Starting phenix.real_space_refine on Sun Jun 15 06:18:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwh_35058/06_2025/8hwh_35058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwh_35058/06_2025/8hwh_35058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwh_35058/06_2025/8hwh_35058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwh_35058/06_2025/8hwh_35058.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwh_35058/06_2025/8hwh_35058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwh_35058/06_2025/8hwh_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-5710/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: 10.95, per 1000 atoms: 0.65 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: 4.49 Conformation dependent library (CDL) restraints added in 2.3 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: 2.07 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: 5.30 Time building geometry restraints manager: 5.39 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: 1.220 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 40.970 Find NCS groups from input model: 0.940 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.090 ------------------------------------------------------------------------------- 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= 0.155 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 Details of bonding type rmsd hydrogen bonds : bond 0.18339 ( 546) hydrogen bonds : angle 6.55138 ( 1533) covalent geometry : bond 0.00309 (17301) covalent geometry : angle 0.70824 (23373) *********************** 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 : 2.075 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: 0.2937 time to fit residues: 82.5031 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 : 2.095 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.143094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097606 restraints weight = 36807.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099528 restraints weight = 21673.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.099430 restraints weight = 14507.968| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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= 0.215 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 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 546) hydrogen bonds : angle 5.19511 ( 1533) covalent geometry : bond 0.00515 (17301) covalent geometry : angle 0.64110 (23373) *********************** 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 : 2.146 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: 0.7993 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: C 474 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7416 (pp20) REVERT: C 554 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7908 (t80) REVERT: D 543 PHE cc_start: 0.7945 (p90) cc_final: 0.7462 (p90) REVERT: D 611 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7545 (p0) REVERT: D 658 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7659 (pttp) REVERT: E 547 MET cc_start: 0.8367 (tmm) cc_final: 0.8069 (ppp) REVERT: F 462 MET cc_start: 0.7141 (ptp) cc_final: 0.6813 (ptp) REVERT: F 547 MET cc_start: 0.7481 (tmm) cc_final: 0.7047 (tmm) outliers start: 80 outliers final: 46 residues processed: 235 average time/residue: 0.2805 time to fit residues: 102.9963 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 : 2.232 ------------------------------------------------------------------------------- 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 202 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN D 680 HIS F 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.145676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102340 restraints weight = 36653.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102623 restraints weight = 20644.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102828 restraints weight = 15978.216| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17301 Z= 0.115 Angle : 0.541 6.850 23373 Z= 0.283 Chirality : 0.042 0.171 2631 Planarity : 0.003 0.042 2953 Dihedral : 8.319 162.202 2307 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.41 % Allowed : 27.20 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.10 (0.18), residues: 2049 helix: 0.78 (0.20), residues: 714 sheet: -1.75 (0.34), residues: 245 loop : -1.55 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 675 HIS 0.003 0.001 HIS F 548 PHE 0.018 0.001 PHE B 543 TYR 0.019 0.001 TYR F 482 ARG 0.005 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 546) hydrogen bonds : angle 4.58377 ( 1533) covalent geometry : bond 0.00273 (17301) covalent geometry : angle 0.54061 (23373) *********************** 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 242 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 2.197 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: 0.8002 (ppp) cc_final: 0.7529 (ppp) REVERT: A 590 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.6811 (t0) REVERT: B 382 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: B 618 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6935 (mpp) REVERT: D 543 PHE cc_start: 0.8134 (p90) cc_final: 0.7569 (p90) REVERT: E 547 MET cc_start: 0.8361 (tmm) cc_final: 0.8115 (ppp) REVERT: E 612 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7160 (tmm-80) REVERT: F 547 MET cc_start: 0.7613 (tmm) cc_final: 0.7154 (tmm) outliers start: 65 outliers final: 42 residues processed: 229 average time/residue: 0.2884 time to fit residues: 101.4183 Evaluate side-chains 211 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 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 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 351 ILE 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 177 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 66 optimal weight: 0.0170 chunk 138 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN A 590 ASN B 662 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.144641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097263 restraints weight = 36650.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100697 restraints weight = 20484.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102981 restraints weight = 14313.827| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1915 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= 0.137 Angle : 0.550 9.078 23373 Z= 0.286 Chirality : 0.042 0.158 2631 Planarity : 0.004 0.042 2953 Dihedral : 8.310 162.533 2307 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.35 % Allowed : 27.20 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.04 (0.18), residues: 2049 helix: 0.83 (0.20), residues: 717 sheet: -1.67 (0.35), residues: 241 loop : -1.53 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 PHE 0.012 0.001 PHE B 543 TYR 0.039 0.001 TYR F 482 ARG 0.005 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 546) hydrogen bonds : angle 4.52227 ( 1533) covalent geometry : bond 0.00327 (17301) covalent geometry : angle 0.55005 (23373) *********************** 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 257 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 174 time to evaluate : 2.140 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: 0.7847 (ppp) cc_final: 0.7391 (ppp) REVERT: A 590 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7089 (t0) REVERT: B 374 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: B 382 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: B 447 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8127 (t70) REVERT: B 618 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6916 (mpp) REVERT: D 543 PHE cc_start: 0.8041 (p90) cc_final: 0.7502 (p90) REVERT: D 658 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7415 (pttp) REVERT: D 684 MET cc_start: 0.8497 (tmm) cc_final: 0.8269 (tmm) REVERT: E 421 ASP cc_start: 0.7536 (t0) cc_final: 0.7192 (p0) REVERT: E 547 MET cc_start: 0.8420 (tmm) cc_final: 0.8125 (ppp) REVERT: E 612 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7126 (tmm-80) REVERT: F 547 MET cc_start: 0.7637 (tmm) cc_final: 0.7196 (tmm) outliers start: 83 outliers final: 58 residues processed: 243 average time/residue: 0.2763 time to fit residues: 104.9024 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 : 2.089 ------------------------------------------------------------------------------- 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 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 590 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU 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 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 435 LYS 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 582 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN D 680 HIS ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.143159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095679 restraints weight = 37033.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099047 restraints weight = 20783.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101271 restraints weight = 14587.559| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2235 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= 0.168 Angle : 0.579 7.364 23373 Z= 0.300 Chirality : 0.043 0.240 2631 Planarity : 0.004 0.038 2953 Dihedral : 8.380 162.749 2307 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.61 % Allowed : 27.31 % 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: -1.04 (0.18), residues: 2049 helix: 0.80 (0.20), residues: 718 sheet: -1.60 (0.34), residues: 247 loop : -1.52 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP F 675 HIS 0.004 0.001 HIS D 347 PHE 0.012 0.001 PHE B 444 TYR 0.034 0.001 TYR F 482 ARG 0.004 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 546) hydrogen bonds : angle 4.61247 ( 1533) covalent geometry : bond 0.00402 (17301) covalent geometry : angle 0.57893 (23373) *********************** 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 259 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 171 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7933 (ppp) cc_final: 0.7461 (ppp) REVERT: A 590 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7251 (t0) REVERT: A 618 MET cc_start: 0.7329 (ppp) cc_final: 0.7115 (ppp) REVERT: B 374 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: B 382 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: B 447 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8166 (t70) REVERT: B 618 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7011 (mpp) REVERT: C 458 MET cc_start: 0.7569 (tpt) cc_final: 0.7358 (tpt) REVERT: C 474 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7180 (pp20) REVERT: C 618 MET cc_start: 0.8553 (ptt) cc_final: 0.8180 (ptt) REVERT: D 543 PHE cc_start: 0.8061 (p90) cc_final: 0.7561 (p90) REVERT: D 658 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7471 (pttp) REVERT: E 421 ASP cc_start: 0.7554 (t0) cc_final: 0.7200 (p0) REVERT: E 612 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7122 (tmm-80) outliers start: 88 outliers final: 64 residues processed: 243 average time/residue: 0.2774 time to fit residues: 103.5975 Evaluate side-chains 235 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 164 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain 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 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 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 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 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 63 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 116 optimal weight: 0.3980 chunk 202 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 30 optimal weight: 30.0000 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.142099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095963 restraints weight = 37110.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098744 restraints weight = 21274.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100162 restraints weight = 14047.113| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2496 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= 0.171 Angle : 0.583 6.778 23373 Z= 0.302 Chirality : 0.043 0.199 2631 Planarity : 0.004 0.041 2953 Dihedral : 8.405 162.879 2307 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.98 % Allowed : 26.94 % 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: -1.02 (0.19), residues: 2049 helix: 0.75 (0.20), residues: 719 sheet: -1.56 (0.35), residues: 246 loop : -1.47 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 PHE 0.012 0.001 PHE B 444 TYR 0.027 0.001 TYR F 482 ARG 0.007 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 546) hydrogen bonds : angle 4.61706 ( 1533) covalent geometry : bond 0.00408 (17301) covalent geometry : angle 0.58342 (23373) *********************** 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 257 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 162 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 CYS cc_start: 0.9041 (m) cc_final: 0.8416 (t) REVERT: A 547 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7520 (ppp) REVERT: A 590 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.6947 (t0) REVERT: B 374 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: B 382 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: B 447 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8200 (t70) REVERT: B 594 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7876 (m110) REVERT: B 618 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7324 (mpp) REVERT: B 689 THR cc_start: 0.7516 (OUTLIER) cc_final: 0.7216 (p) REVERT: C 426 MET cc_start: 0.6533 (mtm) cc_final: 0.6284 (ptm) REVERT: C 474 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7415 (pp20) REVERT: D 543 PHE cc_start: 0.8082 (p90) cc_final: 0.7779 (p90) REVERT: D 658 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7607 (pttp) REVERT: D 660 GLN cc_start: 0.9077 (mp10) cc_final: 0.8864 (pp30) REVERT: E 421 ASP cc_start: 0.7619 (t0) cc_final: 0.7209 (p0) REVERT: E 612 ARG cc_start: 0.7708 (mtm110) cc_final: 0.7169 (tmm-80) REVERT: F 356 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7621 (mtmm) outliers start: 95 outliers final: 69 residues processed: 241 average time/residue: 0.3191 time to fit residues: 119.3247 Evaluate side-chains 236 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 156 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 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 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain 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 527 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 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 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 27 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 198 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 475 ASN F 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.144259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098232 restraints weight = 36541.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101868 restraints weight = 20717.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.104589 restraints weight = 12254.332| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2581 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= 0.107 Angle : 0.559 10.499 23373 Z= 0.287 Chirality : 0.042 0.206 2631 Planarity : 0.003 0.039 2953 Dihedral : 8.297 162.693 2307 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.14 % Allowed : 27.73 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.93 (0.19), residues: 2049 helix: 0.80 (0.20), residues: 728 sheet: -1.54 (0.36), residues: 241 loop : -1.42 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP F 675 HIS 0.002 0.000 HIS A 548 PHE 0.010 0.001 PHE B 543 TYR 0.027 0.001 TYR F 482 ARG 0.006 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 546) hydrogen bonds : angle 4.34389 ( 1533) covalent geometry : bond 0.00252 (17301) covalent geometry : angle 0.55905 (23373) *********************** 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 248 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 169 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7461 (ppp) REVERT: B 374 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: B 382 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: B 447 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8158 (t70) REVERT: B 594 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7889 (m110) REVERT: B 618 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6941 (mpp) REVERT: C 462 MET cc_start: 0.8704 (tpp) cc_final: 0.8473 (mmm) REVERT: C 618 MET cc_start: 0.8535 (ptt) cc_final: 0.7922 (ptt) REVERT: D 543 PHE cc_start: 0.8062 (p90) cc_final: 0.7809 (p90) REVERT: D 658 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7621 (pttp) REVERT: E 421 ASP cc_start: 0.7511 (t0) cc_final: 0.7170 (p0) REVERT: E 612 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7263 (tmm-80) REVERT: E 658 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6999 (ptpp) REVERT: F 356 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7487 (mtmm) REVERT: F 462 MET cc_start: 0.7437 (ptp) cc_final: 0.7148 (ptp) REVERT: F 547 MET cc_start: 0.7653 (tmm) cc_final: 0.7386 (tmm) REVERT: F 618 MET cc_start: 0.7577 (ttt) cc_final: 0.7051 (tpp) outliers start: 79 outliers final: 58 residues processed: 234 average time/residue: 0.3715 time to fit residues: 133.2361 Evaluate side-chains 228 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 2.418 ------------------------------------------------------------------------------- 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 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 538 LYS Chi-restraints excluded: chain A residue 544 ILE 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 A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 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 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 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 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER 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 45 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 200 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 529 GLN F 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092594 restraints weight = 36779.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096023 restraints weight = 20249.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098291 restraints weight = 14090.344| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17301 Z= 0.220 Angle : 0.652 9.503 23373 Z= 0.333 Chirality : 0.044 0.185 2631 Planarity : 0.004 0.046 2953 Dihedral : 8.500 163.738 2307 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.61 % Allowed : 27.67 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2049 helix: 0.54 (0.19), residues: 732 sheet: -1.52 (0.33), residues: 262 loop : -1.49 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP F 675 HIS 0.005 0.001 HIS D 680 PHE 0.014 0.001 PHE B 444 TYR 0.030 0.002 TYR F 482 ARG 0.011 0.001 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 546) hydrogen bonds : angle 4.78073 ( 1533) covalent geometry : bond 0.00530 (17301) covalent geometry : angle 0.65222 (23373) *********************** 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 255 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 167 time to evaluate : 3.111 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 489 CYS cc_start: 0.9058 (m) cc_final: 0.8542 (t) REVERT: A 547 MET cc_start: 0.7997 (ppp) cc_final: 0.7523 (ppp) REVERT: B 374 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: B 382 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: B 481 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8985 (tt) REVERT: B 618 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7307 (mpp) REVERT: C 618 MET cc_start: 0.8492 (ptt) cc_final: 0.7938 (ptt) REVERT: D 543 PHE cc_start: 0.8046 (p90) cc_final: 0.7797 (p90) REVERT: D 658 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7449 (pttp) REVERT: E 421 ASP cc_start: 0.7613 (t0) cc_final: 0.7242 (p0) REVERT: E 597 HIS cc_start: 0.8107 (m170) cc_final: 0.7492 (m-70) REVERT: E 612 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7168 (tmm-80) REVERT: E 658 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7050 (ptpp) REVERT: F 356 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7682 (mtmm) REVERT: F 547 MET cc_start: 0.7706 (tmm) cc_final: 0.7387 (tmm) REVERT: F 618 MET cc_start: 0.7656 (ttt) cc_final: 0.7167 (tpp) outliers start: 88 outliers final: 68 residues processed: 241 average time/residue: 0.3334 time to fit residues: 126.6134 Evaluate side-chains 232 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 157 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 461 LEU 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 531 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain 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 435 LYS 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 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 509 LYS 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 669 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 175 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 179 optimal weight: 0.0980 chunk 159 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 594 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN F 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.143299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097838 restraints weight = 36970.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100666 restraints weight = 22459.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.103478 restraints weight = 13594.308| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3001 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= 0.116 Angle : 0.583 9.924 23373 Z= 0.297 Chirality : 0.042 0.161 2631 Planarity : 0.003 0.043 2953 Dihedral : 8.382 162.896 2307 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.72 % Allowed : 28.46 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.19), residues: 2049 helix: 0.81 (0.20), residues: 725 sheet: -1.48 (0.34), residues: 252 loop : -1.39 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP F 675 HIS 0.002 0.000 HIS D 347 PHE 0.018 0.001 PHE E 668 TYR 0.030 0.001 TYR F 482 ARG 0.007 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 546) hydrogen bonds : angle 4.34623 ( 1533) covalent geometry : bond 0.00276 (17301) covalent geometry : angle 0.58259 (23373) *********************** 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 233 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 162 time to evaluate : 2.980 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: 0.9051 (m) cc_final: 0.8525 (t) REVERT: A 547 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7521 (ppp) REVERT: B 374 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: B 382 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: B 481 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 532 LEU cc_start: 0.8610 (tp) cc_final: 0.8259 (tp) REVERT: B 618 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7225 (mpp) REVERT: C 458 MET cc_start: 0.7694 (tpt) cc_final: 0.7393 (tpt) REVERT: C 618 MET cc_start: 0.8533 (ptt) cc_final: 0.7915 (ptt) REVERT: D 543 PHE cc_start: 0.8088 (p90) cc_final: 0.7804 (p90) REVERT: D 658 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7748 (pttp) REVERT: E 421 ASP cc_start: 0.7555 (t0) cc_final: 0.7187 (p0) REVERT: E 547 MET cc_start: 0.8509 (tmm) cc_final: 0.8266 (tmm) REVERT: E 597 HIS cc_start: 0.8121 (m170) cc_final: 0.7509 (m-70) REVERT: E 612 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7115 (tmm-80) REVERT: E 684 MET cc_start: 0.6247 (tpt) cc_final: 0.5976 (tpt) REVERT: F 547 MET cc_start: 0.7820 (tmm) cc_final: 0.7537 (tmm) REVERT: F 618 MET cc_start: 0.7598 (ttt) cc_final: 0.7134 (tpp) outliers start: 71 outliers final: 60 residues processed: 222 average time/residue: 0.3502 time to fit residues: 124.4341 Evaluate side-chains 227 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 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 461 LEU 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 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 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 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 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 F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 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 95 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 166 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 6 optimal weight: 0.3980 chunk 30 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 C 605 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.142027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096916 restraints weight = 36801.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099554 restraints weight = 22278.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101310 restraints weight = 14476.828| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3177 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= 0.154 Angle : 0.613 11.765 23373 Z= 0.312 Chirality : 0.043 0.164 2631 Planarity : 0.004 0.045 2953 Dihedral : 8.421 163.660 2307 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.88 % Allowed : 28.51 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.94 (0.19), residues: 2049 helix: 0.77 (0.20), residues: 729 sheet: -1.49 (0.34), residues: 249 loop : -1.41 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP F 675 HIS 0.005 0.001 HIS E 548 PHE 0.016 0.001 PHE F 501 TYR 0.029 0.001 TYR F 482 ARG 0.008 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 546) hydrogen bonds : angle 4.48228 ( 1533) covalent geometry : bond 0.00371 (17301) covalent geometry : angle 0.61296 (23373) ********************** 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 234 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 160 time to evaluate : 2.021 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: 0.9058 (m) cc_final: 0.8555 (t) REVERT: A 547 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7513 (ppp) REVERT: B 374 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: B 382 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: B 481 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8937 (tt) REVERT: B 532 LEU cc_start: 0.8610 (tp) cc_final: 0.8276 (tp) REVERT: B 547 MET cc_start: 0.8226 (ptt) cc_final: 0.8017 (ptp) REVERT: B 618 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: C 458 MET cc_start: 0.7673 (tpt) cc_final: 0.7352 (tpt) REVERT: C 618 MET cc_start: 0.8594 (ptt) cc_final: 0.7951 (ptt) REVERT: D 543 PHE cc_start: 0.8102 (p90) cc_final: 0.7823 (p90) REVERT: D 658 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7660 (pttp) REVERT: E 421 ASP cc_start: 0.7585 (t0) cc_final: 0.7205 (p0) REVERT: E 597 HIS cc_start: 0.8141 (m170) cc_final: 0.7535 (m-70) REVERT: E 612 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7096 (tmm-80) REVERT: E 684 MET cc_start: 0.6436 (tpt) cc_final: 0.6130 (tpt) REVERT: F 501 PHE cc_start: 0.7666 (m-80) cc_final: 0.7333 (m-10) REVERT: F 532 LEU cc_start: 0.8053 (tp) cc_final: 0.7503 (pp) REVERT: F 547 MET cc_start: 0.7794 (tmm) cc_final: 0.7475 (tmm) REVERT: F 618 MET cc_start: 0.7578 (ttt) cc_final: 0.7254 (tpp) outliers start: 74 outliers final: 62 residues processed: 221 average time/residue: 0.2926 time to fit residues: 103.2595 Evaluate side-chains 221 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 153 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 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 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 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 461 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 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 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 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 509 LYS 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 669 LEU 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 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 73 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.143087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096345 restraints weight = 36405.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099915 restraints weight = 19741.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.102285 restraints weight = 13587.853| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3283 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= 0.132 Angle : 0.595 11.416 23373 Z= 0.303 Chirality : 0.042 0.169 2631 Planarity : 0.004 0.041 2953 Dihedral : 8.301 163.322 2305 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.72 % Allowed : 28.41 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.89 (0.19), residues: 2049 helix: 0.85 (0.20), residues: 731 sheet: -1.54 (0.35), residues: 240 loop : -1.39 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP F 675 HIS 0.003 0.001 HIS D 347 PHE 0.013 0.001 PHE F 501 TYR 0.029 0.001 TYR F 482 ARG 0.007 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 546) hydrogen bonds : angle 4.34564 ( 1533) covalent geometry : bond 0.00317 (17301) covalent geometry : angle 0.59473 (23373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6246.49 seconds wall clock time: 113 minutes 42.66 seconds (6822.66 seconds total)