Starting phenix.real_space_refine on Mon Nov 18 17:12:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/11_2024/8hwh_35058.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/11_2024/8hwh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/11_2024/8hwh_35058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/11_2024/8hwh_35058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/11_2024/8hwh_35058.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwh_35058/11_2024/8hwh_35058.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 10.52, per 1000 atoms: 0.62 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: 4.46 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.08 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: 5.06 Time building geometry restraints manager: 4.97 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=" 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=" 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 bond pdb=" N ASP A 522 " pdb=" CA ASP A 522 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.17e+00 bond pdb=" N LEU D 532 " pdb=" CA LEU D 532 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.26e+00 ... (remaining 17296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22863 2.09 - 4.19: 438 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=" C SER B 556 " pdb=" N GLU B 557 " pdb=" CA GLU B 557 " ideal model delta sigma weight residual 122.08 127.99 -5.91 1.47e+00 4.63e-01 1.62e+01 angle pdb=" CA MET E 462 " pdb=" CB MET E 462 " pdb=" CG MET E 462 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+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: 431 0.112 - 0.168: 39 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: 1.020 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: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.220 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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= 0.195 Angle : 0.708 10.467 23373 Z= 0.405 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (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 TRP 0.022 0.001 TRP A 675 HIS 0.005 0.001 HIS C 629 PHE 0.021 0.001 PHE C 357 TYR 0.014 0.001 TYR B 482 ARG 0.017 0.000 ARG B 479 *********************** 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 : 2.054 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: 0.3026 time to fit residues: 84.3563 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 : 2.209 ------------------------------------------------------------------------------- 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 173 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 478 ASN B 629 HIS C 529 GLN D 680 HIS E 358 ASN E 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17301 Z= 0.334 Angle : 0.641 7.215 23373 Z= 0.333 Chirality : 0.045 0.169 2631 Planarity : 0.004 0.050 2953 Dihedral : 8.474 161.777 2307 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.19 % Allowed : 26.31 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2049 helix: 0.35 (0.19), residues: 723 sheet: -1.82 (0.34), residues: 245 loop : -1.69 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP F 675 HIS 0.006 0.001 HIS D 347 PHE 0.018 0.001 PHE B 543 TYR 0.019 0.001 TYR F 482 ARG 0.008 0.001 ARG B 479 *********************** 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 251 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 171 time to evaluate : 2.220 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: 0.8000 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: C 474 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: C 554 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7914 (t80) REVERT: D 543 PHE cc_start: 0.7864 (p90) cc_final: 0.7380 (p90) REVERT: D 611 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7504 (p0) REVERT: D 658 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7621 (pttp) REVERT: E 547 MET cc_start: 0.8341 (tmm) cc_final: 0.8068 (ppp) REVERT: F 462 MET cc_start: 0.7141 (ptp) cc_final: 0.6816 (ptp) REVERT: F 547 MET cc_start: 0.7452 (tmm) cc_final: 0.7016 (tmm) outliers start: 80 outliers final: 46 residues processed: 235 average time/residue: 0.2858 time to fit residues: 104.1378 Evaluate side-chains 207 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 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 618 MET Chi-restraints excluded: chain B residue 659 ILE 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 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 606 TYR Chi-restraints excluded: chain D residue 609 VAL 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 103 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN B 662 ASN F 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17301 Z= 0.282 Angle : 0.587 6.959 23373 Z= 0.306 Chirality : 0.043 0.170 2631 Planarity : 0.004 0.044 2953 Dihedral : 8.472 162.645 2307 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.35 % Allowed : 26.78 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2049 helix: 0.59 (0.19), residues: 714 sheet: -1.82 (0.34), residues: 245 loop : -1.62 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 675 HIS 0.004 0.001 HIS D 680 PHE 0.020 0.001 PHE B 543 TYR 0.020 0.001 TYR F 482 ARG 0.005 0.000 ARG B 479 *********************** 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 253 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 170 time to evaluate : 2.054 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: 0.8029 (ppp) cc_final: 0.7526 (ppp) REVERT: A 590 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.6785 (t0) REVERT: B 374 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7132 (mp10) REVERT: B 382 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: B 447 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8182 (t70) REVERT: B 618 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7073 (mpp) REVERT: C 474 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: C 554 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7722 (t80) REVERT: D 543 PHE cc_start: 0.8012 (p90) cc_final: 0.7491 (p90) REVERT: E 421 ASP cc_start: 0.7690 (t0) cc_final: 0.7227 (p0) REVERT: E 547 MET cc_start: 0.8419 (tmm) cc_final: 0.8130 (ppp) REVERT: E 548 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.4659 (t70) REVERT: E 612 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7081 (tmm-80) REVERT: F 388 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8207 (mttp) REVERT: F 486 LEU cc_start: 0.9488 (mt) cc_final: 0.9250 (mp) REVERT: F 547 MET cc_start: 0.7640 (tmm) cc_final: 0.7220 (tmm) outliers start: 83 outliers final: 50 residues processed: 238 average time/residue: 0.2790 time to fit residues: 101.9458 Evaluate side-chains 218 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 159 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 513 LYS 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 569 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 658 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 618 MET Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 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 388 LYS Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17301 Z= 0.206 Angle : 0.552 8.867 23373 Z= 0.288 Chirality : 0.042 0.180 2631 Planarity : 0.004 0.040 2953 Dihedral : 8.385 162.537 2307 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.35 % Allowed : 27.57 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2049 helix: 0.76 (0.20), residues: 716 sheet: -1.72 (0.34), residues: 247 loop : -1.56 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 675 HIS 0.003 0.001 HIS A 548 PHE 0.011 0.001 PHE B 543 TYR 0.016 0.001 TYR F 482 ARG 0.004 0.000 ARG D 627 *********************** 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 263 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 180 time to evaluate : 2.300 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: symmetry clash REVERT: A 547 MET cc_start: 0.7957 (ppp) cc_final: 0.7502 (ppp) REVERT: B 382 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: B 534 ASP cc_start: 0.8149 (t0) cc_final: 0.7934 (t0) REVERT: B 594 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7937 (m110) REVERT: B 603 ASP cc_start: 0.7309 (t70) cc_final: 0.7095 (t70) REVERT: B 618 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: D 543 PHE cc_start: 0.8056 (p90) cc_final: 0.7540 (p90) REVERT: D 611 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7577 (p0) REVERT: D 658 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7651 (pttp) REVERT: E 421 ASP cc_start: 0.7598 (t0) cc_final: 0.7173 (p0) REVERT: E 612 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7122 (tmm-80) REVERT: F 405 GLU cc_start: 0.7810 (mp0) cc_final: 0.7550 (mp0) REVERT: F 486 LEU cc_start: 0.9413 (mt) cc_final: 0.9173 (mp) REVERT: F 547 MET cc_start: 0.7718 (tmm) cc_final: 0.7313 (tmm) outliers start: 83 outliers final: 59 residues processed: 248 average time/residue: 0.2903 time to fit residues: 110.1739 Evaluate side-chains 226 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 346 ASP 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 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 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 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 497 CYS 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 611 ASP 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 659 ILE 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 659 ILE 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 618 MET 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 165 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17301 Z= 0.416 Angle : 0.683 8.068 23373 Z= 0.352 Chirality : 0.046 0.175 2631 Planarity : 0.004 0.043 2953 Dihedral : 8.689 163.680 2307 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.39 % Allowed : 26.52 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2049 helix: 0.37 (0.19), residues: 729 sheet: -1.74 (0.33), residues: 257 loop : -1.66 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP F 675 HIS 0.005 0.001 HIS D 347 PHE 0.017 0.002 PHE B 444 TYR 0.016 0.002 TYR B 482 ARG 0.011 0.001 ARG D 619 *********************** 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 291 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 169 time to evaluate : 2.432 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 343 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: A 411 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8044 (p0) REVERT: A 489 CYS cc_start: 0.9041 (m) cc_final: 0.8451 (t) REVERT: A 547 MET cc_start: 0.8080 (ppp) cc_final: 0.7575 (ppp) REVERT: A 590 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7042 (t0) REVERT: A 602 ILE cc_start: 0.9294 (mm) cc_final: 0.9080 (mm) REVERT: B 374 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: B 382 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: B 532 LEU cc_start: 0.8589 (tp) cc_final: 0.8206 (tp) REVERT: B 534 ASP cc_start: 0.8135 (t0) cc_final: 0.7840 (t0) REVERT: C 474 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7558 (pp20) REVERT: C 554 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7644 (t80) REVERT: D 543 PHE cc_start: 0.8081 (p90) cc_final: 0.7731 (p90) REVERT: D 658 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7908 (pttm) REVERT: D 660 GLN cc_start: 0.9119 (mp10) cc_final: 0.8855 (pp30) REVERT: E 612 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7159 (tmm-80) REVERT: E 658 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7012 (ptpp) REVERT: F 407 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: F 486 LEU cc_start: 0.9480 (mt) cc_final: 0.9232 (mm) outliers start: 122 outliers final: 80 residues processed: 274 average time/residue: 0.2958 time to fit residues: 126.7031 Evaluate side-chains 244 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 154 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 422 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 527 THR 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 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 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 351 ILE 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 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 555 CYS 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 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 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU 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 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 695 ASP 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 516 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 658 LYS Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 439 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 198 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN B 478 ASN B 594 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17301 Z= 0.158 Angle : 0.560 9.284 23373 Z= 0.290 Chirality : 0.042 0.188 2631 Planarity : 0.004 0.038 2953 Dihedral : 8.401 162.709 2307 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.94 % Allowed : 29.77 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 2049 helix: 0.89 (0.20), residues: 719 sheet: -1.57 (0.34), residues: 255 loop : -1.48 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP F 675 HIS 0.002 0.000 HIS C 680 PHE 0.013 0.001 PHE F 501 TYR 0.014 0.001 TYR B 482 ARG 0.005 0.000 ARG B 479 *********************** 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 226 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 2.081 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: A 343 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7788 (tp30) REVERT: A 547 MET cc_start: 0.7922 (ppp) cc_final: 0.7552 (ppp) REVERT: A 602 ILE cc_start: 0.9334 (mm) cc_final: 0.9133 (mm) REVERT: B 374 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: B 382 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: B 534 ASP cc_start: 0.8238 (t0) cc_final: 0.7900 (t0) REVERT: B 618 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7258 (mpp) REVERT: B 689 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7217 (p) REVERT: C 458 MET cc_start: 0.7644 (tpt) cc_final: 0.7320 (tpt) REVERT: D 543 PHE cc_start: 0.8052 (p90) cc_final: 0.7800 (p90) REVERT: D 658 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7669 (pttp) REVERT: D 660 GLN cc_start: 0.9097 (mp10) cc_final: 0.8871 (pp30) REVERT: E 597 HIS cc_start: 0.8117 (m170) cc_final: 0.7504 (m-70) REVERT: E 612 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7115 (tmm-80) REVERT: F 356 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7534 (mtmm) REVERT: F 482 TYR cc_start: 0.8771 (t80) cc_final: 0.8554 (t80) REVERT: F 486 LEU cc_start: 0.9450 (mt) cc_final: 0.9221 (mm) REVERT: F 547 MET cc_start: 0.7812 (tmm) cc_final: 0.7489 (tmm) outliers start: 56 outliers final: 41 residues processed: 216 average time/residue: 0.2905 time to fit residues: 96.0373 Evaluate side-chains 201 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 351 ILE 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 574 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU 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 689 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 558 LEU 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 E residue 349 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17301 Z= 0.241 Angle : 0.592 10.016 23373 Z= 0.305 Chirality : 0.043 0.182 2631 Planarity : 0.004 0.041 2953 Dihedral : 8.442 163.416 2307 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.04 % Allowed : 28.93 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 2049 helix: 0.83 (0.20), residues: 721 sheet: -1.51 (0.33), residues: 260 loop : -1.48 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.003 TRP F 675 HIS 0.005 0.001 HIS E 680 PHE 0.011 0.001 PHE B 543 TYR 0.017 0.001 TYR E 664 ARG 0.009 0.000 ARG D 619 *********************** 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 239 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 162 time to evaluate : 2.033 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 343 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7779 (tp30) REVERT: A 489 CYS cc_start: 0.8975 (m) cc_final: 0.8506 (t) REVERT: A 547 MET cc_start: 0.7939 (ppp) cc_final: 0.7506 (ppp) REVERT: A 602 ILE cc_start: 0.9338 (mm) cc_final: 0.9115 (mm) REVERT: B 374 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: B 382 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: B 534 ASP cc_start: 0.8253 (t0) cc_final: 0.7858 (t0) REVERT: B 618 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7359 (mpp) REVERT: D 543 PHE cc_start: 0.8046 (p90) cc_final: 0.7795 (p90) REVERT: D 658 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7696 (pttp) REVERT: D 660 GLN cc_start: 0.9148 (mp10) cc_final: 0.8946 (pp30) REVERT: E 597 HIS cc_start: 0.8150 (m170) cc_final: 0.7541 (m-70) REVERT: E 612 ARG cc_start: 0.7661 (mtm110) cc_final: 0.7104 (tmm-80) REVERT: E 658 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7070 (ptpp) REVERT: F 486 LEU cc_start: 0.9441 (mt) cc_final: 0.9184 (mm) REVERT: F 501 PHE cc_start: 0.7780 (m-80) cc_final: 0.7315 (m-10) REVERT: F 532 LEU cc_start: 0.7895 (tp) cc_final: 0.7339 (pp) outliers start: 77 outliers final: 56 residues processed: 228 average time/residue: 0.2861 time to fit residues: 102.0277 Evaluate side-chains 216 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 154 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLU 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 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 375 LEU Chi-restraints excluded: chain B residue 382 GLU 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 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 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 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 628 THR 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 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 658 LYS Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 393 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 596 ASN ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17301 Z= 0.322 Angle : 0.640 9.991 23373 Z= 0.327 Chirality : 0.044 0.185 2631 Planarity : 0.004 0.047 2953 Dihedral : 8.601 163.797 2307 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.56 % Allowed : 28.09 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 2049 helix: 0.61 (0.20), residues: 735 sheet: -1.61 (0.33), residues: 260 loop : -1.57 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP F 675 HIS 0.008 0.001 HIS E 680 PHE 0.017 0.001 PHE E 668 TYR 0.021 0.001 TYR F 482 ARG 0.007 0.000 ARG F 514 *********************** 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 243 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 156 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7784 (tp30) REVERT: A 489 CYS cc_start: 0.9040 (m) cc_final: 0.8568 (t) REVERT: A 547 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7563 (ppp) REVERT: A 602 ILE cc_start: 0.9328 (mm) cc_final: 0.9099 (mm) REVERT: B 374 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7211 (mp10) REVERT: B 382 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: B 481 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8984 (tt) REVERT: B 534 ASP cc_start: 0.8267 (t0) cc_final: 0.7888 (t0) REVERT: D 543 PHE cc_start: 0.8014 (p90) cc_final: 0.7770 (p90) REVERT: D 658 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7752 (pttp) REVERT: D 660 GLN cc_start: 0.9190 (mp10) cc_final: 0.8981 (mp10) REVERT: E 360 GLU cc_start: 0.7159 (pm20) cc_final: 0.6945 (pm20) REVERT: E 597 HIS cc_start: 0.8171 (m170) cc_final: 0.7534 (m-70) REVERT: E 612 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7124 (tmm-80) REVERT: E 658 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7085 (ptpp) REVERT: F 390 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7933 (mptt) REVERT: F 491 CYS cc_start: 0.8439 (m) cc_final: 0.8180 (m) REVERT: F 532 LEU cc_start: 0.8113 (tp) cc_final: 0.7610 (pp) REVERT: F 547 MET cc_start: 0.7732 (tmm) cc_final: 0.7499 (tmm) REVERT: F 618 MET cc_start: 0.7531 (ttt) cc_final: 0.6903 (tpp) outliers start: 87 outliers final: 61 residues processed: 233 average time/residue: 0.2596 time to fit residues: 96.2585 Evaluate side-chains 218 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLU 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 527 THR 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 547 MET Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 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 481 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU 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 360 GLU 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 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 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 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 380 SER Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 658 LYS Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain F residue 393 GLU 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 189 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 144 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN F 475 ASN F 680 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17301 Z= 0.205 Angle : 0.592 10.591 23373 Z= 0.304 Chirality : 0.043 0.172 2631 Planarity : 0.004 0.044 2953 Dihedral : 8.413 163.331 2305 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.77 % Allowed : 28.88 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 2049 helix: 0.69 (0.20), residues: 735 sheet: -1.55 (0.33), residues: 257 loop : -1.54 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.003 TRP F 675 HIS 0.006 0.001 HIS E 680 PHE 0.015 0.001 PHE E 668 TYR 0.020 0.001 TYR F 482 ARG 0.007 0.000 ARG D 619 *********************** 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 228 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 156 time to evaluate : 2.166 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: A 489 CYS cc_start: 0.8981 (m) cc_final: 0.8509 (t) REVERT: A 547 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7526 (ppp) REVERT: A 602 ILE cc_start: 0.9342 (mm) cc_final: 0.9115 (mm) REVERT: B 374 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: B 382 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: B 481 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8925 (tt) REVERT: B 534 ASP cc_start: 0.8212 (t0) cc_final: 0.7932 (t0) REVERT: B 618 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7322 (mpp) REVERT: D 543 PHE cc_start: 0.8003 (p90) cc_final: 0.7739 (p90) REVERT: D 658 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7803 (pttp) REVERT: E 547 MET cc_start: 0.8599 (tmm) cc_final: 0.8364 (tmm) REVERT: E 597 HIS cc_start: 0.8155 (m170) cc_final: 0.7657 (m-70) REVERT: E 612 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7081 (tmm-80) REVERT: F 390 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7827 (mptt) REVERT: F 501 PHE cc_start: 0.7663 (m-80) cc_final: 0.7247 (m-10) REVERT: F 532 LEU cc_start: 0.8136 (tp) cc_final: 0.7681 (pp) REVERT: F 547 MET cc_start: 0.7771 (tmm) cc_final: 0.7546 (tmm) REVERT: F 618 MET cc_start: 0.7632 (ttt) cc_final: 0.7000 (tpp) outliers start: 72 outliers final: 57 residues processed: 219 average time/residue: 0.2808 time to fit residues: 96.2039 Evaluate side-chains 215 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 669 LEU 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 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 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 612 ARG 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 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 436 TYR Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 554 PHE 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 380 SER Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain F residue 393 GLU 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 194 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 162 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 597 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 17301 Z= 0.422 Angle : 0.719 11.314 23373 Z= 0.369 Chirality : 0.046 0.202 2631 Planarity : 0.004 0.056 2953 Dihedral : 8.623 164.584 2303 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.04 % Allowed : 28.56 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2049 helix: 0.29 (0.19), residues: 720 sheet: -1.66 (0.33), residues: 257 loop : -1.59 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.137 0.004 TRP F 675 HIS 0.007 0.001 HIS E 680 PHE 0.017 0.002 PHE B 543 TYR 0.041 0.002 TYR F 482 ARG 0.006 0.001 ARG F 514 ********************** 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 236 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 159 time to evaluate : 2.119 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: 0.9026 (m) cc_final: 0.8659 (t) REVERT: A 547 MET cc_start: 0.8031 (ppp) cc_final: 0.7525 (ppp) REVERT: A 602 ILE cc_start: 0.9323 (mm) cc_final: 0.9112 (mm) REVERT: B 374 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: B 382 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: B 481 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9102 (tt) REVERT: B 534 ASP cc_start: 0.7935 (t0) cc_final: 0.7622 (t0) REVERT: D 543 PHE cc_start: 0.8027 (p90) cc_final: 0.7754 (p90) REVERT: D 658 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7678 (pttp) REVERT: E 612 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7105 (tmm-80) REVERT: E 658 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6986 (ptpp) REVERT: F 390 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7983 (mptt) REVERT: F 532 LEU cc_start: 0.8261 (tp) cc_final: 0.7875 (pp) REVERT: F 547 MET cc_start: 0.7799 (tmm) cc_final: 0.7549 (tmm) REVERT: F 618 MET cc_start: 0.7710 (ttt) cc_final: 0.7189 (tpp) REVERT: F 675 TRP cc_start: 0.7815 (m100) cc_final: 0.7544 (t60) outliers start: 77 outliers final: 66 residues processed: 229 average time/residue: 0.2783 time to fit residues: 99.9163 Evaluate side-chains 220 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 148 time to evaluate : 3.224 ------------------------------------------------------------------------------- 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 527 THR 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 569 ILE 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 346 ASP 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 468 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU 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 507 THR 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 360 GLU 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 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 612 ARG 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 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 380 SER Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 658 LYS Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 390 LYS Chi-restraints excluded: chain F residue 393 GLU 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 173 optimal weight: 9.9990 chunk 49 optimal weight: 30.0000 chunk 149 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 162 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 ASN E 548 HIS E 680 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.142986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099975 restraints weight = 36609.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100455 restraints weight = 23359.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101749 restraints weight = 16337.131| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17301 Z= 0.169 Angle : 0.602 10.754 23373 Z= 0.311 Chirality : 0.043 0.200 2631 Planarity : 0.004 0.046 2953 Dihedral : 8.383 163.363 2303 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.04 % Allowed : 29.77 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 2049 helix: 0.70 (0.20), residues: 725 sheet: -1.56 (0.33), residues: 257 loop : -1.45 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.003 TRP F 675 HIS 0.006 0.001 HIS E 680 PHE 0.015 0.001 PHE D 696 TYR 0.014 0.001 TYR C 482 ARG 0.011 0.000 ARG B 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.48 seconds wall clock time: 58 minutes 41.38 seconds (3521.38 seconds total)