Starting phenix.real_space_refine on Tue Sep 24 17:03:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwj_35768/09_2024/8iwj_35768.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwj_35768/09_2024/8iwj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwj_35768/09_2024/8iwj_35768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwj_35768/09_2024/8iwj_35768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwj_35768/09_2024/8iwj_35768.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwj_35768/09_2024/8iwj_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-5461/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: 7.60, per 1000 atoms: 0.90 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: 1.93 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: 0.91 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: 2.33 Time building geometry restraints manager: 2.28 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: 0.00 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: 1.610 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.320 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.530 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.053 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: 1.2575 time to fit residues: 145.9087 Evaluate side-chains 81 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.888 Fit side-chains REVERT: A 565 TYR cc_start: 0.8642 (m-80) cc_final: 0.8375 (m-80) REVERT: B 224 ASN cc_start: 0.8922 (t0) cc_final: 0.8691 (t0) REVERT: B 565 TYR cc_start: 0.8639 (m-80) cc_final: 0.8342 (m-80) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 1.0214 time to fit residues: 99.4285 Evaluate side-chains 74 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 54 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 224 ASN A 389 GLN B 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8660 Z= 0.177 Angle : 0.584 9.255 11740 Z= 0.292 Chirality : 0.041 0.131 1400 Planarity : 0.004 0.043 1440 Dihedral : 5.045 41.910 1180 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.40 % Allowed : 7.56 % Favored : 91.04 % 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: -2.95 (0.23), residues: 1072 helix: -1.53 (0.20), residues: 598 sheet: -0.31 (0.66), residues: 62 loop : -2.75 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 426 HIS 0.004 0.001 HIS B 219 PHE 0.015 0.001 PHE A 502 TYR 0.010 0.001 TYR A 586 ARG 0.005 0.000 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 99 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.004 Fit side-chains REVERT: A 224 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8653 (t0) REVERT: A 565 TYR cc_start: 0.8632 (m-80) cc_final: 0.8307 (m-80) REVERT: B 565 TYR cc_start: 0.8635 (m-80) cc_final: 0.8309 (m-80) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 1.0074 time to fit residues: 102.5450 Evaluate side-chains 91 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 224 ASN 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 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 97 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 0.0020 chunk 28 optimal weight: 0.6980 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 224 ASN B 112 ASN B 130 ASN B 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8660 Z= 0.225 Angle : 0.600 9.587 11740 Z= 0.299 Chirality : 0.042 0.132 1400 Planarity : 0.004 0.047 1440 Dihedral : 5.022 41.618 1180 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.05 % Allowed : 7.67 % Favored : 90.28 % 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: -2.43 (0.24), residues: 1072 helix: -1.03 (0.21), residues: 598 sheet: -0.00 (0.66), residues: 62 loop : -2.67 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 426 HIS 0.004 0.001 HIS B 219 PHE 0.015 0.002 PHE B 502 TYR 0.011 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 91 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 1.021 Fit side-chains REVERT: A 565 TYR cc_start: 0.8646 (m-80) cc_final: 0.8322 (m-80) REVERT: B 224 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8695 (t0) REVERT: B 565 TYR cc_start: 0.8640 (m-80) cc_final: 0.8337 (m-80) outliers start: 19 outliers final: 11 residues processed: 83 average time/residue: 1.0404 time to fit residues: 93.5624 Evaluate side-chains 84 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 224 ASN B 130 ASN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8660 Z= 0.327 Angle : 0.670 9.788 11740 Z= 0.333 Chirality : 0.045 0.141 1400 Planarity : 0.005 0.066 1440 Dihedral : 5.252 43.216 1180 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.05 % Allowed : 7.99 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.27 (0.25), residues: 1072 helix: -0.93 (0.21), residues: 602 sheet: 0.27 (0.66), residues: 62 loop : -2.61 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 426 HIS 0.006 0.001 HIS A 219 PHE 0.016 0.002 PHE B 499 TYR 0.013 0.002 TYR A 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 92 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.984 Fit side-chains REVERT: A 565 TYR cc_start: 0.8647 (m-80) cc_final: 0.8335 (m-80) REVERT: B 224 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8818 (t0) REVERT: B 565 TYR cc_start: 0.8651 (m-80) cc_final: 0.8344 (m-80) outliers start: 19 outliers final: 13 residues processed: 88 average time/residue: 1.0390 time to fit residues: 98.7289 Evaluate side-chains 87 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 224 ASN B 130 ASN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8660 Z= 0.196 Angle : 0.570 8.188 11740 Z= 0.285 Chirality : 0.041 0.134 1400 Planarity : 0.004 0.049 1440 Dihedral : 4.972 41.148 1180 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.73 % Allowed : 8.42 % Favored : 89.85 % 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: -1.92 (0.25), residues: 1072 helix: -0.58 (0.21), residues: 598 sheet: 0.39 (0.66), residues: 62 loop : -2.54 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 426 HIS 0.004 0.001 HIS A 219 PHE 0.015 0.001 PHE B 499 TYR 0.008 0.001 TYR A 586 ARG 0.006 0.000 ARG B 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 85 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.904 Fit side-chains REVERT: A 565 TYR cc_start: 0.8641 (m-80) cc_final: 0.8300 (m-80) REVERT: B 565 TYR cc_start: 0.8639 (m-80) cc_final: 0.8310 (m-80) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 1.0714 time to fit residues: 93.9090 Evaluate side-chains 79 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 0.0370 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8860 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8660 Z= 0.167 Angle : 0.546 8.107 11740 Z= 0.273 Chirality : 0.040 0.134 1400 Planarity : 0.004 0.046 1440 Dihedral : 4.742 39.358 1180 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.38 % Allowed : 8.53 % Favored : 89.09 % 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: -1.62 (0.25), residues: 1072 helix: -0.36 (0.22), residues: 600 sheet: 0.56 (0.66), residues: 62 loop : -2.38 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 426 HIS 0.003 0.001 HIS A 219 PHE 0.017 0.001 PHE B 502 TYR 0.008 0.001 TYR A 586 ARG 0.005 0.000 ARG B 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 90 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 0.988 Fit side-chains REVERT: A 565 TYR cc_start: 0.8623 (m-80) cc_final: 0.8300 (m-80) REVERT: A 635 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7353 (tpt) REVERT: B 565 TYR cc_start: 0.8632 (m-80) cc_final: 0.8322 (m-80) outliers start: 22 outliers final: 12 residues processed: 82 average time/residue: 1.0335 time to fit residues: 91.6500 Evaluate side-chains 80 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.0770 overall best weight: 1.0542 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8660 Z= 0.187 Angle : 0.571 9.625 11740 Z= 0.283 Chirality : 0.041 0.135 1400 Planarity : 0.004 0.047 1440 Dihedral : 4.776 39.619 1180 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.27 % Allowed : 8.75 % Favored : 88.98 % 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: -1.50 (0.26), residues: 1072 helix: -0.30 (0.21), residues: 598 sheet: 0.70 (0.66), residues: 62 loop : -2.28 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 426 HIS 0.004 0.001 HIS B 219 PHE 0.018 0.001 PHE B 502 TYR 0.009 0.001 TYR A 586 ARG 0.004 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 86 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 1.291 Fit side-chains REVERT: A 565 TYR cc_start: 0.8640 (m-80) cc_final: 0.8322 (m-80) REVERT: B 565 TYR cc_start: 0.8639 (m-80) cc_final: 0.8333 (m-80) outliers start: 21 outliers final: 12 residues processed: 80 average time/residue: 1.0639 time to fit residues: 92.4644 Evaluate side-chains 77 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8660 Z= 0.162 Angle : 0.558 10.032 11740 Z= 0.276 Chirality : 0.041 0.135 1400 Planarity : 0.004 0.046 1440 Dihedral : 4.666 38.944 1180 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.73 % Allowed : 9.29 % Favored : 88.98 % 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: -1.31 (0.26), residues: 1072 helix: -0.16 (0.22), residues: 598 sheet: 0.79 (0.66), residues: 62 loop : -2.18 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.006 0.000 ARG B 205 *********************** 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 81 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.873 Fit side-chains REVERT: A 203 PHE cc_start: 0.8248 (m-10) cc_final: 0.8041 (m-80) REVERT: A 565 TYR cc_start: 0.8625 (m-80) cc_final: 0.8305 (m-80) REVERT: A 635 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7359 (tpt) REVERT: B 565 TYR cc_start: 0.8629 (m-80) cc_final: 0.8302 (m-80) outliers start: 16 outliers final: 15 residues processed: 77 average time/residue: 1.1301 time to fit residues: 93.7722 Evaluate side-chains 80 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 102 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 99 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8660 Z= 0.146 Angle : 0.530 8.980 11740 Z= 0.265 Chirality : 0.040 0.134 1400 Planarity : 0.003 0.046 1440 Dihedral : 4.582 38.350 1180 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.94 % Allowed : 9.18 % 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: -1.15 (0.26), residues: 1072 helix: -0.02 (0.22), residues: 600 sheet: 0.82 (0.66), residues: 62 loop : -2.10 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 426 HIS 0.003 0.001 HIS A 219 PHE 0.019 0.001 PHE B 502 TYR 0.007 0.001 TYR B 586 ARG 0.004 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 fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.988 Fit side-chains REVERT: A 203 PHE cc_start: 0.8221 (m-10) cc_final: 0.7987 (m-80) REVERT: A 565 TYR cc_start: 0.8620 (m-80) cc_final: 0.8303 (m-80) REVERT: A 635 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7380 (tpt) REVERT: B 565 TYR cc_start: 0.8636 (m-80) cc_final: 0.8317 (m-80) outliers start: 18 outliers final: 15 residues processed: 83 average time/residue: 1.1697 time to fit residues: 104.4607 Evaluate side-chains 84 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 0.3980 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.150348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107777 restraints weight = 9848.707| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.89 r_work: 0.2980 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2698 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= 0.159 Angle : 0.547 9.738 11740 Z= 0.272 Chirality : 0.040 0.133 1400 Planarity : 0.004 0.047 1440 Dihedral : 4.570 38.316 1180 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.84 % Allowed : 9.83 % 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: -1.07 (0.26), residues: 1072 helix: 0.03 (0.22), residues: 600 sheet: 0.91 (0.66), residues: 62 loop : -2.06 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.003 0.001 HIS A 219 PHE 0.020 0.001 PHE B 502 TYR 0.008 0.001 TYR A 586 ARG 0.006 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2573.50 seconds wall clock time: 46 minutes 11.28 seconds (2771.28 seconds total)