Starting phenix.real_space_refine on Thu Feb 13 00:22:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwj_35768/02_2025/8iwj_35768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwj_35768/02_2025/8iwj_35768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwj_35768/02_2025/8iwj_35768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwj_35768/02_2025/8iwj_35768.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwj_35768/02_2025/8iwj_35768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwj_35768/02_2025/8iwj_35768.cif" } resolution = 3.0 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= 0.013 sd= 0.141 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5524 2.51 5 N 1416 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8484 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4242 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 527} Chain breaks: 4 Restraints were copied for chains: B Time building chain proxies: 7.53, per 1000 atoms: 0.89 Number of scatterers: 8484 At special positions: 0 Unit cell: (111.1, 69.3, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1492 8.00 N 1416 7.00 C 5524 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: 1.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 57.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.579A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.762A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.679A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.732A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.813A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.643A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.615A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.652A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.722A pdb=" N VAL A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.516A pdb=" N LYS A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 397 removed outlier: 4.210A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.516A pdb=" N ARG A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.512A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 454 removed outlier: 3.615A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.764A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.683A pdb=" N GLN A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 462' Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.552A pdb=" N ALA A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.617A pdb=" N MET A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.505A pdb=" N LEU A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 542 removed outlier: 3.549A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.687A pdb=" N VAL A 579 " --> pdb=" O MET A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.878A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.944A pdb=" N GLY A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 658 removed outlier: 3.722A pdb=" N VAL A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.579A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.762A pdb=" N LYS B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.679A pdb=" N LEU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.732A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.813A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.643A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.616A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.652A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.722A pdb=" N VAL B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.517A pdb=" N LYS B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 397 removed outlier: 4.211A pdb=" N TRP B 386 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 395 " --> pdb=" O CYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 removed outlier: 3.516A pdb=" N ARG B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.513A pdb=" N PHE B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 454 removed outlier: 3.615A pdb=" N ARG B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.764A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.682A pdb=" N GLN B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 462' Processing helix chain 'B' and resid 463 through 472 removed outlier: 3.552A pdb=" N ALA B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 removed outlier: 3.617A pdb=" N MET B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.505A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 542 removed outlier: 3.548A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.686A pdb=" N VAL B 579 " --> pdb=" O MET B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.879A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 588 " --> pdb=" O TYR B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.944A pdb=" N GLY B 631 " --> pdb=" O GLU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 658 removed outlier: 3.722A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 5.443A pdb=" N VAL A 45 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 84 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.415A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 47 removed outlier: 5.443A pdb=" N VAL B 45 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 84 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.415A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 978 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: 2.11 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2613 1.34 - 1.46: 1750 1.46 - 1.58: 4213 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 8660 Sorted by residual: bond pdb=" CB PRO A 451 " pdb=" CG PRO A 451 " ideal model delta sigma weight residual 1.492 1.402 0.090 5.00e-02 4.00e+02 3.24e+00 bond pdb=" CB PRO B 451 " pdb=" CG PRO B 451 " ideal model delta sigma weight residual 1.492 1.402 0.090 5.00e-02 4.00e+02 3.22e+00 bond pdb=" CG LEU B 509 " pdb=" CD2 LEU B 509 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.19e+00 bond pdb=" CG LEU A 509 " pdb=" CD2 LEU A 509 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.14e+00 bond pdb=" CB VAL A 185 " pdb=" CG1 VAL A 185 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.04e+00 ... (remaining 8655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11360 2.63 - 5.27: 330 5.27 - 7.90: 38 7.90 - 10.53: 10 10.53 - 13.17: 2 Bond angle restraints: 11740 Sorted by residual: angle pdb=" N VAL B 185 " pdb=" CA VAL B 185 " pdb=" C VAL B 185 " ideal model delta sigma weight residual 112.96 107.28 5.68 1.00e+00 1.00e+00 3.23e+01 angle pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" C VAL A 185 " ideal model delta sigma weight residual 112.96 107.30 5.66 1.00e+00 1.00e+00 3.21e+01 angle pdb=" N SER A 571 " pdb=" CA SER A 571 " pdb=" C SER A 571 " ideal model delta sigma weight residual 110.80 119.38 -8.58 2.13e+00 2.20e-01 1.62e+01 angle pdb=" N SER B 571 " pdb=" CA SER B 571 " pdb=" C SER B 571 " ideal model delta sigma weight residual 110.80 119.36 -8.56 2.13e+00 2.20e-01 1.61e+01 angle pdb=" CB ARG B 436 " pdb=" CG ARG B 436 " pdb=" CD ARG B 436 " ideal model delta sigma weight residual 111.30 120.24 -8.94 2.30e+00 1.89e-01 1.51e+01 ... (remaining 11735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 4828 15.02 - 30.03: 211 30.03 - 45.05: 39 45.05 - 60.06: 6 60.06 - 75.08: 6 Dihedral angle restraints: 5090 sinusoidal: 1968 harmonic: 3122 Sorted by residual: dihedral pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" N LYS A 178 " pdb=" CA LYS A 178 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL B 177 " pdb=" C VAL B 177 " pdb=" N LYS B 178 " pdb=" CA LYS B 178 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA PRO A 570 " pdb=" C PRO A 570 " pdb=" N SER A 571 " pdb=" CA SER A 571 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 5087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 932 0.057 - 0.115: 388 0.115 - 0.172: 62 0.172 - 0.229: 13 0.229 - 0.286: 5 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB VAL B 177 " pdb=" CA VAL B 177 " pdb=" CG1 VAL B 177 " pdb=" CG2 VAL B 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE B 630 " pdb=" CA ILE B 630 " pdb=" CG1 ILE B 630 " pdb=" CG2 ILE B 630 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1397 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 450 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 451 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 450 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 451 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 350 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 351 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.030 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2932 2.87 - 3.38: 7205 3.38 - 3.89: 12546 3.89 - 4.39: 15065 4.39 - 4.90: 26518 Nonbonded interactions: 64266 Sorted by model distance: nonbonded pdb=" O TYR B 298 " pdb=" OG SER B 301 " model vdw 2.363 3.040 nonbonded pdb=" O TYR A 298 " pdb=" OG SER A 301 " model vdw 2.364 3.040 nonbonded pdb=" OG SER A 452 " pdb=" O SER A 530 " model vdw 2.424 3.040 nonbonded pdb=" N GLY A 572 " pdb=" N MET A 573 " model vdw 2.424 2.560 nonbonded pdb=" OG SER B 452 " pdb=" O SER B 530 " model vdw 2.424 3.040 ... (remaining 64261 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.010 0.090 8660 Z= 0.659 Angle : 1.062 13.167 11740 Z= 0.560 Chirality : 0.062 0.286 1400 Planarity : 0.007 0.060 1440 Dihedral : 9.688 75.080 3086 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.84 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -6.16 (0.16), residues: 1072 helix: -4.85 (0.06), residues: 588 sheet: -1.12 (0.62), residues: 62 loop : -3.10 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP B 447 HIS 0.013 0.003 HIS A 219 PHE 0.027 0.004 PHE B 163 TYR 0.023 0.003 TYR A 526 ARG 0.017 0.001 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.853 Fit side-chains REVERT: A 224 ASN cc_start: 0.8933 (t0) cc_final: 0.8724 (t0) REVERT: A 474 MET cc_start: 0.8472 (mtp) cc_final: 0.8095 (mtm) REVERT: A 565 TYR cc_start: 0.8624 (m-80) cc_final: 0.8359 (m-80) REVERT: B 224 ASN cc_start: 0.8886 (t0) cc_final: 0.8621 (t0) REVERT: B 565 TYR cc_start: 0.8642 (m-80) cc_final: 0.8331 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 1.3067 time to fit residues: 151.4993 Evaluate side-chains 81 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 389 GLN A 531 GLN B 130 ASN B 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112074 restraints weight = 9712.599| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.94 r_work: 0.3040 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8660 Z= 0.178 Angle : 0.605 6.770 11740 Z= 0.315 Chirality : 0.042 0.145 1400 Planarity : 0.005 0.041 1440 Dihedral : 5.485 46.781 1180 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.86 % Allowed : 6.37 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.23 (0.21), residues: 1072 helix: -2.77 (0.16), residues: 600 sheet: -0.71 (0.64), residues: 62 loop : -3.00 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 447 HIS 0.004 0.001 HIS B 219 PHE 0.019 0.002 PHE A 502 TYR 0.012 0.001 TYR A 586 ARG 0.009 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.898 Fit side-chains REVERT: A 224 ASN cc_start: 0.9028 (t0) cc_final: 0.8745 (t0) REVERT: A 565 TYR cc_start: 0.8861 (m-80) cc_final: 0.8620 (m-80) REVERT: B 224 ASN cc_start: 0.9009 (t0) cc_final: 0.8687 (t0) REVERT: B 565 TYR cc_start: 0.8863 (m-80) cc_final: 0.8585 (m-80) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 1.0679 time to fit residues: 103.5648 Evaluate side-chains 75 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113800 restraints weight = 9631.230| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.90 r_work: 0.3170 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8660 Z= 0.348 Angle : 0.706 10.801 11740 Z= 0.352 Chirality : 0.046 0.142 1400 Planarity : 0.005 0.065 1440 Dihedral : 5.488 45.109 1180 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.40 % Allowed : 7.88 % Favored : 90.71 % 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: -3.21 (0.23), residues: 1072 helix: -1.76 (0.19), residues: 600 sheet: -0.34 (0.65), residues: 62 loop : -2.86 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 426 HIS 0.006 0.002 HIS B 219 PHE 0.018 0.002 PHE A 96 TYR 0.015 0.002 TYR B 586 ARG 0.005 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.913 Fit side-chains REVERT: A 224 ASN cc_start: 0.8985 (t0) cc_final: 0.8657 (t0) REVERT: A 565 TYR cc_start: 0.8957 (m-80) cc_final: 0.8693 (m-80) REVERT: B 90 MET cc_start: 0.9130 (ptm) cc_final: 0.8897 (ppp) REVERT: B 224 ASN cc_start: 0.8973 (t0) cc_final: 0.8662 (t0) REVERT: B 565 TYR cc_start: 0.8949 (m-80) cc_final: 0.8706 (m-80) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 1.1314 time to fit residues: 99.8383 Evaluate side-chains 82 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 389 GLN B 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118050 restraints weight = 9678.653| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.92 r_work: 0.2928 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 8660 Z= 0.125 Angle : 0.527 7.780 11740 Z= 0.264 Chirality : 0.039 0.137 1400 Planarity : 0.003 0.044 1440 Dihedral : 4.880 40.170 1180 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.62 % Allowed : 7.78 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.36 (0.24), residues: 1072 helix: -0.97 (0.21), residues: 598 sheet: -0.02 (0.66), residues: 62 loop : -2.65 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 426 HIS 0.003 0.001 HIS B 219 PHE 0.014 0.001 PHE A 502 TYR 0.006 0.001 TYR B 586 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.932 Fit side-chains REVERT: A 224 ASN cc_start: 0.9036 (t0) cc_final: 0.8786 (t0) REVERT: A 565 TYR cc_start: 0.8998 (m-80) cc_final: 0.8758 (m-80) REVERT: B 224 ASN cc_start: 0.9016 (t0) cc_final: 0.8759 (t0) REVERT: B 565 TYR cc_start: 0.8996 (m-80) cc_final: 0.8760 (m-80) outliers start: 15 outliers final: 10 residues processed: 94 average time/residue: 0.9763 time to fit residues: 99.6124 Evaluate side-chains 92 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100609 restraints weight = 9985.621| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.05 r_work: 0.2824 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8660 Z= 0.414 Angle : 0.724 11.110 11740 Z= 0.359 Chirality : 0.047 0.155 1400 Planarity : 0.006 0.075 1440 Dihedral : 5.398 44.107 1180 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.27 % Allowed : 7.56 % Favored : 90.17 % 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: -2.42 (0.24), residues: 1072 helix: -1.08 (0.20), residues: 604 sheet: 0.16 (0.66), residues: 62 loop : -2.62 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 426 HIS 0.007 0.001 HIS B 219 PHE 0.019 0.002 PHE A 502 TYR 0.014 0.002 TYR B 586 ARG 0.004 0.001 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.917 Fit side-chains REVERT: A 90 MET cc_start: 0.9170 (ptm) cc_final: 0.8830 (ppp) REVERT: A 224 ASN cc_start: 0.9006 (t0) cc_final: 0.8690 (t0) REVERT: A 565 TYR cc_start: 0.9036 (m-80) cc_final: 0.8820 (m-80) REVERT: B 224 ASN cc_start: 0.9010 (t0) cc_final: 0.8688 (t0) REVERT: B 565 TYR cc_start: 0.9034 (m-80) cc_final: 0.8821 (m-80) outliers start: 21 outliers final: 16 residues processed: 95 average time/residue: 1.1136 time to fit residues: 113.7315 Evaluate side-chains 93 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.3980 chunk 26 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 46 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117635 restraints weight = 9704.826| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.87 r_work: 0.2951 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8660 Z= 0.128 Angle : 0.524 8.306 11740 Z= 0.261 Chirality : 0.039 0.139 1400 Planarity : 0.003 0.046 1440 Dihedral : 4.791 39.227 1180 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.38 % Allowed : 8.10 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.80 (0.25), residues: 1072 helix: -0.48 (0.21), residues: 598 sheet: 0.45 (0.67), residues: 62 loop : -2.49 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.002 0.000 HIS A 219 PHE 0.015 0.001 PHE A 502 TYR 0.005 0.001 TYR B 586 ARG 0.007 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.933 Fit side-chains REVERT: A 90 MET cc_start: 0.9081 (ptm) cc_final: 0.8850 (ppp) REVERT: A 224 ASN cc_start: 0.9014 (t0) cc_final: 0.8770 (t0) REVERT: A 565 TYR cc_start: 0.8995 (m-80) cc_final: 0.8721 (m-80) REVERT: A 635 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7974 (tpt) REVERT: B 224 ASN cc_start: 0.9007 (t0) cc_final: 0.8765 (t0) REVERT: B 565 TYR cc_start: 0.8996 (m-80) cc_final: 0.8727 (m-80) REVERT: B 635 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7991 (tpt) outliers start: 22 outliers final: 11 residues processed: 92 average time/residue: 1.1145 time to fit residues: 110.6112 Evaluate side-chains 91 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119947 restraints weight = 9771.007| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.48 r_work: 0.2935 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8660 Z= 0.345 Angle : 0.681 10.550 11740 Z= 0.336 Chirality : 0.045 0.145 1400 Planarity : 0.005 0.065 1440 Dihedral : 5.194 42.483 1180 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.27 % Allowed : 8.53 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.95 (0.25), residues: 1072 helix: -0.67 (0.21), residues: 600 sheet: 0.49 (0.67), residues: 62 loop : -2.48 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 426 HIS 0.006 0.001 HIS A 219 PHE 0.022 0.002 PHE A 502 TYR 0.012 0.002 TYR B 586 ARG 0.010 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.989 Fit side-chains REVERT: A 90 MET cc_start: 0.9135 (ptm) cc_final: 0.8883 (ppp) REVERT: A 205 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7698 (tmm160) REVERT: A 224 ASN cc_start: 0.9050 (t0) cc_final: 0.8813 (t0) REVERT: A 565 TYR cc_start: 0.8974 (m-80) cc_final: 0.8763 (m-80) REVERT: B 205 ARG cc_start: 0.8092 (tpp-160) cc_final: 0.7695 (tmm160) REVERT: B 224 ASN cc_start: 0.9034 (t0) cc_final: 0.8805 (t0) REVERT: B 565 TYR cc_start: 0.8976 (m-80) cc_final: 0.8767 (m-80) outliers start: 21 outliers final: 17 residues processed: 92 average time/residue: 1.0972 time to fit residues: 108.7529 Evaluate side-chains 91 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 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 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125244 restraints weight = 9912.258| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.15 r_work: 0.3104 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8660 Z= 0.154 Angle : 0.553 8.816 11740 Z= 0.274 Chirality : 0.040 0.138 1400 Planarity : 0.004 0.046 1440 Dihedral : 4.816 39.366 1180 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.94 % Allowed : 8.75 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.58 (0.26), residues: 1072 helix: -0.35 (0.21), residues: 600 sheet: 0.70 (0.67), residues: 62 loop : -2.35 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 426 HIS 0.003 0.000 HIS A 219 PHE 0.018 0.001 PHE B 502 TYR 0.007 0.001 TYR B 586 ARG 0.012 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.939 Fit side-chains REVERT: A 179 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8169 (mt) REVERT: A 565 TYR cc_start: 0.8933 (m-80) cc_final: 0.8679 (m-80) REVERT: B 565 TYR cc_start: 0.8925 (m-80) cc_final: 0.8667 (m-80) outliers start: 18 outliers final: 12 residues processed: 85 average time/residue: 1.1358 time to fit residues: 104.0463 Evaluate side-chains 83 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118721 restraints weight = 9819.228| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.57 r_work: 0.2996 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8660 Z= 0.162 Angle : 0.562 10.066 11740 Z= 0.278 Chirality : 0.040 0.134 1400 Planarity : 0.004 0.046 1440 Dihedral : 4.693 38.699 1180 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.05 % Allowed : 9.07 % Favored : 88.88 % 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: -1.40 (0.26), residues: 1072 helix: -0.21 (0.21), residues: 600 sheet: 0.76 (0.67), residues: 62 loop : -2.26 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.003 0.001 HIS B 219 PHE 0.019 0.001 PHE A 502 TYR 0.008 0.001 TYR B 586 ARG 0.009 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.927 Fit side-chains REVERT: A 565 TYR cc_start: 0.8961 (m-80) cc_final: 0.8727 (m-80) REVERT: A 635 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8088 (tpt) REVERT: B 565 TYR cc_start: 0.8960 (m-80) cc_final: 0.8729 (m-80) REVERT: B 635 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8109 (tpt) outliers start: 19 outliers final: 12 residues processed: 88 average time/residue: 1.0601 time to fit residues: 100.6597 Evaluate side-chains 90 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124500 restraints weight = 9691.291| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.28 r_work: 0.3027 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8660 Z= 0.215 Angle : 0.602 10.682 11740 Z= 0.297 Chirality : 0.042 0.132 1400 Planarity : 0.004 0.048 1440 Dihedral : 4.825 39.781 1180 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.05 % Allowed : 9.61 % Favored : 88.34 % 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 (0.26), residues: 1072 helix: -0.22 (0.21), residues: 596 sheet: 0.81 (0.67), residues: 62 loop : -2.24 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 426 HIS 0.004 0.001 HIS B 219 PHE 0.021 0.002 PHE A 502 TYR 0.010 0.001 TYR B 586 ARG 0.008 0.000 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.885 Fit side-chains REVERT: A 565 TYR cc_start: 0.8957 (m-80) cc_final: 0.8719 (m-80) REVERT: B 565 TYR cc_start: 0.8962 (m-80) cc_final: 0.8723 (m-80) outliers start: 19 outliers final: 17 residues processed: 83 average time/residue: 1.1669 time to fit residues: 104.0739 Evaluate side-chains 86 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124106 restraints weight = 9895.038| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.38 r_work: 0.3038 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8660 Z= 0.147 Angle : 0.549 9.882 11740 Z= 0.272 Chirality : 0.040 0.136 1400 Planarity : 0.004 0.045 1440 Dihedral : 4.645 38.569 1180 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.84 % Allowed : 9.72 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 1072 helix: -0.01 (0.22), residues: 600 sheet: 0.89 (0.68), residues: 62 loop : -2.12 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.003 0.001 HIS B 219 PHE 0.019 0.001 PHE B 502 TYR 0.007 0.001 TYR B 586 ARG 0.008 0.000 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5243.47 seconds wall clock time: 93 minutes 18.30 seconds (5598.30 seconds total)