Starting phenix.real_space_refine on Sun Aug 24 04:36:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwh_35058/08_2025/8hwh_35058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwh_35058/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hwh_35058/08_2025/8hwh_35058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwh_35058/08_2025/8hwh_35058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hwh_35058/08_2025/8hwh_35058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwh_35058/08_2025/8hwh_35058.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 93 5.16 5 C 10815 2.51 5 N 2867 2.21 5 O 3167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16948 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2858 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain breaks: 1 Chain: "B" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2887 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 1 Chain: "C" Number of atoms: 2920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2920 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2940 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 17, 'TRANS': 345} Chain breaks: 1 Chain: "E" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2662 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Chain: "F" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2561 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 14, 'TRANS': 301} Chain breaks: 3 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 4.10, per 1000 atoms: 0.24 Number of scatterers: 16948 At special positions: 0 Unit cell: (109.5, 131.4, 132.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 6 15.00 O 3167 8.00 N 2867 7.00 C 10815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 714.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 23 sheets defined 43.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.716A pdb=" N LEU A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.768A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 571 through 576 removed outlier: 4.000A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 571 through 576' Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.891A pdb=" N MET A 618 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.673A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 660' Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.701A pdb=" N LYS A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 removed outlier: 3.904A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.595A pdb=" N LEU B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.619A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.587A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.954A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.583A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 661' Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.829A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 679 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 692 Processing helix chain 'B' and resid 693 through 700 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.691A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.939A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.535A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.939A pdb=" N THR C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 removed outlier: 3.509A pdb=" N ASP C 432 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.506A pdb=" N LYS C 450 " --> pdb=" O ASP C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.884A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.592A pdb=" N THR C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.561A pdb=" N ASN C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 removed outlier: 4.010A pdb=" N PHE C 668 " --> pdb=" O TYR C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 700 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.539A pdb=" N ILE D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.741A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.600A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 472 through 475 Processing helix chain 'D' and resid 476 through 488 removed outlier: 3.519A pdb=" N TYR D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.603A pdb=" N ALA D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.660A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 577 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 removed outlier: 4.015A pdb=" N MET D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 614 through 619' Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.952A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 661' Processing helix chain 'D' and resid 665 through 680 Processing helix chain 'D' and resid 693 through 700 Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.578A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 400 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.575A pdb=" N ASP E 432 " --> pdb=" O SER E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 removed outlier: 4.008A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 528 through 533 removed outlier: 3.846A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 548 removed outlier: 4.187A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN E 546 " --> pdb=" O PRO E 542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS E 548 " --> pdb=" O ILE E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 614 through 619 removed outlier: 3.859A pdb=" N MET E 618 " --> pdb=" O ASP E 614 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 614 through 619' Processing helix chain 'E' and resid 657 through 661 removed outlier: 4.569A pdb=" N ASN E 661 " --> pdb=" O GLY E 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 657 through 661' Processing helix chain 'E' and resid 665 through 680 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.571A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 387 through 400 Processing helix chain 'F' and resid 429 through 434 Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.838A pdb=" N LYS F 450 " --> pdb=" O ASP F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 removed outlier: 3.882A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.745A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 520 Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.722A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 546 removed outlier: 4.045A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 578 removed outlier: 3.871A pdb=" N THR F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.626A pdb=" N MET F 618 " --> pdb=" O ASP F 614 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 614 through 619' Processing helix chain 'F' and resid 656 through 661 removed outlier: 4.027A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN F 661 " --> pdb=" O GLY F 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 656 through 661' Processing helix chain 'F' and resid 665 through 680 Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 602 removed outlier: 6.646A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.967A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 582 through 583 Processing sheet with id=AA6, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AA7, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.812A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.729A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AB2, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.861A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.940A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB5, first strand: chain 'D' and resid 349 through 350 Processing sheet with id=AB6, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.581A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.430A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AB9, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC1, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AC2, first strand: chain 'E' and resid 525 through 527 removed outlier: 6.447A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 340 through 341 Processing sheet with id=AC4, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AC5, first strand: chain 'F' and resid 525 through 527 removed outlier: 3.597A pdb=" N VAL F 553 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE F 601 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR F 499 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR F 604 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE F 501 " --> pdb=" O THR F 604 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.93 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.19), residues: 2049 helix: 0.57 (0.21), residues: 689 sheet: -1.64 (0.33), residues: 256 loop : -1.69 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 479 TYR 0.014 0.001 TYR B 482 PHE 0.021 0.001 PHE C 357 TRP 0.022 0.001 TRP A 675 HIS 0.005 0.001 HIS C 629 Details of bonding type rmsd covalent geometry : bond 0.00309 (17301) covalent geometry : angle 0.70824 (23373) hydrogen bonds : bond 0.18339 ( 546) hydrogen bonds : angle 6.55138 ( 1533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.663 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: 0.1321 time to fit residues: 37.0873 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 : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 ASN B 478 ASN B 629 HIS D 680 HIS E 358 ASN E 475 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.144219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096284 restraints weight = 36736.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099764 restraints weight = 20408.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101999 restraints weight = 14220.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103476 restraints weight = 11399.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104388 restraints weight = 9925.314| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17301 Z= 0.199 Angle : 0.623 7.320 23373 Z= 0.323 Chirality : 0.044 0.170 2631 Planarity : 0.004 0.049 2953 Dihedral : 8.427 161.793 2307 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.88 % Allowed : 26.42 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.18), residues: 2049 helix: 0.41 (0.19), residues: 723 sheet: -1.80 (0.34), residues: 245 loop : -1.67 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 479 TYR 0.020 0.001 TYR F 482 PHE 0.020 0.001 PHE B 543 TRP 0.027 0.002 TRP F 675 HIS 0.005 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00473 (17301) covalent geometry : angle 0.62303 (23373) hydrogen bonds : bond 0.04228 ( 546) hydrogen bonds : angle 5.12342 ( 1533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 171 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: B 618 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6970 (mpp) REVERT: C 474 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7113 (pp20) REVERT: C 554 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8017 (t80) REVERT: D 543 PHE cc_start: 0.7810 (p90) cc_final: 0.7332 (p90) REVERT: D 658 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7387 (pttp) REVERT: E 547 MET cc_start: 0.8282 (tmm) cc_final: 0.8054 (ppp) outliers start: 74 outliers final: 45 residues processed: 231 average time/residue: 0.1227 time to fit residues: 44.3320 Evaluate side-chains 204 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 C residue 351 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 187 optimal weight: 0.0370 chunk 114 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.146474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100736 restraints weight = 37029.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103863 restraints weight = 20815.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105384 restraints weight = 12906.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105277 restraints weight = 13279.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.105432 restraints weight = 11724.324| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17301 Z= 0.105 Angle : 0.535 6.984 23373 Z= 0.280 Chirality : 0.041 0.180 2631 Planarity : 0.003 0.042 2953 Dihedral : 8.273 161.975 2307 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.20 % Allowed : 26.78 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.18), residues: 2049 helix: 0.80 (0.20), residues: 715 sheet: -1.71 (0.34), residues: 241 loop : -1.52 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 479 TYR 0.016 0.001 TYR F 482 PHE 0.016 0.001 PHE B 543 TRP 0.036 0.001 TRP F 675 HIS 0.003 0.000 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00244 (17301) covalent geometry : angle 0.53489 (23373) hydrogen bonds : bond 0.03140 ( 546) hydrogen bonds : angle 4.53336 ( 1533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 0.466 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: 0.8034 (ppp) cc_final: 0.7523 (ppp) REVERT: A 590 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.6858 (t0) REVERT: B 382 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: B 618 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6898 (mpp) REVERT: D 543 PHE cc_start: 0.8127 (p90) cc_final: 0.7539 (p90) REVERT: D 611 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7554 (p0) REVERT: E 547 MET cc_start: 0.8447 (tmm) cc_final: 0.8110 (ppp) REVERT: E 612 ARG cc_start: 0.7760 (mtm110) cc_final: 0.7116 (tmm-80) REVERT: F 547 MET cc_start: 0.7521 (tmm) cc_final: 0.7120 (tmm) outliers start: 61 outliers final: 39 residues processed: 224 average time/residue: 0.1212 time to fit residues: 42.7120 Evaluate side-chains 211 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 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 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 611 ASP Chi-restraints excluded: chain E residue 346 ASP 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 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 167 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 92 optimal weight: 0.0270 chunk 155 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 chunk 86 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.146324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099405 restraints weight = 36886.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.103033 restraints weight = 20048.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105133 restraints weight = 13783.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106781 restraints weight = 11042.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107654 restraints weight = 9564.684| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17301 Z= 0.101 Angle : 0.521 9.204 23373 Z= 0.271 Chirality : 0.041 0.172 2631 Planarity : 0.003 0.042 2953 Dihedral : 8.198 162.073 2307 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.56 % Allowed : 27.04 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.19), residues: 2049 helix: 0.96 (0.20), residues: 717 sheet: -1.58 (0.35), residues: 242 loop : -1.45 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 479 TYR 0.041 0.001 TYR F 482 PHE 0.008 0.001 PHE B 444 TRP 0.043 0.001 TRP F 675 HIS 0.002 0.000 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00234 (17301) covalent geometry : angle 0.52111 (23373) hydrogen bonds : bond 0.02869 ( 546) hydrogen bonds : angle 4.33342 ( 1533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 177 time to evaluate : 0.680 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: 0.7844 (ppp) cc_final: 0.7392 (ppp) REVERT: A 590 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7084 (t0) REVERT: B 382 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: B 447 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8099 (t70) REVERT: B 603 ASP cc_start: 0.7363 (t70) cc_final: 0.7133 (t70) REVERT: B 618 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6790 (mpp) REVERT: D 543 PHE cc_start: 0.8038 (p90) cc_final: 0.7487 (p90) REVERT: D 658 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7322 (pttp) REVERT: E 421 ASP cc_start: 0.7474 (t0) cc_final: 0.7128 (p0) REVERT: E 612 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7127 (tmm-80) REVERT: F 388 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8241 (mtmm) REVERT: F 547 MET cc_start: 0.7508 (tmm) cc_final: 0.7108 (tmm) outliers start: 68 outliers final: 44 residues processed: 229 average time/residue: 0.1324 time to fit residues: 46.4038 Evaluate side-chains 216 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 423 VAL 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 497 CYS 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 658 LYS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 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 602 ILE 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 158 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 200 optimal weight: 0.0970 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN B 662 ASN D 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.142884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095655 restraints weight = 36939.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098947 restraints weight = 22028.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.102467 restraints weight = 14473.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101924 restraints weight = 11130.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102082 restraints weight = 11389.261| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17301 Z= 0.194 Angle : 0.600 8.056 23373 Z= 0.310 Chirality : 0.044 0.164 2631 Planarity : 0.004 0.040 2953 Dihedral : 8.387 163.050 2307 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.77 % Allowed : 26.68 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.18), residues: 2049 helix: 0.80 (0.20), residues: 712 sheet: -1.61 (0.34), residues: 247 loop : -1.49 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 479 TYR 0.032 0.001 TYR F 482 PHE 0.014 0.001 PHE B 444 TRP 0.060 0.002 TRP F 675 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00462 (17301) covalent geometry : angle 0.59990 (23373) hydrogen bonds : bond 0.03746 ( 546) hydrogen bonds : angle 4.71248 ( 1533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 174 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 374 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: B 382 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: B 447 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8159 (t70) REVERT: B 618 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7034 (mpp) REVERT: D 543 PHE cc_start: 0.8132 (p90) cc_final: 0.7672 (p90) REVERT: D 658 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7551 (pttp) REVERT: E 547 MET cc_start: 0.7697 (ppp) cc_final: 0.6714 (ppp) REVERT: E 612 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7169 (tmm-80) REVERT: F 388 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8321 (mttp) outliers start: 91 outliers final: 62 residues processed: 245 average time/residue: 0.1245 time to fit residues: 47.2386 Evaluate side-chains 230 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 162 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 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 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 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 510 SER Chi-restraints excluded: chain C residue 525 VAL 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 527 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 422 LEU 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 388 LYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 108 optimal weight: 0.0040 chunk 132 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.143290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.095786 restraints weight = 37018.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099384 restraints weight = 20017.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101684 restraints weight = 13756.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103159 restraints weight = 10968.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103946 restraints weight = 9526.961| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2373 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= 0.147 Angle : 0.571 6.571 23373 Z= 0.296 Chirality : 0.043 0.212 2631 Planarity : 0.004 0.037 2953 Dihedral : 8.351 162.486 2307 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.19 % Allowed : 26.83 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.19), residues: 2049 helix: 0.85 (0.20), residues: 717 sheet: -1.62 (0.34), residues: 248 loop : -1.43 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 479 TYR 0.030 0.001 TYR F 482 PHE 0.011 0.001 PHE B 444 TRP 0.085 0.002 TRP F 675 HIS 0.007 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00352 (17301) covalent geometry : angle 0.57144 (23373) hydrogen bonds : bond 0.03272 ( 546) hydrogen bonds : angle 4.50333 ( 1533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 169 time to evaluate : 0.451 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: B 374 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: B 382 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: B 447 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8157 (t70) REVERT: B 618 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6946 (mpp) REVERT: C 458 MET cc_start: 0.7509 (tpt) cc_final: 0.7257 (tpt) REVERT: C 462 MET cc_start: 0.8330 (tpp) cc_final: 0.7797 (mpp) REVERT: C 474 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: D 543 PHE cc_start: 0.7960 (p90) cc_final: 0.7718 (p90) REVERT: D 658 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7334 (pttp) REVERT: E 612 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7182 (tmm-80) outliers start: 80 outliers final: 58 residues processed: 233 average time/residue: 0.1075 time to fit residues: 39.1011 Evaluate side-chains 225 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 161 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 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 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain 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 422 LEU Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.144332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097246 restraints weight = 36629.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100731 restraints weight = 20379.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103006 restraints weight = 14202.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104271 restraints weight = 11341.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105238 restraints weight = 9952.231| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2512 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= 0.118 Angle : 0.562 9.929 23373 Z= 0.289 Chirality : 0.042 0.163 2631 Planarity : 0.003 0.037 2953 Dihedral : 8.297 162.661 2307 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.62 % Allowed : 27.94 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.19), residues: 2049 helix: 0.88 (0.20), residues: 726 sheet: -1.57 (0.35), residues: 241 loop : -1.39 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 619 TYR 0.032 0.001 TYR F 482 PHE 0.014 0.001 PHE E 543 TRP 0.058 0.002 TRP F 675 HIS 0.002 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00279 (17301) covalent geometry : angle 0.56186 (23373) hydrogen bonds : bond 0.02987 ( 546) hydrogen bonds : angle 4.33886 ( 1533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 165 time to evaluate : 0.502 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: B 374 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: B 382 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: B 447 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8165 (t70) REVERT: B 618 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6832 (mpp) REVERT: D 543 PHE cc_start: 0.7972 (p90) cc_final: 0.7770 (p90) REVERT: D 658 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7385 (pttp) REVERT: E 360 GLU cc_start: 0.6857 (pm20) cc_final: 0.6416 (pm20) REVERT: E 612 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7164 (tmm-80) REVERT: F 356 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7512 (mtmm) REVERT: F 547 MET cc_start: 0.7670 (tmm) cc_final: 0.7392 (tmm) REVERT: F 618 MET cc_start: 0.7687 (ttt) cc_final: 0.7216 (tpp) outliers start: 69 outliers final: 58 residues processed: 219 average time/residue: 0.1234 time to fit residues: 41.2268 Evaluate side-chains 221 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 157 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 440 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 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 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 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 422 LEU 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 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 69 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 548 HIS F 680 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.144313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097293 restraints weight = 36968.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100972 restraints weight = 19857.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103382 restraints weight = 13606.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104827 restraints weight = 10756.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105794 restraints weight = 9376.276| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2681 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= 0.115 Angle : 0.568 8.949 23373 Z= 0.291 Chirality : 0.042 0.188 2631 Planarity : 0.004 0.050 2953 Dihedral : 8.268 162.770 2307 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.88 % Allowed : 28.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.19), residues: 2049 helix: 0.88 (0.20), residues: 729 sheet: -1.49 (0.34), residues: 247 loop : -1.35 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 479 TYR 0.025 0.001 TYR F 482 PHE 0.016 0.001 PHE E 668 TRP 0.098 0.002 TRP F 675 HIS 0.002 0.000 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00272 (17301) covalent geometry : angle 0.56794 (23373) hydrogen bonds : bond 0.02994 ( 546) hydrogen bonds : angle 4.29560 ( 1533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 163 time to evaluate : 0.711 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: 0.8959 (m) cc_final: 0.8372 (t) REVERT: A 590 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7345 (t0) REVERT: B 374 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: B 382 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: B 447 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8162 (t70) REVERT: B 618 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6773 (mpp) REVERT: D 543 PHE cc_start: 0.7934 (p90) cc_final: 0.7723 (p90) REVERT: D 658 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7318 (pttp) REVERT: E 597 HIS cc_start: 0.8079 (m170) cc_final: 0.7485 (m-70) REVERT: E 612 ARG cc_start: 0.7762 (mtm110) cc_final: 0.7183 (tmm-80) REVERT: E 684 MET cc_start: 0.6131 (tpt) cc_final: 0.5851 (tpt) REVERT: F 356 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7566 (mtmm) REVERT: F 501 PHE cc_start: 0.7453 (m-80) cc_final: 0.7110 (m-10) REVERT: F 547 MET cc_start: 0.7692 (tmm) cc_final: 0.7377 (tmm) REVERT: F 618 MET cc_start: 0.7638 (ttt) cc_final: 0.7170 (tpp) outliers start: 74 outliers final: 64 residues processed: 224 average time/residue: 0.1226 time to fit residues: 42.5515 Evaluate side-chains 221 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 150 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 440 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 566 SER 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 461 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain 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 F residue 354 SER Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 142 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 30.0000 chunk 140 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 ASN F 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.144178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099239 restraints weight = 36755.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101961 restraints weight = 21128.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.103454 restraints weight = 13061.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.103948 restraints weight = 13251.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.104033 restraints weight = 11134.108| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2808 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= 0.118 Angle : 0.578 9.149 23373 Z= 0.296 Chirality : 0.042 0.160 2631 Planarity : 0.004 0.050 2953 Dihedral : 8.245 162.936 2307 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.19), residues: 2049 helix: 0.83 (0.20), residues: 731 sheet: -1.48 (0.34), residues: 247 loop : -1.32 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.020 0.001 TYR F 482 PHE 0.016 0.001 PHE E 668 TRP 0.127 0.003 TRP F 675 HIS 0.004 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00280 (17301) covalent geometry : angle 0.57827 (23373) hydrogen bonds : bond 0.03040 ( 546) hydrogen bonds : angle 4.28526 ( 1533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 160 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 CYS cc_start: 0.9041 (m) cc_final: 0.8518 (t) REVERT: A 590 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7180 (t0) REVERT: B 374 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: B 382 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: B 447 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8186 (t70) REVERT: B 481 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8863 (tt) REVERT: B 618 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6804 (mpp) REVERT: D 543 PHE cc_start: 0.8039 (p90) cc_final: 0.7793 (p90) REVERT: D 658 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7718 (pttp) REVERT: E 421 ASP cc_start: 0.7511 (t0) cc_final: 0.7183 (p0) REVERT: E 445 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8512 (mmmm) REVERT: E 597 HIS cc_start: 0.8084 (m170) cc_final: 0.7521 (m-70) REVERT: E 612 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7191 (tmm-80) REVERT: E 684 MET cc_start: 0.6240 (tpt) cc_final: 0.5923 (tpt) REVERT: F 356 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7545 (mtmm) REVERT: F 501 PHE cc_start: 0.7669 (m-80) cc_final: 0.7314 (m-10) REVERT: F 547 MET cc_start: 0.7695 (tmm) cc_final: 0.7384 (tmm) REVERT: F 618 MET cc_start: 0.7637 (ttt) cc_final: 0.7174 (tpp) outliers start: 79 outliers final: 66 residues processed: 224 average time/residue: 0.1217 time to fit residues: 41.8935 Evaluate side-chains 227 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 153 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 440 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 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 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 C residue 351 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 0.0470 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.145033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100424 restraints weight = 36949.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.103442 restraints weight = 21202.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105670 restraints weight = 12927.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.106014 restraints weight = 12493.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105935 restraints weight = 10592.160| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17301 Z= 0.106 Angle : 0.590 15.829 23373 Z= 0.301 Chirality : 0.042 0.157 2631 Planarity : 0.004 0.060 2953 Dihedral : 8.174 162.871 2307 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.46 % Allowed : 28.41 % Favored : 68.13 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.19), residues: 2049 helix: 0.93 (0.20), residues: 724 sheet: -1.50 (0.35), residues: 237 loop : -1.25 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.025 0.001 TYR F 482 PHE 0.012 0.001 PHE B 543 TRP 0.152 0.003 TRP F 675 HIS 0.004 0.000 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00246 (17301) covalent geometry : angle 0.59004 (23373) hydrogen bonds : bond 0.02927 ( 546) hydrogen bonds : angle 4.15369 ( 1533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 0.440 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: 0.9031 (m) cc_final: 0.8484 (t) REVERT: A 590 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7204 (t0) REVERT: B 374 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: B 481 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 618 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6761 (mpp) REVERT: D 543 PHE cc_start: 0.8046 (p90) cc_final: 0.7779 (p90) REVERT: D 658 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7600 (pttp) REVERT: E 421 ASP cc_start: 0.7464 (t0) cc_final: 0.7176 (p0) REVERT: E 445 LYS cc_start: 0.8841 (ttpp) cc_final: 0.8525 (mmmm) REVERT: E 612 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7192 (tmm-80) REVERT: E 684 MET cc_start: 0.6204 (tpt) cc_final: 0.5880 (tpt) REVERT: F 469 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6542 (tp40) REVERT: F 501 PHE cc_start: 0.7696 (m-80) cc_final: 0.7352 (m-10) REVERT: F 547 MET cc_start: 0.7700 (tmm) cc_final: 0.7392 (tmm) REVERT: F 618 MET cc_start: 0.7589 (ttt) cc_final: 0.7281 (tpp) outliers start: 66 outliers final: 53 residues processed: 222 average time/residue: 0.1060 time to fit residues: 36.8100 Evaluate side-chains 216 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 157 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 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 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 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 C residue 380 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 509 LYS Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 25 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.144868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100178 restraints weight = 36869.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102877 restraints weight = 21697.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105544 restraints weight = 13195.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105729 restraints weight = 12123.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.105413 restraints weight = 10593.113| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 17301 Z= 0.199 Angle : 0.776 59.192 23373 Z= 0.435 Chirality : 0.042 0.340 2631 Planarity : 0.004 0.046 2953 Dihedral : 8.152 162.892 2305 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.20 % Allowed : 28.93 % Favored : 67.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.19), residues: 2049 helix: 0.93 (0.20), residues: 723 sheet: -1.49 (0.35), residues: 237 loop : -1.25 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 479 TYR 0.024 0.001 TYR F 482 PHE 0.018 0.001 PHE A 698 TRP 0.121 0.002 TRP F 675 HIS 0.003 0.000 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00417 (17301) covalent geometry : angle 0.77612 (23373) hydrogen bonds : bond 0.03014 ( 546) hydrogen bonds : angle 4.16187 ( 1533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.40 seconds wall clock time: 50 minutes 59.57 seconds (3059.57 seconds total)