Starting phenix.real_space_refine on Fri Jul 3 23:59:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwh_35058/07_2026/8hwh_35058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwh_35058/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwh_35058/07_2026/8hwh_35058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwh_35058/07_2026/8hwh_35058.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwh_35058/07_2026/8hwh_35058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwh_35058/07_2026/8hwh_35058.cif" } 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-dev-6108/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: 3.21, 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: 1.18 Conformation dependent library (CDL) restraints added in 755.3 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: 0.54 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: 2.89 Time building geometry restraints manager: 1.61 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.720 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- 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= 0.419 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 0.71265 / 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 : 0.673 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: 0.1139 time to fit residues: 32.1991 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 : 0.666 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.144240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098407 restraints weight = 36724.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100867 restraints weight = 21582.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101730 restraints weight = 14533.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.102198 restraints weight = 14558.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.102252 restraints weight = 12978.135| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17301 Z= 0.200 Angle : 0.638 7.897 23373 Z= 0.330 Chirality : 0.045 0.228 2631 Planarity : 0.004 0.047 2953 Dihedral : 8.410 163.419 2307 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.25 % Allowed : 26.42 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.41 (0.18), residues: 2049 helix: 0.35 (0.19), residues: 725 sheet: -1.78 (0.34), residues: 245 loop : -1.65 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 479 TYR 0.017 0.001 TYR F 482 PHE 0.014 0.001 PHE B 543 TRP 0.023 0.002 TRP F 675 HIS 0.005 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (17301) covalent geometry : angle 0.63774 / 0.33 (23373) hydrogen bonds : bond 0.04124 / 2.68 ( 546) hydrogen bonds : angle 5.13291 / 3.54 ( 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 254 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 173 time to evaluate : 0.426 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 382 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: B 479 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7662 (ttp80) REVERT: B 618 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7003 (mpp) REVERT: C 474 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7343 (pp20) REVERT: C 554 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8024 (t80) REVERT: D 543 PHE cc_start: 0.7902 (p90) cc_final: 0.7410 (p90) REVERT: D 611 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7391 (p0) REVERT: D 658 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7684 (pttp) REVERT: E 458 MET cc_start: 0.4855 (ppp) cc_final: 0.4633 (ppp) REVERT: E 547 MET cc_start: 0.8334 (tmm) cc_final: 0.7972 (ppp) REVERT: F 462 MET cc_start: 0.7121 (ptp) cc_final: 0.6722 (ptp) outliers start: 81 outliers final: 49 residues processed: 235 average time/residue: 0.1076 time to fit residues: 39.5419 Evaluate side-chains 216 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 382 GLU 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 610 PHE Chi-restraints excluded: chain D residue 611 ASP 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 617 LEU 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: 2.9990 chunk 49 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.144423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096558 restraints weight = 37082.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100128 restraints weight = 20420.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102450 restraints weight = 14138.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103874 restraints weight = 11256.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104799 restraints weight = 9812.927| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17301 Z= 0.161 Angle : 0.572 6.972 23373 Z= 0.299 Chirality : 0.043 0.238 2631 Planarity : 0.004 0.042 2953 Dihedral : 8.388 163.009 2307 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.09 % Allowed : 26.73 % Favored : 69.18 % 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: -1.22 (0.18), residues: 2049 helix: 0.63 (0.19), residues: 717 sheet: -1.75 (0.34), residues: 245 loop : -1.60 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 619 TYR 0.021 0.001 TYR F 482 PHE 0.020 0.001 PHE B 543 TRP 0.049 0.002 TRP F 675 HIS 0.004 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (17301) covalent geometry : angle 0.57194 / 0.30 (23373) hydrogen bonds : bond 0.03723 / 2.38 ( 546) hydrogen bonds : angle 4.77069 / 3.31 ( 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 254 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 176 time to evaluate : 0.688 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: 0.7993 (ppp) cc_final: 0.7509 (ppp) REVERT: A 590 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.6984 (t0) REVERT: B 382 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: B 479 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7259 (ttp80) REVERT: B 618 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7003 (mpp) REVERT: C 554 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7825 (t80) REVERT: D 543 PHE cc_start: 0.8051 (p90) cc_final: 0.7551 (p90) REVERT: E 547 MET cc_start: 0.8297 (tmm) cc_final: 0.7896 (tmm) REVERT: E 557 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8249 (tp30) REVERT: F 458 MET cc_start: 0.7403 (ppp) cc_final: 0.7057 (ppp) REVERT: F 486 LEU cc_start: 0.9427 (mt) cc_final: 0.9223 (mp) REVERT: F 547 MET cc_start: 0.7532 (tmm) cc_final: 0.7127 (tmm) outliers start: 78 outliers final: 46 residues processed: 240 average time/residue: 0.1106 time to fit residues: 41.3767 Evaluate side-chains 214 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 382 GLU 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 618 MET Chi-restraints excluded: chain B residue 659 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 510 SER Chi-restraints excluded: chain C residue 547 MET 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 623 VAL 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 533 THR 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 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: 7.9990 chunk 190 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.144300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099330 restraints weight = 37027.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100523 restraints weight = 21586.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101476 restraints weight = 15483.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101793 restraints weight = 14888.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102032 restraints weight = 13397.996| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17301 Z= 0.134 Angle : 0.557 9.404 23373 Z= 0.290 Chirality : 0.043 0.236 2631 Planarity : 0.004 0.041 2953 Dihedral : 8.364 163.138 2307 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.51 % Allowed : 26.99 % Favored : 68.50 % 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: -1.11 (0.18), residues: 2049 helix: 0.74 (0.20), residues: 717 sheet: -1.68 (0.35), residues: 241 loop : -1.56 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 665 TYR 0.019 0.001 TYR F 482 PHE 0.010 0.001 PHE B 444 TRP 0.047 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (17301) covalent geometry : angle 0.55686 / 0.29 (23373) hydrogen bonds : bond 0.03312 / 2.12 ( 546) hydrogen bonds : angle 4.60085 / 3.21 ( 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 259 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 173 time to evaluate : 0.688 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: 0.7959 (ppp) cc_final: 0.7478 (ppp) REVERT: B 374 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: B 382 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: B 447 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8184 (t70) REVERT: B 479 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7117 (ttp80) REVERT: B 594 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7938 (m110) REVERT: B 603 ASP cc_start: 0.7399 (t70) cc_final: 0.7183 (t70) REVERT: B 618 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7002 (mpp) REVERT: C 554 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7751 (t80) REVERT: C 618 MET cc_start: 0.9052 (ptp) cc_final: 0.8012 (ptp) REVERT: D 543 PHE cc_start: 0.8104 (p90) cc_final: 0.7556 (p90) REVERT: D 611 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7564 (p0) REVERT: D 658 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7647 (pttp) REVERT: E 547 MET cc_start: 0.8315 (tmm) cc_final: 0.7855 (tmm) REVERT: E 548 HIS cc_start: 0.6388 (OUTLIER) cc_final: 0.5061 (t70) REVERT: E 557 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8336 (tp30) REVERT: E 612 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7110 (tmm-80) REVERT: F 547 MET cc_start: 0.7609 (tmm) cc_final: 0.7189 (tmm) outliers start: 86 outliers final: 62 residues processed: 245 average time/residue: 0.1171 time to fit residues: 44.8391 Evaluate side-chains 234 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 163 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 569 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 334 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU 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 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 594 ASN 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 554 PHE Chi-restraints excluded: chain C residue 659 ILE 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 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 611 ASP 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 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 548 HIS 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 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 158 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.144613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096976 restraints weight = 37010.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100612 restraints weight = 20086.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102964 restraints weight = 13816.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.104365 restraints weight = 10986.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105326 restraints weight = 9597.040| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17301 Z= 0.125 Angle : 0.551 7.996 23373 Z= 0.286 Chirality : 0.043 0.241 2631 Planarity : 0.004 0.050 2953 Dihedral : 8.331 162.961 2307 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.40 % Allowed : 27.20 % Favored : 68.40 % 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: -1.02 (0.18), residues: 2049 helix: 0.83 (0.20), residues: 718 sheet: -1.60 (0.35), residues: 241 loop : -1.52 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 332 TYR 0.045 0.001 TYR F 482 PHE 0.010 0.001 PHE B 444 TRP 0.064 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (17301) covalent geometry : angle 0.55085 / 0.29 (23373) hydrogen bonds : bond 0.03204 / 2.06 ( 546) hydrogen bonds : angle 4.50239 / 3.16 ( 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 253 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 169 time to evaluate : 0.693 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 590 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7176 (t0) REVERT: B 374 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: B 382 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: B 447 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8163 (t70) REVERT: B 618 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6947 (mpp) REVERT: C 618 MET cc_start: 0.8880 (ptp) cc_final: 0.8055 (ptp) REVERT: D 543 PHE cc_start: 0.8033 (p90) cc_final: 0.7535 (p90) REVERT: D 658 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7403 (pttp) REVERT: E 421 ASP cc_start: 0.7505 (t0) cc_final: 0.7170 (p0) REVERT: E 557 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8353 (tp30) REVERT: E 612 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7147 (tmm-80) REVERT: F 547 MET cc_start: 0.7613 (tmm) cc_final: 0.7180 (tmm) outliers start: 84 outliers final: 63 residues processed: 237 average time/residue: 0.1199 time to fit residues: 44.6010 Evaluate side-chains 231 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 404 VAL 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 574 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 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 382 GLU 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 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 592 ILE 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 659 ILE Chi-restraints excluded: chain C residue 683 ILE 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 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 623 VAL Chi-restraints excluded: chain D residue 628 THR 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 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 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 108 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 44 optimal weight: 0.1980 chunk 160 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.144585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097691 restraints weight = 37060.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101220 restraints weight = 20535.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103489 restraints weight = 14249.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104925 restraints weight = 11387.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.105605 restraints weight = 9924.512| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17301 Z= 0.107 Angle : 0.542 7.275 23373 Z= 0.282 Chirality : 0.042 0.241 2631 Planarity : 0.003 0.037 2953 Dihedral : 8.284 162.722 2307 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.35 % Allowed : 27.52 % Favored : 68.13 % 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: 0.92 (0.20), residues: 712 sheet: -1.55 (0.35), residues: 241 loop : -1.45 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.042 0.001 TYR F 482 PHE 0.013 0.001 PHE F 501 TRP 0.081 0.002 TRP F 675 HIS 0.002 0.000 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (17301) covalent geometry : angle 0.54181 / 0.28 (23373) hydrogen bonds : bond 0.02988 / 1.91 ( 546) hydrogen bonds : angle 4.37711 / 3.07 ( 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 248 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 165 time to evaluate : 0.635 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 374 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: B 382 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 447 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8171 (t70) REVERT: B 618 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6891 (mpp) REVERT: C 618 MET cc_start: 0.8890 (ptp) cc_final: 0.8029 (ptp) REVERT: D 543 PHE cc_start: 0.8024 (p90) cc_final: 0.7695 (p90) REVERT: D 658 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7319 (pttp) REVERT: E 421 ASP cc_start: 0.7486 (t0) cc_final: 0.7173 (p0) REVERT: E 612 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7135 (tmm-80) outliers start: 83 outliers final: 65 residues processed: 233 average time/residue: 0.1238 time to fit residues: 44.9727 Evaluate side-chains 231 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 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 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL 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 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 351 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 C residue 659 ILE Chi-restraints excluded: chain C residue 683 ILE 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 435 LYS 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 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 602 ILE 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: 5.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.142860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095419 restraints weight = 36737.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098965 restraints weight = 19994.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101293 restraints weight = 13773.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102715 restraints weight = 10953.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.103588 restraints weight = 9540.554| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2384 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= 0.167 Angle : 0.595 11.335 23373 Z= 0.305 Chirality : 0.043 0.250 2631 Planarity : 0.004 0.040 2953 Dihedral : 8.363 162.965 2307 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.77 % Allowed : 27.52 % Favored : 67.71 % 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: -0.98 (0.19), residues: 2049 helix: 0.85 (0.20), residues: 713 sheet: -1.59 (0.35), residues: 246 loop : -1.47 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 479 TYR 0.042 0.001 TYR F 482 PHE 0.012 0.001 PHE B 444 TRP 0.102 0.002 TRP F 675 HIS 0.004 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (17301) covalent geometry : angle 0.59472 / 0.31 (23373) hydrogen bonds : bond 0.03485 / 2.23 ( 546) hydrogen bonds : angle 4.58567 / 3.22 ( 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 260 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 169 time to evaluate : 0.674 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 590 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7227 (t0) REVERT: B 374 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: B 382 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: B 447 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8184 (t70) REVERT: B 594 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7996 (m110) REVERT: B 618 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7037 (mpp) REVERT: C 474 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: C 618 MET cc_start: 0.8892 (ptp) cc_final: 0.8068 (ptp) REVERT: D 543 PHE cc_start: 0.8013 (p90) cc_final: 0.7757 (p90) REVERT: D 658 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7367 (pttp) REVERT: E 421 ASP cc_start: 0.7538 (t0) cc_final: 0.7209 (p0) REVERT: E 612 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7199 (tmm-80) REVERT: F 356 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7538 (mtmm) REVERT: F 405 GLU cc_start: 0.7650 (mp0) cc_final: 0.7429 (mp0) REVERT: F 618 MET cc_start: 0.7604 (ttt) cc_final: 0.7096 (tpp) outliers start: 91 outliers final: 72 residues processed: 243 average time/residue: 0.1287 time to fit residues: 48.1879 Evaluate side-chains 243 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 162 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL 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 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 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 674 LYS 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 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU 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 510 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR 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 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 659 ILE 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 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 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 381 SER 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 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 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: 5.9990 chunk 49 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** 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 = 0.4044 r_free = 0.4044 target = 0.142352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096714 restraints weight = 37068.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099459 restraints weight = 22192.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102538 restraints weight = 13612.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102229 restraints weight = 12352.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102020 restraints weight = 10929.787| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17301 Z= 0.167 Angle : 0.602 8.722 23373 Z= 0.310 Chirality : 0.044 0.266 2631 Planarity : 0.004 0.042 2953 Dihedral : 8.400 162.765 2307 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.93 % Allowed : 27.20 % 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: -1.01 (0.19), residues: 2049 helix: 0.77 (0.20), residues: 720 sheet: -1.58 (0.34), residues: 252 loop : -1.46 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 479 TYR 0.034 0.001 TYR F 482 PHE 0.012 0.001 PHE B 444 TRP 0.079 0.002 TRP F 675 HIS 0.005 0.001 HIS E 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (17301) covalent geometry : angle 0.60196 / 0.31 (23373) hydrogen bonds : bond 0.03425 / 2.20 ( 546) hydrogen bonds : angle 4.58897 / 3.22 ( 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 259 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 165 time to evaluate : 0.759 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 469 GLN cc_start: 0.7465 (tt0) cc_final: 0.6761 (tp40) REVERT: A 489 CYS cc_start: 0.9036 (m) cc_final: 0.8434 (t) REVERT: B 374 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: B 382 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: B 447 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8235 (t70) REVERT: B 532 LEU cc_start: 0.8587 (tp) cc_final: 0.8217 (tp) REVERT: B 594 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7865 (m110) REVERT: B 618 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7280 (mpp) REVERT: B 689 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7234 (p) REVERT: C 462 MET cc_start: 0.8234 (tpp) cc_final: 0.7849 (mpp) REVERT: C 474 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7379 (pp20) REVERT: C 618 MET cc_start: 0.9047 (ptp) cc_final: 0.8149 (ptp) REVERT: D 543 PHE cc_start: 0.8089 (p90) cc_final: 0.7818 (p90) REVERT: D 658 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7557 (pttp) REVERT: D 660 GLN cc_start: 0.9021 (mp10) cc_final: 0.8751 (pp30) REVERT: E 421 ASP cc_start: 0.7586 (t0) cc_final: 0.7228 (p0) REVERT: E 612 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7191 (tmm-80) REVERT: F 356 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7614 (mtmm) REVERT: F 501 PHE cc_start: 0.7780 (m-10) cc_final: 0.7489 (m-10) REVERT: F 547 MET cc_start: 0.7722 (tmm) cc_final: 0.7454 (tmm) REVERT: F 618 MET cc_start: 0.7616 (ttt) cc_final: 0.7097 (tpp) outliers start: 94 outliers final: 77 residues processed: 244 average time/residue: 0.1252 time to fit residues: 47.6308 Evaluate side-chains 239 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 153 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 659 ILE 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 334 LEU 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 375 LEU Chi-restraints excluded: chain B residue 382 GLU 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 468 ILE 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 587 CYS Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 689 THR 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 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 659 ILE 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 527 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 628 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 142 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 140 optimal weight: 0.0980 chunk 105 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 ASN F 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.144037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097203 restraints weight = 36724.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.100840 restraints weight = 19741.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103205 restraints weight = 13535.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104667 restraints weight = 10727.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105448 restraints weight = 9325.234| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17301 Z= 0.110 Angle : 0.571 9.011 23373 Z= 0.293 Chirality : 0.043 0.248 2631 Planarity : 0.003 0.038 2953 Dihedral : 8.332 162.330 2307 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.04 % Allowed : 28.09 % 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: -0.91 (0.19), residues: 2049 helix: 0.89 (0.20), residues: 722 sheet: -1.53 (0.35), residues: 247 loop : -1.43 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.033 0.001 TYR F 482 PHE 0.009 0.001 PHE B 444 TRP 0.068 0.002 TRP F 675 HIS 0.009 0.001 HIS E 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (17301) covalent geometry : angle 0.57090 / 0.29 (23373) hydrogen bonds : bond 0.02980 / 1.92 ( 546) hydrogen bonds : angle 4.35341 / 3.06 ( 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 238 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 161 time to evaluate : 0.614 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: 0.8970 (m) cc_final: 0.8348 (t) REVERT: B 374 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: B 382 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: B 447 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8222 (t70) REVERT: B 618 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6839 (mpp) REVERT: C 462 MET cc_start: 0.7989 (tpp) cc_final: 0.7765 (mpp) REVERT: C 618 MET cc_start: 0.8956 (ptp) cc_final: 0.8134 (ptp) REVERT: D 543 PHE cc_start: 0.7994 (p90) cc_final: 0.7725 (p90) REVERT: D 658 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7398 (pttp) REVERT: E 421 ASP cc_start: 0.7473 (t0) cc_final: 0.7192 (p0) REVERT: E 597 HIS cc_start: 0.8052 (m170) cc_final: 0.7408 (m-70) REVERT: E 612 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7165 (tmm-80) REVERT: E 686 LEU cc_start: 0.7941 (pt) cc_final: 0.7697 (tt) REVERT: F 356 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7565 (mtmm) REVERT: F 547 MET cc_start: 0.7718 (tmm) cc_final: 0.7434 (tmm) REVERT: F 618 MET cc_start: 0.7621 (ttt) cc_final: 0.7102 (tpp) outliers start: 77 outliers final: 65 residues processed: 225 average time/residue: 0.1188 time to fit residues: 42.3147 Evaluate side-chains 223 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 589 SER 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 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU 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 531 ILE 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 B residue 669 LEU Chi-restraints excluded: chain B residue 689 THR 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 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 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 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 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: 10.0000 chunk 105 optimal weight: 0.2980 chunk 69 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.143724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.098825 restraints weight = 36648.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.101130 restraints weight = 22296.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103090 restraints weight = 13997.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103459 restraints weight = 13370.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103466 restraints weight = 11464.417| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17301 Z= 0.130 Angle : 0.598 11.433 23373 Z= 0.306 Chirality : 0.043 0.251 2631 Planarity : 0.004 0.037 2953 Dihedral : 8.346 162.407 2307 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.88 % Allowed : 28.41 % Favored : 67.71 % 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: -0.92 (0.19), residues: 2049 helix: 0.87 (0.20), residues: 723 sheet: -1.57 (0.35), residues: 247 loop : -1.43 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.031 0.001 TYR F 482 PHE 0.011 0.001 PHE F 501 TRP 0.063 0.002 TRP F 675 HIS 0.008 0.001 HIS E 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (17301) covalent geometry : angle 0.59838 / 0.31 (23373) hydrogen bonds : bond 0.03128 / 2.02 ( 546) hydrogen bonds : angle 4.41451 / 3.08 ( 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 226 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 152 time to evaluate : 0.552 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: A 489 CYS cc_start: 0.9011 (m) cc_final: 0.8406 (t) REVERT: B 374 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: B 382 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: B 447 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8225 (t70) REVERT: B 618 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7107 (mpp) REVERT: B 689 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7211 (p) REVERT: C 462 MET cc_start: 0.8208 (tpp) cc_final: 0.7943 (mpp) REVERT: C 618 MET cc_start: 0.9135 (ptp) cc_final: 0.8086 (ptp) REVERT: D 543 PHE cc_start: 0.8030 (p90) cc_final: 0.7761 (p90) REVERT: D 658 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7612 (pttp) REVERT: D 660 GLN cc_start: 0.9060 (mp10) cc_final: 0.8770 (pp30) REVERT: E 421 ASP cc_start: 0.7545 (t0) cc_final: 0.7207 (p0) REVERT: E 597 HIS cc_start: 0.8078 (m170) cc_final: 0.7483 (m-70) REVERT: E 612 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7211 (tmm-80) REVERT: E 686 LEU cc_start: 0.7955 (pt) cc_final: 0.7724 (tt) REVERT: F 356 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7607 (mtmm) REVERT: F 405 GLU cc_start: 0.7212 (tp30) cc_final: 0.6985 (tp30) REVERT: F 547 MET cc_start: 0.7748 (tmm) cc_final: 0.7454 (tmm) REVERT: F 618 MET cc_start: 0.7601 (ttt) cc_final: 0.7114 (tpp) outliers start: 74 outliers final: 67 residues processed: 213 average time/residue: 0.1144 time to fit residues: 39.0421 Evaluate side-chains 224 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 589 SER 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 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU 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 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 689 THR 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 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 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 25 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 200 optimal weight: 30.0000 chunk 102 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** F 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097305 restraints weight = 36664.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.100521 restraints weight = 22108.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.102841 restraints weight = 13876.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103067 restraints weight = 11844.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.103287 restraints weight = 11663.718| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17301 Z= 0.118 Angle : 0.586 10.920 23373 Z= 0.298 Chirality : 0.043 0.254 2631 Planarity : 0.004 0.036 2953 Dihedral : 8.326 161.969 2307 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.04 % Allowed : 28.14 % Favored : 67.82 % 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: -0.86 (0.19), residues: 2049 helix: 0.94 (0.20), residues: 722 sheet: -1.45 (0.34), residues: 252 loop : -1.42 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.031 0.001 TYR F 482 PHE 0.022 0.001 PHE F 501 TRP 0.060 0.002 TRP F 675 HIS 0.006 0.001 HIS E 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17301) covalent geometry : angle 0.58603 / 0.30 (23373) hydrogen bonds : bond 0.02919 / 1.89 ( 546) hydrogen bonds : angle 4.33063 / 3.02 ( 1533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.15 seconds wall clock time: 49 minutes 48.12 seconds (2988.12 seconds total)