Starting phenix.real_space_refine on Thu Aug 6 19:47:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwh_35058/08_2026/8hwh_35058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwh_35058/08_2026/8hwh_35058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hwh_35058/08_2026/8hwh_35058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwh_35058/08_2026/8hwh_35058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hwh_35058/08_2026/8hwh_35058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwh_35058/08_2026/8hwh_35058.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.074 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 93 5.16 5 C 10815 2.51 5 N 2867 2.21 5 O 3167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16948 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2858 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain breaks: 1 Chain: "B" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2887 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 1 Chain: "C" Number of atoms: 2920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2920 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2940 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 17, 'TRANS': 345} Chain breaks: 1 Chain: "E" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2662 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Chain: "F" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2561 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 14, 'TRANS': 301} Chain breaks: 3 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 3.24, per 1000 atoms: 0.19 Number of scatterers: 16948 At special positions: 0 Unit cell: (109.5, 131.4, 132.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 6 15.00 O 3167 8.00 N 2867 7.00 C 10815 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: 1.04 Conformation dependent library (CDL) restraints added in 747.8 milliseconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 23 sheets defined 43.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.716A pdb=" N LEU A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.768A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 571 through 576 removed outlier: 4.000A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 571 through 576' Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.891A pdb=" N MET A 618 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.673A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 660' Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.701A pdb=" N LYS A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 removed outlier: 3.904A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.595A pdb=" N LEU B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.619A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.587A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.954A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.583A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 661' Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.829A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 679 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 692 Processing helix chain 'B' and resid 693 through 700 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.691A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.939A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.535A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.939A pdb=" N THR C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 removed outlier: 3.509A pdb=" N ASP C 432 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.506A pdb=" N LYS C 450 " --> pdb=" O ASP C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.884A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.592A pdb=" N THR C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.561A pdb=" N ASN C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 removed outlier: 4.010A pdb=" N PHE C 668 " --> pdb=" O TYR C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 700 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.539A pdb=" N ILE D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.741A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.600A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 472 through 475 Processing helix chain 'D' and resid 476 through 488 removed outlier: 3.519A pdb=" N TYR D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.603A pdb=" N ALA D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.660A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 577 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 removed outlier: 4.015A pdb=" N MET D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 614 through 619' Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.952A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 661' Processing helix chain 'D' and resid 665 through 680 Processing helix chain 'D' and resid 693 through 700 Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.578A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 400 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.575A pdb=" N ASP E 432 " --> pdb=" O SER E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 removed outlier: 4.008A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 528 through 533 removed outlier: 3.846A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 548 removed outlier: 4.187A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN E 546 " --> pdb=" O PRO E 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS E 548 " --> pdb=" O ILE E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 614 through 619 removed outlier: 3.859A pdb=" N MET E 618 " --> pdb=" O ASP E 614 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 614 through 619' Processing helix chain 'E' and resid 657 through 661 removed outlier: 4.569A pdb=" N ASN E 661 " --> pdb=" O GLY E 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 657 through 661' Processing helix chain 'E' and resid 665 through 680 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.571A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 387 through 400 Processing helix chain 'F' and resid 429 through 434 Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.838A pdb=" N LYS F 450 " --> pdb=" O ASP F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 removed outlier: 3.882A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.745A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 520 Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.722A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 546 removed outlier: 4.045A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 578 removed outlier: 3.871A pdb=" N THR F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.626A pdb=" N MET F 618 " --> pdb=" O ASP F 614 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 614 through 619' Processing helix chain 'F' and resid 656 through 661 removed outlier: 4.027A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN F 661 " --> pdb=" O GLY F 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 656 through 661' Processing helix chain 'F' and resid 665 through 680 Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 602 removed outlier: 6.646A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.967A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 582 through 583 Processing sheet with id=AA6, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AA7, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.812A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.729A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AB2, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.861A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.940A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB5, first strand: chain 'D' and resid 349 through 350 Processing sheet with id=AB6, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.581A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.430A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AB9, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC1, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AC2, first strand: chain 'E' and resid 525 through 527 removed outlier: 6.447A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 340 through 341 Processing sheet with id=AC4, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AC5, first strand: chain 'F' and resid 525 through 527 removed outlier: 3.597A pdb=" N VAL F 553 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE F 601 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR F 499 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR F 604 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE F 501 " --> pdb=" O THR F 604 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1533 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: 2.27 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3535 1.33 - 1.45: 3800 1.45 - 1.57: 9819 1.57 - 1.69: 12 1.69 - 1.82: 135 Bond restraints: 17301 Sorted by residual: bond pdb=" C3' DT S 2 " pdb=" C2' DT S 2 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.38e+00 bond pdb=" N ILE D 531 " pdb=" CA ILE D 531 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.21e+00 bond pdb=" C3' DT S 3 " pdb=" C2' DT S 3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.30e+00 bond pdb=" CB PRO D 362 " pdb=" CG PRO D 362 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.93e+00 bond pdb=" N MET A 462 " pdb=" CA MET A 462 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.23e+00 ... (remaining 17296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22844 2.09 - 4.19: 457 4.19 - 6.28: 54 6.28 - 8.37: 16 8.37 - 10.47: 2 Bond angle restraints: 23373 Sorted by residual: angle pdb=" CA PRO D 362 " pdb=" N PRO D 362 " pdb=" CD PRO D 362 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" N GLY A 418 " pdb=" CA GLY A 418 " pdb=" C GLY A 418 " ideal model delta sigma weight residual 110.96 116.61 -5.65 1.19e+00 7.06e-01 2.25e+01 angle pdb=" N LYS E 434 " pdb=" CA LYS E 434 " pdb=" C LYS E 434 " ideal model delta sigma weight residual 114.75 109.35 5.40 1.26e+00 6.30e-01 1.83e+01 angle pdb=" N3 DT S 4 " pdb=" C4 DT S 4 " pdb=" O4 DT S 4 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT S 6 " pdb=" C4 DT S 6 " pdb=" O4 DT S 6 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 23368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.90: 10084 32.90 - 65.79: 441 65.79 - 98.69: 26 98.69 - 131.59: 0 131.59 - 164.48: 2 Dihedral angle restraints: 10553 sinusoidal: 4452 harmonic: 6101 Sorted by residual: dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 55.52 164.48 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT S 2 " pdb=" C3' DT S 2 " pdb=" O3' DT S 2 " pdb=" P DT S 3 " ideal model delta sinusoidal sigma weight residual 220.00 81.23 138.77 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA HIS D 680 " pdb=" C HIS D 680 " pdb=" N ILE D 681 " pdb=" CA ILE D 681 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 10550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2156 0.056 - 0.112: 428 0.112 - 0.168: 42 0.168 - 0.224: 4 0.224 - 0.280: 1 Chirality restraints: 2631 Sorted by residual: chirality pdb=" CA LEU D 532 " pdb=" N LEU D 532 " pdb=" C LEU D 532 " pdb=" CB LEU D 532 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE F 600 " pdb=" CA ILE F 600 " pdb=" CG1 ILE F 600 " pdb=" CG2 ILE F 600 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 2628 not shown) Planarity restraints: 2953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 385 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO C 386 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 386 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 386 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 479 " -0.161 9.50e-02 1.11e+02 7.27e-02 4.19e+00 pdb=" NE ARG B 479 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 479 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 479 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 479 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 558 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO E 559 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 559 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 559 " 0.027 5.00e-02 4.00e+02 ... (remaining 2950 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1308 2.74 - 3.28: 17034 3.28 - 3.82: 27009 3.82 - 4.36: 32189 4.36 - 4.90: 55076 Nonbonded interactions: 132616 Sorted by model distance: nonbonded pdb=" O GLU D 504 " pdb=" OG1 THR D 507 " model vdw 2.198 3.040 nonbonded pdb=" NH1 ARG D 389 " pdb=" OD2 ASP E 398 " model vdw 2.201 3.120 nonbonded pdb=" OG SER B 455 " pdb=" OE1 GLU B 457 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP A 411 " pdb=" NZ LYS A 412 " model vdw 2.231 3.120 nonbonded pdb=" NH1 ARG A 389 " pdb=" OD2 ASP B 398 " model vdw 2.237 3.120 ... (remaining 132611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 656 through 689)) selection = (chain 'B' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 652 or resid 657 through 689)) selection = (chain 'C' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 656 through 689)) selection = (chain 'D' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 656 through 689)) selection = (chain 'E' and (resid 323 through 557 or resid 570 through 581 or resid 596 thro \ ugh 628 or resid 656 through 689)) selection = (chain 'F' and (resid 323 through 628 or resid 656 through 689)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.320 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.003 0.132 17301 Z= 0.169 Angle : 0.713 10.467 23373 Z= 0.420 Chirality : 0.044 0.280 2631 Planarity : 0.004 0.073 2953 Dihedral : 17.523 164.482 6587 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 0.42 % Allowed : 30.03 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.19), residues: 2049 helix: 0.57 (0.21), residues: 689 sheet: -1.64 (0.33), residues: 256 loop : -1.69 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 479 TYR 0.014 0.001 TYR B 482 PHE 0.021 0.001 PHE C 357 TRP 0.022 0.001 TRP A 675 HIS 0.005 0.001 HIS C 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (17301) covalent geometry : angle 0.71296 / 0.42 (23373) hydrogen bonds : bond 0.18339 / 12.07 ( 546) hydrogen bonds : angle 6.55138 / 4.45 ( 1533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 CYS cc_start: 0.8859 (m) cc_final: 0.7812 (t) REVERT: D 660 GLN cc_start: 0.8906 (mp10) cc_final: 0.8625 (mp10) outliers start: 8 outliers final: 2 residues processed: 184 average time/residue: 0.1144 time to fit residues: 32.3458 Evaluate side-chains 161 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 475 ASN B 478 ASN B 629 HIS C 529 GLN E 358 ASN E 475 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.144316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096423 restraints weight = 36735.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099932 restraints weight = 20307.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102237 restraints weight = 14102.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103653 restraints weight = 11252.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104590 restraints weight = 9817.721| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17301 Z= 0.196 Angle : 0.634 7.968 23373 Z= 0.328 Chirality : 0.045 0.261 2631 Planarity : 0.004 0.048 2953 Dihedral : 8.374 161.975 2307 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.25 % Allowed : 26.36 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.18), residues: 2049 helix: 0.42 (0.19), residues: 717 sheet: -1.78 (0.34), residues: 245 loop : -1.66 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 479 TYR 0.018 0.001 TYR F 482 PHE 0.014 0.001 PHE B 543 TRP 0.026 0.002 TRP F 675 HIS 0.005 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (17301) covalent geometry : angle 0.63404 / 0.33 (23373) hydrogen bonds : bond 0.04491 / 2.91 ( 546) hydrogen bonds : angle 5.14662 / 3.55 ( 1533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 479 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7625 (ttp80) REVERT: B 618 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6948 (mpp) REVERT: C 474 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7137 (pp20) REVERT: C 554 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8045 (t80) REVERT: D 543 PHE cc_start: 0.7784 (p90) cc_final: 0.7305 (p90) REVERT: D 658 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7440 (pttp) REVERT: E 458 MET cc_start: 0.4790 (ppp) cc_final: 0.4561 (ppp) REVERT: E 547 MET cc_start: 0.8260 (tmm) cc_final: 0.7966 (ppp) REVERT: F 462 MET cc_start: 0.7158 (ptp) cc_final: 0.6783 (ptp) outliers start: 81 outliers final: 47 residues processed: 235 average time/residue: 0.0990 time to fit residues: 36.4695 Evaluate side-chains 213 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 177 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 662 ASN F 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.143837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098266 restraints weight = 37069.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100322 restraints weight = 21833.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100373 restraints weight = 15213.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101027 restraints weight = 15217.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101153 restraints weight = 14324.726| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17301 Z= 0.172 Angle : 0.585 6.998 23373 Z= 0.305 Chirality : 0.044 0.266 2631 Planarity : 0.004 0.042 2953 Dihedral : 8.394 161.994 2307 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.14 % Allowed : 26.62 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2049 helix: 0.57 (0.19), residues: 717 sheet: -1.75 (0.34), residues: 245 loop : -1.61 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 387 TYR 0.023 0.001 TYR F 482 PHE 0.021 0.001 PHE B 543 TRP 0.044 0.002 TRP F 675 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (17301) covalent geometry : angle 0.58503 / 0.30 (23373) hydrogen bonds : bond 0.03847 / 2.46 ( 546) hydrogen bonds : angle 4.81546 / 3.34 ( 1533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.8051 (ppp) cc_final: 0.7568 (ppp) REVERT: A 590 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.6765 (t0) REVERT: B 479 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7348 (ttp80) REVERT: B 618 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7071 (mpp) REVERT: C 474 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7467 (pp20) REVERT: C 554 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7798 (t80) REVERT: D 543 PHE cc_start: 0.8089 (p90) cc_final: 0.7575 (p90) REVERT: E 547 MET cc_start: 0.8369 (tmm) cc_final: 0.8108 (ppp) REVERT: E 557 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8281 (tp30) REVERT: F 388 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8248 (mttp) REVERT: F 462 MET cc_start: 0.7037 (ptp) cc_final: 0.6811 (ptp) REVERT: F 547 MET cc_start: 0.7614 (tmm) cc_final: 0.7204 (tmm) outliers start: 79 outliers final: 49 residues processed: 237 average time/residue: 0.1107 time to fit residues: 41.4015 Evaluate side-chains 216 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 388 LYS Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 167 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 110 optimal weight: 0.0570 chunk 92 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 148 optimal weight: 0.0870 chunk 183 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 ASN A 590 ASN C 529 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.146025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.100415 restraints weight = 37059.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.103497 restraints weight = 21211.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.104895 restraints weight = 13020.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104967 restraints weight = 13832.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.105145 restraints weight = 11680.300| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17301 Z= 0.100 Angle : 0.540 9.381 23373 Z= 0.282 Chirality : 0.042 0.260 2631 Planarity : 0.003 0.042 2953 Dihedral : 8.273 161.825 2307 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.20 % Allowed : 27.88 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.18), residues: 2049 helix: 0.81 (0.20), residues: 717 sheet: -1.63 (0.35), residues: 241 loop : -1.52 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 665 TYR 0.044 0.001 TYR F 482 PHE 0.010 0.001 PHE B 543 TRP 0.045 0.001 TRP F 675 HIS 0.002 0.000 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (17301) covalent geometry : angle 0.53975 / 0.28 (23373) hydrogen bonds : bond 0.03020 / 1.93 ( 546) hydrogen bonds : angle 4.43438 / 3.10 ( 1533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7903 (ppp) cc_final: 0.7439 (ppp) REVERT: B 374 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: B 447 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8165 (t70) REVERT: B 479 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7037 (ttp80) REVERT: B 603 ASP cc_start: 0.7342 (t70) cc_final: 0.7118 (t70) REVERT: B 618 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6927 (mpp) REVERT: C 554 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7718 (t80) REVERT: C 618 MET cc_start: 0.8669 (ptt) cc_final: 0.8166 (ptt) REVERT: D 543 PHE cc_start: 0.8094 (p90) cc_final: 0.7530 (p90) REVERT: D 658 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7629 (pttp) REVERT: E 421 ASP cc_start: 0.7552 (t0) cc_final: 0.7126 (p0) REVERT: E 547 MET cc_start: 0.8370 (tmm) cc_final: 0.7834 (tmm) REVERT: E 612 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7082 (tmm-80) REVERT: F 486 LEU cc_start: 0.9443 (mt) cc_final: 0.9216 (mt) REVERT: F 547 MET cc_start: 0.7568 (tmm) cc_final: 0.7160 (tmm) outliers start: 61 outliers final: 41 residues processed: 229 average time/residue: 0.1223 time to fit residues: 43.4233 Evaluate side-chains 216 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 158 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 0.0270 chunk 83 optimal weight: 0.5980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.146178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.100756 restraints weight = 37143.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103610 restraints weight = 21182.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105695 restraints weight = 13057.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106130 restraints weight = 12706.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106083 restraints weight = 10717.369| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17301 Z= 0.099 Angle : 0.529 8.324 23373 Z= 0.275 Chirality : 0.042 0.265 2631 Planarity : 0.003 0.038 2953 Dihedral : 8.208 161.704 2307 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.67 % Allowed : 27.62 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 2049 helix: 0.92 (0.20), residues: 717 sheet: -1.54 (0.35), residues: 242 loop : -1.42 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 332 TYR 0.039 0.001 TYR F 482 PHE 0.010 0.001 PHE B 543 TRP 0.063 0.002 TRP F 675 HIS 0.002 0.000 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (17301) covalent geometry : angle 0.52942 / 0.27 (23373) hydrogen bonds : bond 0.02898 / 1.87 ( 546) hydrogen bonds : angle 4.29813 / 3.01 ( 1533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7436 (ppp) REVERT: B 374 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: B 447 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8159 (t70) REVERT: B 479 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7052 (ttp80) REVERT: B 603 ASP cc_start: 0.7433 (t70) cc_final: 0.7198 (t70) REVERT: B 618 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6860 (mpp) REVERT: C 618 MET cc_start: 0.8537 (ptt) cc_final: 0.7976 (ptt) REVERT: D 543 PHE cc_start: 0.8129 (p90) cc_final: 0.7587 (p90) REVERT: D 658 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7622 (pttp) REVERT: E 421 ASP cc_start: 0.7520 (t0) cc_final: 0.7137 (p0) REVERT: E 612 ARG cc_start: 0.7747 (mtm110) cc_final: 0.7143 (tmm-80) REVERT: F 388 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8238 (mtmm) REVERT: F 547 MET cc_start: 0.7482 (tmm) cc_final: 0.7032 (tmm) outliers start: 70 outliers final: 50 residues processed: 225 average time/residue: 0.1225 time to fit residues: 43.4293 Evaluate side-chains 223 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 388 LYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 108 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.143482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095896 restraints weight = 37340.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099512 restraints weight = 20391.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101841 restraints weight = 14034.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.103306 restraints weight = 11176.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104095 restraints weight = 9725.061| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17301 Z= 0.155 Angle : 0.573 6.892 23373 Z= 0.296 Chirality : 0.043 0.277 2631 Planarity : 0.004 0.036 2953 Dihedral : 8.292 161.958 2307 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.40 % Allowed : 27.15 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 2049 helix: 0.91 (0.20), residues: 711 sheet: -1.55 (0.35), residues: 241 loop : -1.45 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 619 TYR 0.038 0.001 TYR F 482 PHE 0.011 0.001 PHE B 444 TRP 0.082 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (17301) covalent geometry : angle 0.57273 / 0.30 (23373) hydrogen bonds : bond 0.03385 / 2.17 ( 546) hydrogen bonds : angle 4.53404 / 3.17 ( 1533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 174 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7347 (ppp) REVERT: B 374 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: B 447 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8147 (t70) REVERT: B 618 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6909 (mpp) REVERT: D 543 PHE cc_start: 0.8091 (p90) cc_final: 0.7720 (p90) REVERT: D 658 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7337 (pttp) REVERT: E 421 ASP cc_start: 0.7489 (t0) cc_final: 0.7196 (p0) REVERT: E 612 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7143 (tmm-80) outliers start: 84 outliers final: 62 residues processed: 240 average time/residue: 0.1217 time to fit residues: 45.5491 Evaluate side-chains 227 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 160 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.144458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099636 restraints weight = 36914.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101738 restraints weight = 22683.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103424 restraints weight = 14274.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.103762 restraints weight = 14148.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.103809 restraints weight = 12186.791| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17301 Z= 0.132 Angle : 0.576 10.989 23373 Z= 0.297 Chirality : 0.043 0.276 2631 Planarity : 0.004 0.035 2953 Dihedral : 8.277 161.578 2307 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.14 % Allowed : 27.99 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 2049 helix: 0.87 (0.20), residues: 719 sheet: -1.54 (0.35), residues: 242 loop : -1.39 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 479 TYR 0.032 0.001 TYR F 482 PHE 0.010 0.001 PHE B 444 TRP 0.056 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (17301) covalent geometry : angle 0.57553 / 0.30 (23373) hydrogen bonds : bond 0.03094 / 1.99 ( 546) hydrogen bonds : angle 4.41845 / 3.10 ( 1533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 167 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7505 (ppp) REVERT: B 374 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: B 447 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8173 (t70) REVERT: B 618 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6915 (mpp) REVERT: C 462 MET cc_start: 0.8316 (tpp) cc_final: 0.7946 (mpp) REVERT: C 618 MET cc_start: 0.8314 (ptt) cc_final: 0.7798 (ptt) REVERT: D 543 PHE cc_start: 0.8140 (p90) cc_final: 0.7889 (p90) REVERT: D 658 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7642 (pttp) REVERT: E 421 ASP cc_start: 0.7555 (t0) cc_final: 0.7193 (p0) REVERT: E 612 ARG cc_start: 0.7772 (mtm110) cc_final: 0.7277 (tmm-80) REVERT: F 405 GLU cc_start: 0.7729 (mp0) cc_final: 0.7508 (mp0) REVERT: F 618 MET cc_start: 0.7570 (ttt) cc_final: 0.7054 (tpp) outliers start: 79 outliers final: 64 residues processed: 228 average time/residue: 0.1193 time to fit residues: 43.1536 Evaluate side-chains 227 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 158 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 69 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 GLN A 475 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 ASN F 548 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.144042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098815 restraints weight = 36953.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101849 restraints weight = 21014.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102427 restraints weight = 13105.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102993 restraints weight = 13681.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103286 restraints weight = 12008.275| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17301 Z= 0.132 Angle : 0.574 9.864 23373 Z= 0.295 Chirality : 0.043 0.278 2631 Planarity : 0.004 0.035 2953 Dihedral : 8.264 161.570 2307 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.40 % Allowed : 27.94 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 2049 helix: 0.87 (0.20), residues: 721 sheet: -1.54 (0.35), residues: 247 loop : -1.39 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.038 0.001 TYR F 482 PHE 0.010 0.001 PHE B 444 TRP 0.087 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (17301) covalent geometry : angle 0.57355 / 0.29 (23373) hydrogen bonds : bond 0.03155 / 2.03 ( 546) hydrogen bonds : angle 4.41324 / 3.10 ( 1533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 161 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7504 (ppp) REVERT: B 374 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: B 447 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8208 (t70) REVERT: B 618 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6899 (mpp) REVERT: C 462 MET cc_start: 0.8340 (tpp) cc_final: 0.7900 (mpp) REVERT: C 618 MET cc_start: 0.8342 (ptt) cc_final: 0.7798 (ptt) REVERT: D 543 PHE cc_start: 0.8066 (p90) cc_final: 0.7823 (p90) REVERT: D 658 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7571 (pttp) REVERT: E 421 ASP cc_start: 0.7562 (t0) cc_final: 0.7196 (p0) REVERT: E 612 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7276 (tmm-80) REVERT: E 684 MET cc_start: 0.6167 (tpt) cc_final: 0.5874 (tpt) REVERT: F 356 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7579 (mtmm) REVERT: F 501 PHE cc_start: 0.7795 (m-10) cc_final: 0.7532 (m-10) REVERT: F 618 MET cc_start: 0.7643 (ttt) cc_final: 0.7151 (tpp) outliers start: 84 outliers final: 71 residues processed: 230 average time/residue: 0.1284 time to fit residues: 46.3611 Evaluate side-chains 229 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 152 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 142 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 49 optimal weight: 0.0060 chunk 140 optimal weight: 0.0270 chunk 105 optimal weight: 0.0010 chunk 149 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.146067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103169 restraints weight = 36868.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.103648 restraints weight = 24372.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105236 restraints weight = 16364.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.105525 restraints weight = 14902.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105654 restraints weight = 13815.382| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 17301 Z= 0.100 Angle : 0.570 11.414 23373 Z= 0.293 Chirality : 0.043 0.274 2631 Planarity : 0.003 0.044 2953 Dihedral : 8.192 161.227 2307 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.78 % Allowed : 29.61 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 2049 helix: 1.00 (0.20), residues: 718 sheet: -1.33 (0.35), residues: 246 loop : -1.34 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 479 TYR 0.042 0.001 TYR F 482 PHE 0.009 0.001 PHE B 327 TRP 0.115 0.002 TRP F 675 HIS 0.002 0.000 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (17301) covalent geometry : angle 0.57030 / 0.29 (23373) hydrogen bonds : bond 0.02782 / 1.80 ( 546) hydrogen bonds : angle 4.16709 / 2.94 ( 1533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7362 (ppp) REVERT: B 374 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: B 447 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8235 (t70) REVERT: B 618 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6750 (mpp) REVERT: B 656 ASP cc_start: 0.8562 (m-30) cc_final: 0.8294 (m-30) REVERT: C 618 MET cc_start: 0.8312 (ptt) cc_final: 0.8079 (ptt) REVERT: D 543 PHE cc_start: 0.8005 (p90) cc_final: 0.7785 (p90) REVERT: D 658 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7631 (pttp) REVERT: E 421 ASP cc_start: 0.7527 (t0) cc_final: 0.7179 (p0) REVERT: E 445 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8498 (mmmm) REVERT: E 597 HIS cc_start: 0.8004 (m170) cc_final: 0.7425 (m-70) REVERT: E 612 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7229 (tmm-80) REVERT: E 684 MET cc_start: 0.6108 (tpt) cc_final: 0.5793 (tpt) REVERT: E 686 LEU cc_start: 0.7814 (pt) cc_final: 0.7552 (tt) REVERT: F 356 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7471 (mtmm) REVERT: F 618 MET cc_start: 0.7637 (ttt) cc_final: 0.7154 (tpp) outliers start: 53 outliers final: 41 residues processed: 204 average time/residue: 0.1220 time to fit residues: 39.1823 Evaluate side-chains 202 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 185 optimal weight: 0.0980 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 187 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.144144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099257 restraints weight = 36943.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101841 restraints weight = 22007.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.104213 restraints weight = 13460.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104550 restraints weight = 12615.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.104427 restraints weight = 10975.707| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17301 Z= 0.128 Angle : 0.594 11.352 23373 Z= 0.304 Chirality : 0.043 0.281 2631 Planarity : 0.004 0.042 2953 Dihedral : 8.206 161.453 2307 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.67 % Allowed : 29.82 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 2049 helix: 0.87 (0.20), residues: 724 sheet: -1.34 (0.35), residues: 251 loop : -1.35 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 479 TYR 0.032 0.001 TYR F 482 PHE 0.010 0.001 PHE F 501 TRP 0.110 0.002 TRP F 675 HIS 0.002 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (17301) covalent geometry : angle 0.59425 / 0.30 (23373) hydrogen bonds : bond 0.03076 / 2.00 ( 546) hydrogen bonds : angle 4.31162 / 3.02 ( 1533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7426 (ppp) REVERT: B 374 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: B 447 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8239 (t70) REVERT: B 618 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6803 (mpp) REVERT: C 618 MET cc_start: 0.8567 (ptt) cc_final: 0.7949 (ptt) REVERT: D 543 PHE cc_start: 0.8004 (p90) cc_final: 0.7789 (p90) REVERT: D 658 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7577 (pttp) REVERT: E 421 ASP cc_start: 0.7538 (t0) cc_final: 0.7207 (p0) REVERT: E 445 LYS cc_start: 0.8899 (ttpp) cc_final: 0.8520 (mmmm) REVERT: E 597 HIS cc_start: 0.8080 (m170) cc_final: 0.7500 (m-70) REVERT: E 612 ARG cc_start: 0.7772 (mtm110) cc_final: 0.7291 (tmm-80) REVERT: F 356 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7582 (mtmm) REVERT: F 469 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6350 (tp40) REVERT: F 618 MET cc_start: 0.7610 (ttt) cc_final: 0.7294 (tpp) outliers start: 51 outliers final: 43 residues processed: 196 average time/residue: 0.1134 time to fit residues: 34.8674 Evaluate side-chains 203 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 25 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 165 optimal weight: 0.0980 chunk 36 optimal weight: 0.1980 chunk 126 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 200 optimal weight: 0.0020 chunk 102 optimal weight: 8.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.144807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097980 restraints weight = 36874.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101602 restraints weight = 20030.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103974 restraints weight = 13762.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105282 restraints weight = 10928.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106328 restraints weight = 9547.072| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.219 17301 Z= 0.199 Angle : 0.785 59.193 23373 Z= 0.439 Chirality : 0.043 0.282 2631 Planarity : 0.004 0.036 2953 Dihedral : 8.207 161.417 2307 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.04 % Allowed : 29.45 % Favored : 67.51 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.19), residues: 2049 helix: 0.88 (0.20), residues: 724 sheet: -1.34 (0.35), residues: 251 loop : -1.35 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 479 TYR 0.031 0.001 TYR F 482 PHE 0.029 0.001 PHE E 668 TRP 0.095 0.002 TRP F 675 HIS 0.002 0.000 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (17301) covalent geometry : angle 0.78452 / 0.44 (23373) hydrogen bonds : bond 0.03060 / 1.99 ( 546) hydrogen bonds : angle 4.33366 / 3.03 ( 1533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2645.13 seconds wall clock time: 46 minutes 35.44 seconds (2795.44 seconds total)