Starting phenix.real_space_refine on Thu Sep 26 10:49:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/09_2024/6n7n_0359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/09_2024/6n7n_0359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/09_2024/6n7n_0359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/09_2024/6n7n_0359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/09_2024/6n7n_0359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/09_2024/6n7n_0359.cif" } resolution = 3.5 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 5 5.21 5 S 78 5.16 5 C 7962 2.51 5 N 2257 2.21 5 O 2522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12854 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: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1984 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 252} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 8.06, per 1000 atoms: 0.63 Number of scatterers: 12854 At special positions: 0 Unit cell: (80.25, 127.33, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 30 15.00 Mg 5 11.99 O 2522 8.00 N 2257 7.00 C 7962 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: 3.08 Conformation dependent library (CDL) restraints added in 1.7 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 7 sheets defined 37.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 273 through 280 removed outlier: 4.008A pdb=" N SER A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.160A pdb=" N ASN A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.666A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.689A 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: 3.947A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 375' Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.831A pdb=" N ASP A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.537A pdb=" N TYR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.104A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.769A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 4.257A 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 269 through 272 removed outlier: 3.786A pdb=" N ARG B 272 " --> pdb=" O LEU B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.574A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 4.319A pdb=" N ASN B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 297' Processing helix chain 'B' and resid 317 through 332 Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.682A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.677A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.532A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.966A pdb=" N VAL B 430 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.759A pdb=" N ASP B 485 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 486 " --> pdb=" O ILE B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 486' Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.666A pdb=" N ILE C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 300 removed outlier: 4.426A pdb=" N ASN C 296 " --> pdb=" O CYS C 292 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 removed outlier: 3.769A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 removed outlier: 3.697A pdb=" N THR C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.748A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 4.138A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 416 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 437 through 457 removed outlier: 4.072A pdb=" N MET C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.830A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 318 through 329 removed outlier: 3.648A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.696A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.660A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 4.032A 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: 3.557A pdb=" N GLU D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.509A pdb=" N ASP D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 440 through 457 removed outlier: 3.621A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.563A pdb=" N GLU D 477 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 317 through 329 removed outlier: 3.732A pdb=" N PHE E 321 " --> pdb=" O GLY E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.651A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.615A pdb=" N LYS E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 387 removed outlier: 3.970A 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: 3.968A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.610A pdb=" N GLU E 477 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 495 removed outlier: 3.512A pdb=" N GLN E 494 " --> pdb=" O GLY E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 317 through 329 Processing helix chain 'F' and resid 347 through 358 removed outlier: 3.632A pdb=" N LEU F 353 " --> pdb=" O THR F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 372 removed outlier: 3.975A pdb=" N ARG F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 387 removed outlier: 3.677A pdb=" N GLU F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) removed outlier: 4.170A 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 441 through 457 removed outlier: 3.619A pdb=" N LEU F 445 " --> pdb=" O MET F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 478 removed outlier: 3.778A pdb=" N GLY F 478 " --> pdb=" O HIS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 494 removed outlier: 3.894A 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: 3.508A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 307 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE B 500 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 309 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU B 502 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B 311 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.059A 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: 7.121A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A 308 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 338 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.754A pdb=" N LEU C 393 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 394 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE C 308 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 516 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.564A 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: 6.748A pdb=" N GLY D 338 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 421 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE D 463 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU D 423 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N CYS D 464 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL D 310 " --> pdb=" O CYS D 464 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 265 through 267 removed outlier: 3.588A pdb=" N VAL D 266 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 265 through 267 removed outlier: 3.737A pdb=" N VAL E 266 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL F 337 " --> pdb=" O HIS F 392 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N TYR F 394 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE F 421 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL F 310 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR F 498 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.531A pdb=" N ILE E 421 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE E 308 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET E 309 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N LEU E 502 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR E 311 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1188 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: 3.52 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: 2150 1.31 - 1.44: 3220 1.44 - 1.57: 7473 1.57 - 1.70: 54 1.70 - 1.83: 132 Bond restraints: 13029 Sorted by residual: bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C6 TTP F 700 " pdb=" N1 TTP F 700 " ideal model delta sigma weight residual 1.337 1.426 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.425 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.420 -0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 13024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 17194 2.64 - 5.28: 297 5.28 - 7.92: 60 7.92 - 10.56: 17 10.56 - 13.20: 6 Bond angle restraints: 17574 Sorted by residual: angle pdb=" N ILE E 442 " pdb=" CA ILE E 442 " pdb=" C ILE E 442 " ideal model delta sigma weight residual 111.81 107.50 4.31 8.60e-01 1.35e+00 2.51e+01 angle pdb=" O3' DT T 5 " pdb=" C3' DT T 5 " pdb=" C2' DT T 5 " ideal model delta sigma weight residual 111.50 118.65 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" PA TTP D 700 " pdb=" O3A TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sigma weight residual 120.50 133.70 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" PB TTP C 700 " pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 120.50 132.63 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" PA TTP C 700 " pdb=" O3A TTP C 700 " pdb=" PB TTP C 700 " ideal model delta sigma weight residual 120.50 132.60 -12.10 3.00e+00 1.11e-01 1.63e+01 ... (remaining 17569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 7631 35.60 - 71.20: 127 71.20 - 106.80: 11 106.80 - 142.40: 5 142.40 - 178.00: 7 Dihedral angle restraints: 7781 sinusoidal: 3305 harmonic: 4476 Sorted by residual: dihedral pdb=" O2G TTP F 700 " pdb=" O3B TTP F 700 " pdb=" PG TTP F 700 " pdb=" PB TTP F 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.00 -178.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G TTP D 700 " pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.43 -177.57 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 700 " pdb=" C1' TTP B 700 " pdb=" N1 TTP B 700 " pdb=" O4' TTP B 700 " ideal model delta sinusoidal sigma weight residual -58.32 114.32 -172.64 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 7778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1560 0.064 - 0.128: 377 0.128 - 0.193: 55 0.193 - 0.257: 7 0.257 - 0.321: 3 Chirality restraints: 2002 Sorted by residual: chirality pdb=" C3' DT T 5 " pdb=" C4' DT T 5 " pdb=" O3' DT T 5 " pdb=" C2' DT T 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C4' TTP B 700 " pdb=" C3' TTP B 700 " pdb=" C5' TTP B 700 " pdb=" O4' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' TTP F 700 " pdb=" C2' TTP F 700 " pdb=" C4' TTP F 700 " pdb=" O3' TTP F 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1999 not shown) Planarity restraints: 2166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 358 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ASN B 358 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN B 358 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG B 359 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 342 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C LEU C 342 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU C 342 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN C 343 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO D 511 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.027 5.00e-02 4.00e+02 ... (remaining 2163 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 62 2.56 - 3.15: 9191 3.15 - 3.73: 18570 3.73 - 4.32: 26525 4.32 - 4.90: 44708 Nonbonded interactions: 99056 Sorted by model distance: nonbonded pdb=" OE1 GLN D 343 " pdb="MG MG D 701 " model vdw 1.975 2.170 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 1.985 2.170 nonbonded pdb=" NE2 GLN B 343 " pdb="MG MG B 701 " model vdw 2.041 2.250 nonbonded pdb=" O2B TTP F 700 " pdb="MG MG F 701 " model vdw 2.054 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.116 2.170 ... (remaining 99051 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 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or (resid 440 and (name N or name CA or name C or name O or name CB )) o \ r resid 441 through 506 or resid 510 through 545)) selection = (chain 'B' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or (resid 440 and (name N or name CA or name C \ or name O or name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 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 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 440 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 264 through 429 or resid 440 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: 0.760 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.340 Find NCS groups from input model: 0.630 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 13029 Z= 0.371 Angle : 0.987 13.201 17574 Z= 0.519 Chirality : 0.057 0.321 2002 Planarity : 0.004 0.048 2166 Dihedral : 14.773 177.997 4915 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.74 % Allowed : 3.48 % Favored : 95.78 % 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: -3.49 (0.18), residues: 1556 helix: -2.73 (0.17), residues: 521 sheet: -0.65 (0.30), residues: 318 loop : -2.75 (0.19), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 541 HIS 0.008 0.002 HIS A 357 PHE 0.016 0.002 PHE D 386 TYR 0.013 0.002 TYR A 535 ARG 0.006 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 329 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 368 LEU cc_start: 0.7895 (tt) cc_final: 0.7687 (tt) REVERT: D 504 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6289 (ptm-80) REVERT: F 309 MET cc_start: 0.7792 (mmm) cc_final: 0.7273 (mmt) outliers start: 10 outliers final: 1 residues processed: 338 average time/residue: 0.2903 time to fit residues: 133.5456 Evaluate side-chains 177 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D 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: 6.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** A 512 ASN B 357 HIS C 325 GLN C 380 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 475 HIS D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN E 425 HIS E 507 GLN F 325 GLN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13029 Z= 0.180 Angle : 0.584 7.117 17574 Z= 0.290 Chirality : 0.043 0.146 2002 Planarity : 0.003 0.037 2166 Dihedral : 16.134 179.777 1934 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.37 % Allowed : 9.84 % Favored : 87.79 % 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: -2.21 (0.20), residues: 1556 helix: -1.01 (0.21), residues: 514 sheet: -0.43 (0.30), residues: 322 loop : -2.30 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 381 HIS 0.007 0.001 HIS E 278 PHE 0.020 0.001 PHE B 321 TYR 0.017 0.001 TYR A 547 ARG 0.006 0.001 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ARG cc_start: 0.6525 (ttp80) cc_final: 0.5357 (ttt-90) REVERT: A 542 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7507 (pp) REVERT: C 438 GLU cc_start: 0.6032 (tt0) cc_final: 0.5676 (pm20) REVERT: D 441 MET cc_start: 0.6896 (mmt) cc_final: 0.6643 (mmm) REVERT: D 482 SER cc_start: 0.7392 (m) cc_final: 0.7091 (p) REVERT: E 499 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6650 (mt) REVERT: E 503 GLU cc_start: 0.6269 (mp0) cc_final: 0.5515 (mp0) REVERT: E 517 ARG cc_start: 0.7207 (ttm-80) cc_final: 0.6977 (ttm-80) outliers start: 32 outliers final: 18 residues processed: 223 average time/residue: 0.2358 time to fit residues: 76.7461 Evaluate side-chains 183 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 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** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13029 Z= 0.306 Angle : 0.694 8.669 17574 Z= 0.344 Chirality : 0.047 0.162 2002 Planarity : 0.004 0.036 2166 Dihedral : 16.377 177.765 1929 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.55 % Allowed : 12.07 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.05 (0.20), residues: 1556 helix: -0.73 (0.22), residues: 532 sheet: -0.51 (0.30), residues: 314 loop : -2.24 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 541 HIS 0.009 0.001 HIS B 392 PHE 0.030 0.002 PHE C 321 TYR 0.016 0.002 TYR A 547 ARG 0.006 0.001 ARG E 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3843 (ptmt) cc_final: 0.3230 (ttmt) REVERT: A 487 ARG cc_start: 0.6757 (ttp80) cc_final: 0.5504 (ttt-90) REVERT: A 542 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7568 (pp) REVERT: D 441 MET cc_start: 0.6931 (mmt) cc_final: 0.6590 (mmm) REVERT: E 499 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6868 (mt) REVERT: F 379 ASP cc_start: 0.5482 (OUTLIER) cc_final: 0.4977 (m-30) outliers start: 48 outliers final: 28 residues processed: 192 average time/residue: 0.2212 time to fit residues: 63.8101 Evaluate side-chains 173 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.0470 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 0.0970 chunk 153 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 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** E 506 GLN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13029 Z= 0.136 Angle : 0.524 6.864 17574 Z= 0.262 Chirality : 0.042 0.147 2002 Planarity : 0.002 0.028 2166 Dihedral : 15.414 174.586 1929 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.37 % Allowed : 13.69 % Favored : 83.94 % 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: -1.41 (0.21), residues: 1556 helix: 0.01 (0.23), residues: 531 sheet: -0.31 (0.30), residues: 332 loop : -2.01 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 541 HIS 0.004 0.001 HIS C 425 PHE 0.021 0.001 PHE C 321 TYR 0.014 0.001 TYR A 547 ARG 0.003 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7782 (mmt) cc_final: 0.7471 (mmp) REVERT: A 473 LYS cc_start: 0.3813 (ptmt) cc_final: 0.3223 (ttmt) REVERT: A 487 ARG cc_start: 0.6820 (ttp80) cc_final: 0.5451 (ttt-90) REVERT: A 542 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7397 (pp) REVERT: D 441 MET cc_start: 0.6789 (mmt) cc_final: 0.6487 (mmm) REVERT: E 503 GLU cc_start: 0.6205 (mp0) cc_final: 0.5472 (mp0) outliers start: 32 outliers final: 16 residues processed: 181 average time/residue: 0.2255 time to fit residues: 60.7951 Evaluate side-chains 158 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.0050 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 506 GLN E 358 ASN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13029 Z= 0.150 Angle : 0.521 6.787 17574 Z= 0.258 Chirality : 0.042 0.146 2002 Planarity : 0.002 0.020 2166 Dihedral : 15.108 170.792 1929 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.66 % Allowed : 13.77 % Favored : 83.57 % 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: -1.06 (0.22), residues: 1556 helix: 0.31 (0.24), residues: 527 sheet: -0.05 (0.31), residues: 313 loop : -1.80 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 329 HIS 0.004 0.001 HIS C 425 PHE 0.020 0.001 PHE C 321 TYR 0.012 0.001 TYR A 547 ARG 0.003 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7751 (mmt) cc_final: 0.7462 (mmp) REVERT: A 473 LYS cc_start: 0.3926 (ptmt) cc_final: 0.3156 (ttmt) REVERT: A 487 ARG cc_start: 0.6893 (ttp80) cc_final: 0.5579 (ttt-90) REVERT: A 542 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7365 (pp) REVERT: D 288 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6505 (mt) REVERT: E 503 GLU cc_start: 0.6312 (mp0) cc_final: 0.5626 (mp0) REVERT: F 379 ASP cc_start: 0.5210 (OUTLIER) cc_final: 0.4845 (m-30) outliers start: 36 outliers final: 23 residues processed: 173 average time/residue: 0.2167 time to fit residues: 56.9447 Evaluate side-chains 168 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 148 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13029 Z= 0.178 Angle : 0.540 7.732 17574 Z= 0.268 Chirality : 0.043 0.145 2002 Planarity : 0.002 0.022 2166 Dihedral : 14.830 169.020 1929 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.44 % Allowed : 14.21 % Favored : 83.35 % 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: -1.02 (0.22), residues: 1556 helix: 0.38 (0.23), residues: 531 sheet: -0.02 (0.31), residues: 316 loop : -1.82 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 329 HIS 0.004 0.001 HIS B 392 PHE 0.019 0.001 PHE C 321 TYR 0.012 0.001 TYR A 547 ARG 0.002 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7761 (mmt) cc_final: 0.7398 (mmp) REVERT: A 473 LYS cc_start: 0.3951 (ptmt) cc_final: 0.3220 (ttmt) REVERT: A 542 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7271 (pp) REVERT: C 441 MET cc_start: 0.6677 (tpp) cc_final: 0.6464 (tpp) REVERT: E 499 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6722 (mt) REVERT: E 503 GLU cc_start: 0.6391 (mp0) cc_final: 0.5695 (mp0) outliers start: 33 outliers final: 27 residues processed: 166 average time/residue: 0.2073 time to fit residues: 52.9896 Evaluate side-chains 166 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 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** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13029 Z= 0.179 Angle : 0.533 7.079 17574 Z= 0.265 Chirality : 0.043 0.142 2002 Planarity : 0.002 0.026 2166 Dihedral : 14.666 163.326 1929 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.75 % 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: -0.96 (0.22), residues: 1556 helix: 0.44 (0.23), residues: 534 sheet: -0.02 (0.31), residues: 314 loop : -1.79 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 329 HIS 0.004 0.001 HIS B 392 PHE 0.017 0.001 PHE C 321 TYR 0.011 0.001 TYR A 547 ARG 0.003 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7759 (mmt) cc_final: 0.7435 (mmp) REVERT: A 473 LYS cc_start: 0.3931 (ptmt) cc_final: 0.3196 (ttmt) REVERT: A 542 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7189 (pp) REVERT: C 370 ARG cc_start: 0.6868 (mtm180) cc_final: 0.6340 (tpm170) REVERT: E 499 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6754 (mt) REVERT: E 503 GLU cc_start: 0.6481 (mp0) cc_final: 0.5719 (mp0) outliers start: 35 outliers final: 26 residues processed: 166 average time/residue: 0.2230 time to fit residues: 57.3032 Evaluate side-chains 164 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 104 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13029 Z= 0.136 Angle : 0.508 9.092 17574 Z= 0.251 Chirality : 0.042 0.146 2002 Planarity : 0.002 0.038 2166 Dihedral : 14.239 150.023 1929 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.59 % Allowed : 15.03 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.22), residues: 1556 helix: 0.68 (0.24), residues: 531 sheet: 0.18 (0.31), residues: 314 loop : -1.73 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 381 HIS 0.003 0.001 HIS B 392 PHE 0.016 0.001 PHE C 321 TYR 0.011 0.001 TYR A 547 ARG 0.002 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7668 (mmt) cc_final: 0.7312 (mmp) REVERT: A 473 LYS cc_start: 0.4059 (ptmt) cc_final: 0.3377 (ttmt) REVERT: B 316 MET cc_start: 0.7115 (mmt) cc_final: 0.6809 (mmt) REVERT: C 370 ARG cc_start: 0.6853 (mtm180) cc_final: 0.6266 (tpm170) REVERT: D 288 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6466 (mt) REVERT: E 499 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6682 (mt) REVERT: E 503 GLU cc_start: 0.6296 (mp0) cc_final: 0.5699 (mp0) outliers start: 35 outliers final: 24 residues processed: 169 average time/residue: 0.2135 time to fit residues: 54.7159 Evaluate side-chains 166 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 5.9990 chunk 142 optimal weight: 0.2980 chunk 146 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 0.0050 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 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** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13029 Z= 0.231 Angle : 0.588 9.414 17574 Z= 0.290 Chirality : 0.044 0.144 2002 Planarity : 0.003 0.044 2166 Dihedral : 14.479 148.593 1929 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.37 % Allowed : 15.62 % Favored : 82.01 % 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: -0.98 (0.22), residues: 1556 helix: 0.41 (0.23), residues: 528 sheet: 0.01 (0.31), residues: 313 loop : -1.80 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 329 HIS 0.006 0.001 HIS B 392 PHE 0.026 0.002 PHE C 321 TYR 0.011 0.001 TYR A 547 ARG 0.004 0.000 ARG E 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.575 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7758 (mmt) cc_final: 0.7479 (mmp) REVERT: A 473 LYS cc_start: 0.3644 (ptmt) cc_final: 0.3009 (ttmt) REVERT: A 533 MET cc_start: 0.3346 (mtm) cc_final: 0.3015 (ttp) REVERT: C 370 ARG cc_start: 0.6936 (mtm180) cc_final: 0.6307 (tpm170) REVERT: D 341 MET cc_start: 0.8012 (mmm) cc_final: 0.7805 (mmm) REVERT: E 499 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6818 (mt) outliers start: 32 outliers final: 25 residues processed: 169 average time/residue: 0.2189 time to fit residues: 56.0095 Evaluate side-chains 166 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13029 Z= 0.372 Angle : 0.729 9.450 17574 Z= 0.361 Chirality : 0.048 0.165 2002 Planarity : 0.004 0.046 2166 Dihedral : 15.076 152.881 1929 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.44 % Allowed : 15.99 % Favored : 81.57 % 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: -1.65 (0.21), residues: 1556 helix: -0.30 (0.22), residues: 531 sheet: -0.50 (0.30), residues: 315 loop : -1.98 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 541 HIS 0.010 0.002 HIS B 392 PHE 0.029 0.002 PHE C 321 TYR 0.014 0.002 TYR C 394 ARG 0.005 0.001 ARG B 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: C 370 ARG cc_start: 0.7023 (mtm180) cc_final: 0.6427 (tpp-160) REVERT: E 285 VAL cc_start: 0.7417 (t) cc_final: 0.7209 (m) REVERT: E 499 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.7049 (mt) outliers start: 33 outliers final: 28 residues processed: 166 average time/residue: 0.2214 time to fit residues: 55.4350 Evaluate side-chains 164 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.159639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.143652 restraints weight = 19926.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.145722 restraints weight = 13023.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.147174 restraints weight = 9426.542| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13029 Z= 0.168 Angle : 0.559 7.671 17574 Z= 0.279 Chirality : 0.043 0.142 2002 Planarity : 0.003 0.094 2166 Dihedral : 14.503 146.826 1929 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.07 % Allowed : 16.51 % Favored : 81.42 % 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: -1.13 (0.21), residues: 1556 helix: 0.29 (0.23), residues: 530 sheet: -0.19 (0.31), residues: 311 loop : -1.82 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 381 HIS 0.003 0.001 HIS B 392 PHE 0.029 0.002 PHE B 523 TYR 0.010 0.001 TYR A 547 ARG 0.008 0.000 ARG F 522 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.63 seconds wall clock time: 43 minutes 36.89 seconds (2616.89 seconds total)