Starting phenix.real_space_refine on Mon Nov 18 01:30:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/11_2024/8hwd_35054.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/11_2024/8hwd_35054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/11_2024/8hwd_35054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/11_2024/8hwd_35054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/11_2024/8hwd_35054.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/11_2024/8hwd_35054.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.092 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 12 5.49 5 S 79 5.16 5 C 9553 2.51 5 N 2554 2.21 5 O 2831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15029 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2505 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 11, 'TRANS': 296} Chain breaks: 5 Chain: "F" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2092 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 9, 'TRANS': 248} Chain breaks: 4 Chain: "D" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2427 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 11, 'TRANS': 287} Chain breaks: 4 Chain: "E" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2012 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 4 Chain: "C" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 3 Chain: "B" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3045 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.84, per 1000 atoms: 0.59 Number of scatterers: 15029 At special positions: 0 Unit cell: (107.2, 127.568, 128.64, 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 79 16.00 P 12 15.00 O 2831 8.00 N 2554 7.00 C 9553 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: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3498 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 22 sheets defined 44.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.563A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.912A 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: 3.934A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 390 through 398 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.665A pdb=" N PHE A 451 " --> pdb=" O ASP A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 571 through 577 Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.784A pdb=" N ASN A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.772A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.504A pdb=" N LEU F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 375 removed outlier: 3.796A pdb=" N LEU F 375 " --> pdb=" O ARG F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 372 through 375' Processing helix chain 'F' and resid 387 through 398 removed outlier: 3.959A pdb=" N THR F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 435 removed outlier: 3.745A pdb=" N LYS F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.731A pdb=" N LYS F 450 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 451 " --> pdb=" O ASP F 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 447 through 451' Processing helix chain 'F' and resid 457 through 469 Processing helix chain 'F' and resid 475 through 488 Processing helix chain 'F' and resid 508 through 520 Processing helix chain 'F' and resid 657 through 661 removed outlier: 4.202A pdb=" N ASN F 661 " --> pdb=" O GLY F 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 657 through 661' Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.680A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.745A pdb=" N LEU D 375 " --> pdb=" O ARG D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.556A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 399 removed outlier: 3.626A pdb=" N LYS D 390 " --> pdb=" O PRO D 386 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 434 Processing helix chain 'D' and resid 447 through 451 removed outlier: 3.673A pdb=" N PHE D 451 " --> pdb=" O ASP D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 469 Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.724A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 575 through 579 removed outlier: 4.050A pdb=" N GLU D 579 " --> pdb=" O LYS D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 639 Processing helix chain 'D' and resid 652 through 661 removed outlier: 4.151A pdb=" N ASP D 656 " --> pdb=" O ASP D 652 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.884A pdb=" N LYS D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR D 679 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.826A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 388 through 400 removed outlier: 3.935A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 434 removed outlier: 3.767A pdb=" N ASP E 432 " --> pdb=" O SER E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 455 through 469 removed outlier: 3.677A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 475 Processing helix chain 'E' and resid 476 through 489 removed outlier: 3.649A pdb=" N CYS E 489 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 667 through 680 Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.932A pdb=" N LEU C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.614A 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 380 through 384 removed outlier: 3.534A pdb=" N LEU C 384 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 388 Processing helix chain 'C' and resid 389 through 398 Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.906A pdb=" N LYS C 450 " --> pdb=" O ASP C 447 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 451 " --> pdb=" O ASP C 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 447 through 451' Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 472 through 475 Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.765A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.750A pdb=" N LYS C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.599A pdb=" N MET C 618 " --> pdb=" O ASP C 614 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 619 " --> pdb=" O ASN C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 614 through 619' Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.686A pdb=" N PHE C 668 " --> pdb=" O TYR C 664 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS C 678 " --> pdb=" O LYS C 674 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 679 " --> pdb=" O TRP C 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.520A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.659A 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 380 through 384 removed outlier: 3.641A pdb=" N LEU B 384 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 removed outlier: 3.740A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.785A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.749A pdb=" N LYS B 450 " --> pdb=" O ASP B 447 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 451 " --> pdb=" O ASP B 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 447 through 451' Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.577A pdb=" N ILE B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.876A pdb=" N ALA B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 removed outlier: 4.089A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.616A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 641 removed outlier: 4.353A pdb=" N GLU B 637 " --> pdb=" O PRO B 633 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.660A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 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 525 through 526 removed outlier: 6.432A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA5, first strand: chain 'F' and resid 339 through 342 Processing sheet with id=AA6, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.772A pdb=" N MET F 426 " --> pdb=" O ASP F 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 339 through 341 removed outlier: 3.557A pdb=" N ILE D 351 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.668A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 499 through 500 removed outlier: 6.632A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 629 through 631 removed outlier: 3.834A pdb=" N LYS D 649 " --> pdb=" O HIS D 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 340 through 342 Processing sheet with id=AB3, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AB4, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB5, first strand: chain 'C' and resid 412 through 415 Processing sheet with id=AB6, first strand: chain 'C' and resid 498 through 500 removed outlier: 6.915A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB8, first strand: chain 'C' and resid 628 through 631 removed outlier: 3.795A pdb=" N SER C 631 " --> pdb=" O LYS C 649 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AC1, first strand: chain 'B' and resid 412 through 415 removed outlier: 4.016A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 419 " --> pdb=" O TYR B 428 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.198A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'B' and resid 628 through 631 removed outlier: 3.548A pdb=" N SER B 631 " --> pdb=" O LYS B 649 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1419 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: 4.54 Time building geometry restraints manager: 4.26 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: 4318 1.33 - 1.46: 2555 1.46 - 1.58: 8313 1.58 - 1.70: 18 1.70 - 1.82: 118 Bond restraints: 15322 Sorted by residual: bond pdb=" N VAL D 673 " pdb=" CA VAL D 673 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.18e+00 bond pdb=" N HIS F 548 " pdb=" CA HIS F 548 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.22e-02 6.72e+03 6.31e+00 bond pdb=" N THR B 342 " pdb=" CA THR B 342 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.16e-02 7.43e+03 6.13e+00 bond pdb=" N ASP B 522 " pdb=" CA ASP B 522 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" N LYS D 674 " pdb=" CA LYS D 674 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 5.01e+00 ... (remaining 15317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 20206 2.16 - 4.32: 375 4.32 - 6.48: 76 6.48 - 8.63: 12 8.63 - 10.79: 5 Bond angle restraints: 20674 Sorted by residual: angle pdb=" N LYS D 450 " pdb=" CA LYS D 450 " pdb=" C LYS D 450 " ideal model delta sigma weight residual 114.56 107.59 6.97 1.27e+00 6.20e-01 3.01e+01 angle pdb=" CB GLU D 457 " pdb=" CG GLU D 457 " pdb=" CD GLU D 457 " ideal model delta sigma weight residual 112.60 104.04 8.56 1.70e+00 3.46e-01 2.53e+01 angle pdb=" N GLY D 521 " pdb=" CA GLY D 521 " pdb=" C GLY D 521 " ideal model delta sigma weight residual 111.67 116.07 -4.40 9.20e-01 1.18e+00 2.28e+01 angle pdb=" CB LYS C 647 " pdb=" CG LYS C 647 " pdb=" CD LYS C 647 " ideal model delta sigma weight residual 111.30 122.09 -10.79 2.30e+00 1.89e-01 2.20e+01 angle pdb=" C GLU D 457 " pdb=" CA GLU D 457 " pdb=" CB GLU D 457 " ideal model delta sigma weight residual 110.42 118.41 -7.99 1.99e+00 2.53e-01 1.61e+01 ... (remaining 20669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.77: 8803 31.77 - 63.54: 483 63.54 - 95.30: 24 95.30 - 127.07: 1 127.07 - 158.84: 2 Dihedral angle restraints: 9313 sinusoidal: 3942 harmonic: 5371 Sorted by residual: dihedral pdb=" C2' ADP B1001 " pdb=" C1' ADP B1001 " pdb=" N9 ADP B1001 " pdb=" C4 ADP B1001 " ideal model delta sinusoidal sigma weight residual 91.55 -67.29 158.84 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C2' ADP E1001 " pdb=" C1' ADP E1001 " pdb=" N9 ADP E1001 " pdb=" C4 ADP E1001 " ideal model delta sinusoidal sigma weight residual 91.55 -129.70 -138.76 1 2.00e+01 2.50e-03 4.20e+01 dihedral pdb=" O2A ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PA ADP E1001 " pdb=" PB ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 66.45 -126.45 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 9310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1588 0.038 - 0.077: 559 0.077 - 0.115: 146 0.115 - 0.153: 25 0.153 - 0.191: 3 Chirality restraints: 2321 Sorted by residual: chirality pdb=" CA ASN D 641 " pdb=" N ASN D 641 " pdb=" C ASN D 641 " pdb=" CB ASN D 641 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CB ILE B 464 " pdb=" CA ILE B 464 " pdb=" CG1 ILE B 464 " pdb=" CG2 ILE B 464 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CB ILE B 681 " pdb=" CA ILE B 681 " pdb=" CG1 ILE B 681 " pdb=" CG2 ILE B 681 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 2318 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 456 " -0.028 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C PRO D 456 " 0.102 2.00e-02 2.50e+03 pdb=" O PRO D 456 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU D 457 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 628 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C THR D 628 " -0.057 2.00e-02 2.50e+03 pdb=" O THR D 628 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS D 629 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 448 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ASP D 448 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP D 448 " 0.017 2.00e-02 2.50e+03 pdb=" N THR D 449 " 0.015 2.00e-02 2.50e+03 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1297 2.74 - 3.28: 15292 3.28 - 3.82: 24878 3.82 - 4.36: 29589 4.36 - 4.90: 50232 Nonbonded interactions: 121288 Sorted by model distance: nonbonded pdb=" OG SER F 510 " pdb=" O2A ADP F1001 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR B 365 " pdb=" OE1 GLU B 393 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 455 " pdb=" OE1 GLU A 457 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN D 395 " pdb=" NH2 ARG C 389 " model vdw 2.221 3.120 nonbonded pdb=" O LEU D 369 " pdb=" NH1 ARG D 372 " model vdw 2.237 3.120 ... (remaining 121283 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 526 or resid 544 through 554 or resid 575 thro \ ugh 581 or resid 595 through 614 or resid 623 through 688 or resid 1001)) selection = (chain 'C' and (resid 323 through 526 or resid 544 through 554 or resid 575 thro \ ugh 581 or resid 595 through 603 or resid 623 through 631 or resid 645 through 6 \ 88 or resid 1001)) selection = (chain 'D' and (resid 323 through 603 or resid 623 through 631 or resid 645 thro \ ugh 688 or resid 1001)) } ncs_group { reference = (chain 'E' and (resid 323 through 525 or resid 547 through 553 or resid 575 thro \ ugh 686 or resid 1001)) selection = (chain 'F' and (resid 323 through 525 or resid 547 through 580 or resid 595 thro \ ugh 600 or resid 664 through 686 or resid 1001)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.020 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.004 0.076 15322 Z= 0.240 Angle : 0.734 10.793 20674 Z= 0.382 Chirality : 0.042 0.191 2321 Planarity : 0.005 0.059 2583 Dihedral : 18.031 158.839 5815 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.64 % Favored : 91.30 % Rotamer: Outliers : 1.25 % Allowed : 32.48 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.20), residues: 1782 helix: 0.00 (0.20), residues: 689 sheet: -1.31 (0.35), residues: 232 loop : -2.03 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 355 HIS 0.005 0.001 HIS F 597 PHE 0.016 0.001 PHE E 666 TYR 0.018 0.001 TYR B 482 ARG 0.005 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7910 (mmmm) REVERT: A 618 MET cc_start: 0.8179 (tmm) cc_final: 0.7017 (tpp) REVERT: D 390 LYS cc_start: 0.6517 (mptt) cc_final: 0.6086 (mtmm) REVERT: D 500 PHE cc_start: 0.6804 (m-10) cc_final: 0.6602 (m-10) REVERT: D 650 LEU cc_start: 0.8161 (pp) cc_final: 0.7833 (pt) REVERT: D 651 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8472 (tt) REVERT: D 660 GLN cc_start: 0.7633 (mp10) cc_final: 0.7420 (mm-40) REVERT: C 436 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: B 374 GLN cc_start: 0.7550 (mt0) cc_final: 0.7344 (mt0) outliers start: 21 outliers final: 7 residues processed: 277 average time/residue: 0.2944 time to fit residues: 117.8061 Evaluate side-chains 255 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 246 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain B residue 351 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 GLN D 478 ASN E 331 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN C 573 ASN ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15322 Z= 0.208 Angle : 0.643 8.975 20674 Z= 0.309 Chirality : 0.041 0.155 2321 Planarity : 0.005 0.051 2583 Dihedral : 8.664 154.137 2051 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.87 % Allowed : 28.78 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1782 helix: 0.12 (0.20), residues: 705 sheet: -1.43 (0.35), residues: 211 loop : -1.92 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 675 HIS 0.003 0.001 HIS F 597 PHE 0.016 0.001 PHE D 630 TYR 0.019 0.001 TYR B 482 ARG 0.010 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 267 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 THR cc_start: 0.8385 (p) cc_final: 0.8161 (m) REVERT: F 361 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.4932 (pp20) REVERT: D 458 MET cc_start: 0.6067 (ppp) cc_final: 0.5815 (tmm) REVERT: D 481 LEU cc_start: 0.8433 (tp) cc_final: 0.8067 (tp) REVERT: D 502 PHE cc_start: 0.6575 (t80) cc_final: 0.6347 (t80) REVERT: D 645 TYR cc_start: 0.7488 (m-10) cc_final: 0.6591 (m-10) REVERT: D 666 PHE cc_start: 0.7228 (m-80) cc_final: 0.7016 (m-10) REVERT: E 382 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: C 375 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7255 (mt) REVERT: C 484 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7669 (ttmm) REVERT: B 374 GLN cc_start: 0.7569 (mt0) cc_final: 0.7332 (mt0) REVERT: B 501 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6621 (m-10) REVERT: B 677 LYS cc_start: 0.8283 (tmtt) cc_final: 0.7999 (mttp) outliers start: 65 outliers final: 36 residues processed: 311 average time/residue: 0.2839 time to fit residues: 130.3871 Evaluate side-chains 276 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 620 ARG Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 645 TYR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 555 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 162 optimal weight: 0.1980 chunk 175 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN C 358 ASN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15322 Z= 0.298 Angle : 0.671 8.371 20674 Z= 0.323 Chirality : 0.043 0.196 2321 Planarity : 0.005 0.066 2583 Dihedral : 8.251 150.836 2037 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.24 % Allowed : 27.00 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1782 helix: -0.07 (0.19), residues: 707 sheet: -1.49 (0.36), residues: 197 loop : -2.02 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 350 HIS 0.005 0.001 HIS B 629 PHE 0.020 0.002 PHE B 554 TYR 0.020 0.001 TYR B 482 ARG 0.004 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 261 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 343 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7472 (mp0) REVERT: F 361 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.4954 (pp20) REVERT: D 458 MET cc_start: 0.6250 (ppp) cc_final: 0.5912 (tmm) REVERT: D 481 LEU cc_start: 0.8488 (tp) cc_final: 0.8171 (tp) REVERT: D 502 PHE cc_start: 0.6752 (t80) cc_final: 0.6382 (t80) REVERT: E 382 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: E 384 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8290 (mt) REVERT: E 421 ASP cc_start: 0.7308 (t0) cc_final: 0.7066 (t0) REVERT: C 375 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7272 (mt) REVERT: C 436 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: C 484 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7780 (ttmm) REVERT: B 374 GLN cc_start: 0.7612 (mt0) cc_final: 0.7367 (mt0) REVERT: B 501 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6797 (m-10) outliers start: 88 outliers final: 49 residues processed: 319 average time/residue: 0.2666 time to fit residues: 125.9128 Evaluate side-chains 304 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 645 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 673 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 10.0000 chunk 122 optimal weight: 0.1980 chunk 84 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN F 475 ASN F 478 ASN D 469 GLN D 478 ASN E 331 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN C 661 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15322 Z= 0.219 Angle : 0.644 12.151 20674 Z= 0.307 Chirality : 0.042 0.150 2321 Planarity : 0.004 0.067 2583 Dihedral : 8.112 151.618 2037 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.01 % Allowed : 27.47 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1782 helix: 0.07 (0.20), residues: 707 sheet: -1.51 (0.37), residues: 187 loop : -1.90 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 350 HIS 0.003 0.001 HIS B 629 PHE 0.014 0.001 PHE B 554 TYR 0.019 0.001 TYR D 645 ARG 0.003 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 256 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: F 361 GLU cc_start: 0.5268 (OUTLIER) cc_final: 0.4928 (pp20) REVERT: D 481 LEU cc_start: 0.8490 (tp) cc_final: 0.8166 (tp) REVERT: D 502 PHE cc_start: 0.6850 (t80) cc_final: 0.6605 (t80) REVERT: E 382 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: E 384 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8265 (mt) REVERT: C 343 GLU cc_start: 0.7187 (mp0) cc_final: 0.6832 (mp0) REVERT: C 436 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: C 484 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7663 (ttmm) REVERT: C 509 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6810 (mttp) REVERT: B 374 GLN cc_start: 0.7591 (mt0) cc_final: 0.7379 (mt0) REVERT: B 501 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6942 (m-10) outliers start: 84 outliers final: 58 residues processed: 311 average time/residue: 0.2648 time to fit residues: 122.7103 Evaluate side-chains 309 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 43 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: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN E 331 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15322 Z= 0.228 Angle : 0.645 9.372 20674 Z= 0.308 Chirality : 0.042 0.147 2321 Planarity : 0.004 0.066 2583 Dihedral : 8.049 150.491 2037 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.60 % Allowed : 27.77 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1782 helix: 0.10 (0.20), residues: 708 sheet: -1.51 (0.37), residues: 187 loop : -1.85 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.004 0.001 HIS C 629 PHE 0.013 0.001 PHE B 501 TYR 0.018 0.001 TYR F 482 ARG 0.002 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 254 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 361 GLU cc_start: 0.5254 (OUTLIER) cc_final: 0.5003 (pp20) REVERT: D 481 LEU cc_start: 0.8521 (tp) cc_final: 0.8192 (tp) REVERT: D 502 PHE cc_start: 0.6883 (t80) cc_final: 0.6681 (t80) REVERT: D 651 LEU cc_start: 0.8637 (mp) cc_final: 0.8388 (mp) REVERT: D 670 TYR cc_start: 0.7200 (t80) cc_final: 0.6968 (t80) REVERT: E 382 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: E 384 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8250 (mt) REVERT: C 375 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7289 (mt) REVERT: C 436 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: C 484 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7668 (ttmm) REVERT: C 509 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6872 (mttp) REVERT: C 606 TYR cc_start: 0.6612 (OUTLIER) cc_final: 0.5630 (m-80) REVERT: B 374 GLN cc_start: 0.7495 (mt0) cc_final: 0.7273 (mt0) REVERT: B 501 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: B 677 LYS cc_start: 0.8296 (tmtt) cc_final: 0.7893 (mttm) outliers start: 94 outliers final: 64 residues processed: 318 average time/residue: 0.2670 time to fit residues: 126.1203 Evaluate side-chains 313 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 240 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15322 Z= 0.204 Angle : 0.640 14.334 20674 Z= 0.305 Chirality : 0.041 0.154 2321 Planarity : 0.004 0.067 2583 Dihedral : 7.953 150.952 2037 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.07 % Allowed : 29.32 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1782 helix: 0.22 (0.20), residues: 708 sheet: -1.49 (0.37), residues: 187 loop : -1.80 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.004 0.001 HIS C 629 PHE 0.013 0.001 PHE B 501 TYR 0.017 0.001 TYR F 482 ARG 0.003 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 244 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8340 (mt) REVERT: A 618 MET cc_start: 0.8135 (tmm) cc_final: 0.6992 (tpp) REVERT: F 361 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4953 (pp20) REVERT: D 481 LEU cc_start: 0.8464 (tp) cc_final: 0.8143 (tp) REVERT: D 651 LEU cc_start: 0.8708 (mp) cc_final: 0.8496 (mp) REVERT: E 382 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: E 384 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8210 (mt) REVERT: C 375 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7325 (mt) REVERT: C 436 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: C 484 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7683 (ttmm) REVERT: C 509 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6822 (mttp) REVERT: C 606 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5617 (m-80) REVERT: C 690 PRO cc_start: 0.7515 (Cg_endo) cc_final: 0.7313 (Cg_exo) REVERT: B 501 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6860 (m-10) REVERT: B 677 LYS cc_start: 0.8274 (tmtt) cc_final: 0.7903 (mttm) outliers start: 85 outliers final: 64 residues processed: 300 average time/residue: 0.2523 time to fit residues: 113.9552 Evaluate side-chains 306 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 232 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15322 Z= 0.331 Angle : 0.714 15.337 20674 Z= 0.342 Chirality : 0.044 0.197 2321 Planarity : 0.005 0.067 2583 Dihedral : 8.116 146.583 2037 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 5.90 % Allowed : 29.02 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.20), residues: 1782 helix: -0.04 (0.19), residues: 698 sheet: -1.54 (0.37), residues: 197 loop : -1.91 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 350 HIS 0.004 0.001 HIS C 629 PHE 0.016 0.002 PHE B 501 TYR 0.030 0.002 TYR F 482 ARG 0.003 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 246 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7053 (pm20) cc_final: 0.6097 (mp0) REVERT: A 523 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7569 (mt) REVERT: A 618 MET cc_start: 0.8121 (tmm) cc_final: 0.7059 (tpp) REVERT: F 361 GLU cc_start: 0.5399 (OUTLIER) cc_final: 0.5097 (pp20) REVERT: D 390 LYS cc_start: 0.6725 (mptt) cc_final: 0.6452 (mtmm) REVERT: D 481 LEU cc_start: 0.8517 (tp) cc_final: 0.8219 (tp) REVERT: D 651 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8442 (mp) REVERT: E 365 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.6575 (t) REVERT: E 382 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: E 384 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8252 (mt) REVERT: E 405 GLU cc_start: 0.6610 (pm20) cc_final: 0.5962 (pt0) REVERT: C 375 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7224 (mt) REVERT: C 436 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: C 484 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7764 (ttmm) REVERT: C 509 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6936 (mttp) REVERT: C 606 TYR cc_start: 0.6565 (OUTLIER) cc_final: 0.5561 (m-80) REVERT: C 690 PRO cc_start: 0.7686 (Cg_endo) cc_final: 0.7486 (Cg_exo) REVERT: B 409 TYR cc_start: 0.8060 (m-80) cc_final: 0.7777 (m-80) REVERT: B 501 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6903 (m-10) REVERT: B 677 LYS cc_start: 0.8342 (tmtt) cc_final: 0.8018 (mttp) outliers start: 99 outliers final: 75 residues processed: 317 average time/residue: 0.2596 time to fit residues: 122.7489 Evaluate side-chains 324 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 237 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 609 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN E 331 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15322 Z= 0.246 Angle : 0.676 14.524 20674 Z= 0.322 Chirality : 0.042 0.165 2321 Planarity : 0.004 0.064 2583 Dihedral : 7.999 148.969 2037 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 5.36 % Allowed : 29.38 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.20), residues: 1782 helix: 0.08 (0.20), residues: 699 sheet: -1.54 (0.38), residues: 187 loop : -1.86 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.003 0.001 HIS D 629 PHE 0.015 0.001 PHE D 502 TYR 0.026 0.001 TYR F 482 ARG 0.002 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 242 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7208 (pm20) cc_final: 0.6017 (mp0) REVERT: A 523 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7546 (mt) REVERT: A 618 MET cc_start: 0.8127 (tmm) cc_final: 0.7149 (tpp) REVERT: F 361 GLU cc_start: 0.5334 (OUTLIER) cc_final: 0.4996 (pp20) REVERT: D 390 LYS cc_start: 0.6607 (mptt) cc_final: 0.6035 (mtmm) REVERT: D 481 LEU cc_start: 0.8481 (tp) cc_final: 0.8164 (tp) REVERT: D 651 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8429 (mp) REVERT: E 365 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.6594 (t) REVERT: E 382 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: E 384 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8235 (mt) REVERT: E 405 GLU cc_start: 0.6652 (pm20) cc_final: 0.6058 (pt0) REVERT: C 375 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7242 (mt) REVERT: C 436 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: C 484 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7649 (ttmm) REVERT: C 509 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6808 (mttp) REVERT: C 606 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5505 (m-80) REVERT: C 690 PRO cc_start: 0.7704 (Cg_endo) cc_final: 0.7503 (Cg_exo) REVERT: B 409 TYR cc_start: 0.8037 (m-80) cc_final: 0.7776 (m-80) REVERT: B 501 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6929 (m-10) REVERT: B 677 LYS cc_start: 0.8253 (tmtt) cc_final: 0.7930 (mttp) outliers start: 90 outliers final: 70 residues processed: 307 average time/residue: 0.2678 time to fit residues: 121.9962 Evaluate side-chains 314 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 232 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 609 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 2.9990 chunk 150 optimal weight: 0.0020 chunk 160 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 ASN E 331 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 15322 Z= 0.194 Angle : 0.655 13.931 20674 Z= 0.312 Chirality : 0.041 0.184 2321 Planarity : 0.004 0.068 2583 Dihedral : 7.857 150.795 2037 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 5.24 % Allowed : 29.44 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1782 helix: 0.27 (0.20), residues: 703 sheet: -1.45 (0.37), residues: 197 loop : -1.81 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 355 HIS 0.004 0.001 HIS C 629 PHE 0.012 0.001 PHE B 501 TYR 0.026 0.001 TYR F 482 ARG 0.002 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 245 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7214 (pm20) cc_final: 0.6046 (mp0) REVERT: A 523 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7599 (mt) REVERT: A 618 MET cc_start: 0.8174 (tmm) cc_final: 0.7258 (tpp) REVERT: D 390 LYS cc_start: 0.6545 (mptt) cc_final: 0.5926 (mtmm) REVERT: D 481 LEU cc_start: 0.8458 (tp) cc_final: 0.8176 (tp) REVERT: E 365 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.6591 (t) REVERT: E 382 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: E 384 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8207 (mt) REVERT: E 405 GLU cc_start: 0.6719 (pm20) cc_final: 0.6130 (pt0) REVERT: C 375 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7304 (mt) REVERT: C 436 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: C 484 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7681 (ttmm) REVERT: C 606 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.5524 (m-80) REVERT: C 690 PRO cc_start: 0.7689 (Cg_endo) cc_final: 0.7485 (Cg_exo) REVERT: B 409 TYR cc_start: 0.7993 (m-80) cc_final: 0.7698 (m-80) REVERT: B 501 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6933 (m-10) REVERT: B 677 LYS cc_start: 0.8227 (tmtt) cc_final: 0.7920 (mttp) outliers start: 88 outliers final: 59 residues processed: 307 average time/residue: 0.2667 time to fit residues: 121.5078 Evaluate side-chains 301 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 233 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 609 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 5.9990 chunk 80 optimal weight: 0.0370 chunk 118 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 109 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 331 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15322 Z= 0.184 Angle : 0.664 13.241 20674 Z= 0.315 Chirality : 0.041 0.175 2321 Planarity : 0.004 0.072 2583 Dihedral : 7.724 152.101 2037 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.99 % Allowed : 30.69 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1782 helix: 0.41 (0.20), residues: 704 sheet: -1.38 (0.40), residues: 172 loop : -1.84 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 355 HIS 0.004 0.001 HIS C 629 PHE 0.017 0.001 PHE B 502 TYR 0.025 0.001 TYR F 482 ARG 0.002 0.000 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7104 (pm20) cc_final: 0.5992 (mp0) REVERT: A 523 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7659 (mt) REVERT: A 618 MET cc_start: 0.8149 (tmm) cc_final: 0.7259 (tpp) REVERT: F 348 ILE cc_start: 0.8599 (pt) cc_final: 0.8094 (pt) REVERT: F 684 MET cc_start: 0.6999 (tmm) cc_final: 0.5800 (ptp) REVERT: D 481 LEU cc_start: 0.8428 (tp) cc_final: 0.8163 (tp) REVERT: E 365 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.6655 (t) REVERT: E 382 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: E 384 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8250 (mt) REVERT: E 405 GLU cc_start: 0.6679 (pm20) cc_final: 0.6109 (pt0) REVERT: C 436 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: C 484 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7699 (ttmm) REVERT: C 606 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: C 690 PRO cc_start: 0.7645 (Cg_endo) cc_final: 0.7437 (Cg_exo) REVERT: B 409 TYR cc_start: 0.8019 (m-80) cc_final: 0.7687 (m-80) REVERT: B 501 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: B 649 LYS cc_start: 0.7518 (mmtm) cc_final: 0.7202 (mmpt) REVERT: B 677 LYS cc_start: 0.8324 (tmtt) cc_final: 0.7958 (mttp) outliers start: 67 outliers final: 51 residues processed: 293 average time/residue: 0.2619 time to fit residues: 114.7417 Evaluate side-chains 295 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 609 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 18 optimal weight: 0.0040 chunk 26 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN E 331 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.216524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162077 restraints weight = 18176.096| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.26 r_work: 0.3735 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15322 Z= 0.195 Angle : 0.671 13.219 20674 Z= 0.318 Chirality : 0.041 0.173 2321 Planarity : 0.004 0.076 2583 Dihedral : 7.681 151.999 2037 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.99 % Allowed : 30.45 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1782 helix: 0.41 (0.20), residues: 705 sheet: -1.23 (0.41), residues: 162 loop : -1.88 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 355 HIS 0.004 0.001 HIS B 347 PHE 0.017 0.001 PHE B 502 TYR 0.025 0.001 TYR F 482 ARG 0.002 0.000 ARG C 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.99 seconds wall clock time: 63 minutes 14.69 seconds (3794.69 seconds total)