues processed: 196 average time/residue: 0.2350 time to fit residues: 68.3852 Evaluate side-chains 187 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 341 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 356 LEU 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 430 VAL Chi-restraints excluded: chain C residue 449 LEU 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 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 388 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 109 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 129 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS ** B 425 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 ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.115505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094865 restraints weight = 31477.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.097295 restraints weight = 19361.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.098978 restraints weight = 13491.547| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4823 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= 0.109 Angle : 0.581 8.853 17588 Z= 0.278 Chirality : 0.042 0.156 2003 Planarity : 0.003 0.072 2165 Dihedral : 14.416 161.937 1938 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.45 % Allowed : 16.23 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1554 helix: 0.90 (0.23), residues: 545 sheet: -0.25 (0.30), residues: 309 loop : -1.56 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 381 HIS 0.013 0.001 HIS B 425 PHE 0.012 0.001 PHE E 321 TYR 0.018 0.001 TYR D 547 ARG 0.004 0.000 ARG D 323 Details of bonding type rmsd hydrogen bonds : bond 0.02576 ( 429) hydrogen bonds : angle 4.34462 ( 1224) covalent geometry : bond 0.00250 (13037) covalent geometry : angle 0.58065 (17588) *********************** 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 202 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.7152 (tp40) cc_final: 0.6744 (tp40) REVERT: A 356 LEU cc_start: 0.8528 (tp) cc_final: 0.8107 (mt) REVERT: A 380 GLN cc_start: 0.8566 (mp10) cc_final: 0.8281 (mp10) REVERT: A 411 TYR cc_start: 0.6761 (t80) cc_final: 0.6181 (t80) REVERT: A 438 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6605 (pp20) REVERT: A 510 MET cc_start: 0.6336 (mpp) cc_final: 0.5590 (mpp) REVERT: B 445 LEU cc_start: 0.8873 (tp) cc_final: 0.8599 (tp) REVERT: D 311 THR cc_start: 0.8926 (p) cc_final: 0.8536 (p) REVERT: D 323 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7776 (ptp-110) REVERT: D 470 ASP cc_start: 0.8920 (p0) cc_final: 0.8687 (p0) REVERT: E 306 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6651 (mt-10) REVERT: E 510 MET cc_start: 0.8548 (mmm) cc_final: 0.8075 (mpp) REVERT: F 298 LYS cc_start: 0.7385 (ttmm) cc_final: 0.7027 (mmtp) REVERT: F 510 MET cc_start: 0.6459 (tpp) cc_final: 0.6196 (ptm) outliers start: 33 outliers final: 28 residues processed: 193 average time/residue: 0.2283 time to fit residues: 65.7319 Evaluate side-chains 195 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 341 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 429 VAL 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 430 VAL Chi-restraints excluded: chain C residue 449 LEU 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 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 322 VAL Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 118 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 0.0270 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.116370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096616 restraints weight = 31885.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099163 restraints weight = 19439.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.100840 restraints weight = 13328.192| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13037 Z= 0.194 Angle : 0.668 9.285 17588 Z= 0.324 Chirality : 0.045 0.153 2003 Planarity : 0.004 0.077 2165 Dihedral : 14.638 166.584 1938 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.37 % Allowed : 16.46 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1554 helix: 0.64 (0.23), residues: 552 sheet: -0.49 (0.30), residues: 316 loop : -1.65 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 381 HIS 0.012 0.001 HIS B 465 PHE 0.022 0.002 PHE E 321 TYR 0.023 0.002 TYR A 547 ARG 0.005 0.001 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 429) hydrogen bonds : angle 4.63196 ( 1224) covalent geometry : bond 0.00444 (13037) covalent geometry : angle 0.66793 (17588) *********************** 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 199 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6826 (tp40) cc_final: 0.6571 (mm-40) REVERT: A 333 MET cc_start: 0.8097 (mtt) cc_final: 0.7619 (mpp) REVERT: A 356 LEU cc_start: 0.8486 (tp) cc_final: 0.8129 (mt) REVERT: A 411 TYR cc_start: 0.6833 (t80) cc_final: 0.6197 (t80) REVERT: A 438 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6658 (pp20) REVERT: A 510 MET cc_start: 0.6455 (mpp) cc_final: 0.5682 (mpp) REVERT: B 445 LEU cc_start: 0.8949 (tp) cc_final: 0.8703 (tp) REVERT: B 477 GLU cc_start: 0.6920 (mp0) cc_final: 0.6511 (mp0) REVERT: D 311 THR cc_start: 0.9145 (p) cc_final: 0.8794 (p) REVERT: D 323 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7833 (ptp-110) REVERT: D 470 ASP cc_start: 0.8887 (p0) cc_final: 0.8671 (p0) REVERT: E 306 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6831 (mt-10) REVERT: F 298 LYS cc_start: 0.7658 (ttmm) cc_final: 0.7380 (mmtp) REVERT: F 454 LYS cc_start: 0.6763 (mmpt) cc_final: 0.6547 (mmpt) outliers start: 32 outliers final: 30 residues processed: 188 average time/residue: 0.2309 time to fit residues: 64.9477 Evaluate side-chains 190 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 341 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 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 471 LYS 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 292 CYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 449 LEU 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 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 310 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 141 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 132 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** F 364 GLN ** 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 = 0.3886 r_free = 0.3886 target = 0.113753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093245 restraints weight = 31489.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095653 restraints weight = 19333.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.097339 restraints weight = 13434.764| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5185 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= 0.134 Angle : 0.619 9.120 17588 Z= 0.299 Chirality : 0.043 0.151 2003 Planarity : 0.003 0.077 2165 Dihedral : 14.489 171.993 1938 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.22 % Allowed : 16.75 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1554 helix: 0.86 (0.23), residues: 543 sheet: -0.41 (0.31), residues: 304 loop : -1.56 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 381 HIS 0.006 0.001 HIS B 465 PHE 0.021 0.001 PHE E 321 TYR 0.013 0.001 TYR D 547 ARG 0.005 0.000 ARG D 323 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 429) hydrogen bonds : angle 4.48628 ( 1224) covalent geometry : bond 0.00310 (13037) covalent geometry : angle 0.61914 (17588) ********************** 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 188 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6821 (tp40) cc_final: 0.6531 (mm-40) REVERT: A 333 MET cc_start: 0.8167 (mtt) cc_final: 0.7704 (mpp) REVERT: A 356 LEU cc_start: 0.8556 (tp) cc_final: 0.8157 (mt) REVERT: A 438 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6761 (pp20) REVERT: A 510 MET cc_start: 0.6542 (mpp) cc_final: 0.5840 (mpp) REVERT: B 445 LEU cc_start: 0.8892 (tp) cc_final: 0.8625 (tp) REVERT: B 477 GLU cc_start: 0.6922 (mp0) cc_final: 0.6601 (mp0) REVERT: D 311 THR cc_start: 0.9090 (p) cc_final: 0.8720 (p) REVERT: D 323 ARG cc_start: 0.8238 (mtm110) cc_final: 0.7971 (ptp-110) REVERT: D 470 ASP cc_start: 0.9004 (p0) cc_final: 0.8783 (p0) REVERT: E 306 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6786 (mt-10) REVERT: E 510 MET cc_start: 0.8574 (mmm) cc_final: 0.8279 (mpp) REVERT: F 344 GLU cc_start: 0.7772 (mp0) cc_final: 0.7467 (mp0) outliers start: 30 outliers final: 27 residues processed: 180 average time/residue: 0.2228 time to fit residues: 60.4057 Evaluate side-chains 183 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 341 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 356 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 430 VAL Chi-restraints excluded: chain C residue 449 LEU 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 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 322 VAL Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.113131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092984 restraints weight = 31325.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095325 restraints weight = 19103.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096989 restraints weight = 13272.158| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13037 Z= 0.143 Angle : 0.623 9.037 17588 Z= 0.301 Chirality : 0.043 0.150 2003 Planarity : 0.003 0.080 2165 Dihedral : 14.385 177.429 1938 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.08 % Allowed : 17.35 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1554 helix: 0.78 (0.23), residues: 550 sheet: -0.46 (0.31), residues: 304 loop : -1.55 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 381 HIS 0.007 0.001 HIS B 465 PHE 0.021 0.001 PHE E 321 TYR 0.024 0.001 TYR A 547 ARG 0.004 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 429) hydrogen bonds : angle 4.48171 ( 1224) covalent geometry : bond 0.00331 (13037) covalent geometry : angle 0.62275 (17588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4004.37 seconds wall clock time: 71 minutes 38.96 seconds (4298.96 seconds total)