Starting phenix.real_space_refine on Wed Feb 14 18:01:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f75_28895/02_2024/8f75_28895.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f75_28895/02_2024/8f75_28895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f75_28895/02_2024/8f75_28895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f75_28895/02_2024/8f75_28895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f75_28895/02_2024/8f75_28895.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f75_28895/02_2024/8f75_28895.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6369 2.51 5 N 1713 2.21 5 O 1785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "F PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 595": "OE1" <-> "OE2" Residue "F GLU 628": "OE1" <-> "OE2" Residue "F PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 795": "OD1" <-> "OD2" Residue "F GLU 798": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9899 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "B" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "F" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3257 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 17, 'TRANS': 386} Time building chain proxies: 5.46, per 1000 atoms: 0.55 Number of scatterers: 9899 At special positions: 0 Unit cell: (128.904, 112.136, 91.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1785 8.00 N 1713 7.00 C 6369 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 - 3.50 Amino acid : False - 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: 3.64 Conformation dependent library (CDL) restraints added in 1.7 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 33.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.637A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.528A pdb=" N ILE A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.888A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.695A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.910A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.954A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.606A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.645A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.549A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.656A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.648A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.877A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 508 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.012A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.513A pdb=" N LEU B 613 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.757A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.718A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.866A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.619A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.637A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.510A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'F' and resid 401 through 409 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.649A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'F' and resid 508 through 513 removed outlier: 3.711A pdb=" N TYR F 511 " --> pdb=" O PRO F 508 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 540 removed outlier: 4.042A pdb=" N ARG F 539 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 removed outlier: 3.574A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 605 through 610 Processing helix chain 'F' and resid 629 through 636 removed outlier: 4.564A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.797A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 682 removed outlier: 3.939A pdb=" N PHE F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS F 682 " --> pdb=" O HIS F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.537A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY F 703 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 728 Processing helix chain 'F' and resid 768 through 774 removed outlier: 3.696A pdb=" N CYS F 774 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 791 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.838A pdb=" N MET F 800 " --> pdb=" O VAL F 796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.378A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 596 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.352A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 668 removed outlier: 3.660A pdb=" N ASP A 691 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 760 removed outlier: 6.342A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.517A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 501 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA7, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.029A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 419 through 420 removed outlier: 6.080A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS F 735 " --> pdb=" O PHE F 711 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP F 758 " --> pdb=" O LEU F 734 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 757 " --> pdb=" O VAL F 783 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 457 through 459 removed outlier: 5.735A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 242 hydrogen bonds defined for protein. 513 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: 3.01 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3157 1.34 - 1.46: 1064 1.46 - 1.57: 5806 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 10071 Sorted by residual: bond pdb=" N THR B 412 " pdb=" CA THR B 412 " ideal model delta sigma weight residual 1.453 1.489 -0.037 1.31e-02 5.83e+03 7.89e+00 bond pdb=" N ARG B 688 " pdb=" CA ARG B 688 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE A 606 " pdb=" CA ILE A 606 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.57e+00 bond pdb=" N HIS A 608 " pdb=" CA HIS A 608 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.44e+00 bond pdb=" N ASP B 414 " pdb=" CA ASP B 414 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.37e+00 ... (remaining 10066 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.03: 222 106.03 - 113.14: 5729 113.14 - 120.26: 3618 120.26 - 127.37: 3976 127.37 - 134.48: 97 Bond angle restraints: 13642 Sorted by residual: angle pdb=" N ARG B 685 " pdb=" CA ARG B 685 " pdb=" C ARG B 685 " ideal model delta sigma weight residual 113.16 122.65 -9.49 1.24e+00 6.50e-01 5.86e+01 angle pdb=" CA LYS F 555 " pdb=" CB LYS F 555 " pdb=" CG LYS F 555 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.91e+01 angle pdb=" N ILE F 713 " pdb=" CA ILE F 713 " pdb=" C ILE F 713 " ideal model delta sigma weight residual 112.17 108.07 4.10 9.50e-01 1.11e+00 1.87e+01 angle pdb=" CA LEU B 687 " pdb=" C LEU B 687 " pdb=" O LEU B 687 " ideal model delta sigma weight residual 122.64 117.83 4.81 1.25e+00 6.40e-01 1.48e+01 angle pdb=" CA VAL B 715 " pdb=" CB VAL B 715 " pdb=" CG1 VAL B 715 " ideal model delta sigma weight residual 110.40 116.86 -6.46 1.70e+00 3.46e-01 1.44e+01 ... (remaining 13637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5500 17.82 - 35.63: 576 35.63 - 53.45: 148 53.45 - 71.26: 22 71.26 - 89.08: 4 Dihedral angle restraints: 6250 sinusoidal: 2646 harmonic: 3604 Sorted by residual: dihedral pdb=" CA ASP B 703 " pdb=" C ASP B 703 " pdb=" N ILE B 704 " pdb=" CA ILE B 704 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO B 747 " pdb=" C PRO B 747 " pdb=" N SER B 748 " pdb=" CA SER B 748 " ideal model delta harmonic sigma weight residual 180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LYS A 552 " pdb=" C LYS A 552 " pdb=" N SER A 553 " pdb=" CA SER A 553 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 6247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1299 0.055 - 0.111: 279 0.111 - 0.166: 46 0.166 - 0.222: 5 0.222 - 0.277: 4 Chirality restraints: 1633 Sorted by residual: chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE B 456 " pdb=" CA ILE B 456 " pdb=" CG1 ILE B 456 " pdb=" CG2 ILE B 456 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1630 not shown) Planarity restraints: 1715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 795 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO A 796 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 438 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO B 439 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 439 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 439 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.009 2.00e-02 2.50e+03 1.44e-02 5.17e+00 pdb=" CG TRP A 475 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 475 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 475 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 475 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 475 " 0.004 2.00e-02 2.50e+03 ... (remaining 1712 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2062 2.79 - 3.31: 9318 3.31 - 3.84: 16982 3.84 - 4.37: 21247 4.37 - 4.90: 33546 Nonbonded interactions: 83155 Sorted by model distance: nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.258 2.520 nonbonded pdb=" O TRP A 411 " pdb=" OG1 THR A 441 " model vdw 2.271 2.440 nonbonded pdb=" O GLN A 560 " pdb=" OG1 THR A 563 " model vdw 2.278 2.440 nonbonded pdb=" O GLU F 790 " pdb=" NH2 ARG F 797 " model vdw 2.310 2.520 nonbonded pdb=" NH1 ARG B 749 " pdb=" OE1 GLU B 752 " model vdw 2.313 2.520 ... (remaining 83150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 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: 15.500 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.920 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 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 0.065 10071 Z= 0.258 Angle : 0.804 9.710 13642 Z= 0.453 Chirality : 0.049 0.277 1633 Planarity : 0.006 0.072 1715 Dihedral : 15.362 89.081 3886 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.62 % Allowed : 19.24 % Favored : 80.14 % 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: -2.96 (0.23), residues: 1212 helix: -2.75 (0.23), residues: 369 sheet: -2.58 (0.37), residues: 182 loop : -1.19 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 475 HIS 0.009 0.001 HIS B 499 PHE 0.029 0.002 PHE F 609 TYR 0.017 0.001 TYR F 756 ARG 0.006 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 385 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.8195 (tp) cc_final: 0.7310 (mt) REVERT: A 448 LEU cc_start: 0.8331 (tp) cc_final: 0.7879 (tp) REVERT: A 471 LEU cc_start: 0.8452 (tt) cc_final: 0.8162 (tp) REVERT: A 546 LEU cc_start: 0.8464 (tp) cc_final: 0.8127 (tp) REVERT: A 569 LEU cc_start: 0.8404 (mt) cc_final: 0.8129 (mt) REVERT: A 572 LEU cc_start: 0.8994 (tp) cc_final: 0.8558 (tp) REVERT: A 611 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: A 621 LEU cc_start: 0.8903 (mt) cc_final: 0.8654 (mt) REVERT: A 623 ASP cc_start: 0.8758 (t0) cc_final: 0.8031 (t70) REVERT: A 643 CYS cc_start: 0.7469 (t) cc_final: 0.7090 (m) REVERT: A 710 LEU cc_start: 0.9117 (tp) cc_final: 0.8611 (mt) REVERT: A 720 ILE cc_start: 0.9366 (mt) cc_final: 0.9148 (mm) REVERT: A 736 LEU cc_start: 0.9170 (mt) cc_final: 0.8951 (mt) REVERT: A 794 LEU cc_start: 0.9110 (mt) cc_final: 0.8784 (mt) REVERT: A 799 LYS cc_start: 0.9261 (mtmt) cc_final: 0.9034 (ttmt) REVERT: B 443 PHE cc_start: 0.7575 (m-10) cc_final: 0.7304 (m-80) REVERT: B 475 TRP cc_start: 0.8269 (m-10) cc_final: 0.7400 (m-10) REVERT: B 513 TYR cc_start: 0.6183 (m-80) cc_final: 0.5371 (m-10) REVERT: B 549 LEU cc_start: 0.9121 (tp) cc_final: 0.8833 (tp) REVERT: F 458 MET cc_start: 0.7017 (tpt) cc_final: 0.6781 (tpt) REVERT: F 505 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6343 (mm-30) REVERT: F 516 LEU cc_start: 0.8752 (mt) cc_final: 0.8371 (tp) REVERT: F 550 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8804 (mppt) REVERT: F 581 MET cc_start: 0.7455 (tpp) cc_final: 0.7084 (tpp) REVERT: F 583 ASN cc_start: 0.8785 (m-40) cc_final: 0.8530 (p0) REVERT: F 594 LEU cc_start: 0.8165 (tp) cc_final: 0.7671 (tp) REVERT: F 612 LEU cc_start: 0.7415 (mt) cc_final: 0.6945 (pp) REVERT: F 623 ASN cc_start: 0.7476 (m-40) cc_final: 0.6586 (p0) REVERT: F 642 LEU cc_start: 0.7566 (tp) cc_final: 0.7240 (tp) REVERT: F 644 LEU cc_start: 0.9414 (mt) cc_final: 0.9202 (tt) REVERT: F 701 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7095 (tp30) REVERT: F 704 VAL cc_start: 0.7392 (t) cc_final: 0.6964 (t) REVERT: F 777 LEU cc_start: 0.8244 (tp) cc_final: 0.8037 (tt) outliers start: 7 outliers final: 0 residues processed: 389 average time/residue: 0.2683 time to fit residues: 136.5950 Evaluate side-chains 228 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A 592 ASN A 636 GLN A 637 HIS A 755 ASN B 409 ASN B 478 HIS B 575 ASN B 576 ASN ** B 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 ASN ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS F 635 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10071 Z= 0.281 Angle : 0.765 12.231 13642 Z= 0.380 Chirality : 0.045 0.180 1633 Planarity : 0.005 0.056 1715 Dihedral : 5.126 22.914 1305 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.83 % Allowed : 23.90 % Favored : 71.27 % 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: -2.66 (0.24), residues: 1212 helix: -2.41 (0.25), residues: 373 sheet: -2.55 (0.37), residues: 186 loop : -0.99 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 475 HIS 0.007 0.001 HIS A 694 PHE 0.019 0.002 PHE B 682 TYR 0.021 0.002 TYR A 689 ARG 0.008 0.001 ARG B 781 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 219 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ARG cc_start: 0.8303 (mmt90) cc_final: 0.7878 (mmt-90) REVERT: A 560 GLN cc_start: 0.5592 (pm20) cc_final: 0.5277 (pp30) REVERT: A 710 LEU cc_start: 0.9107 (tp) cc_final: 0.8494 (mt) REVERT: A 712 ASN cc_start: 0.8752 (m-40) cc_final: 0.8477 (t0) REVERT: A 736 LEU cc_start: 0.9209 (mt) cc_final: 0.8856 (mp) REVERT: A 791 PHE cc_start: 0.7378 (t80) cc_final: 0.6867 (t80) REVERT: A 802 LEU cc_start: 0.8944 (tp) cc_final: 0.8346 (tp) REVERT: B 434 MET cc_start: 0.7542 (tmm) cc_final: 0.6787 (tmm) REVERT: B 477 TYR cc_start: 0.7263 (m-10) cc_final: 0.7029 (m-10) REVERT: B 575 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7389 (m-40) REVERT: B 599 ILE cc_start: 0.8626 (mm) cc_final: 0.8151 (mp) REVERT: B 620 ASP cc_start: 0.7031 (t0) cc_final: 0.6200 (m-30) REVERT: B 621 LEU cc_start: 0.8516 (mt) cc_final: 0.8164 (mt) REVERT: B 684 CYS cc_start: 0.5349 (OUTLIER) cc_final: 0.3471 (m) REVERT: F 516 LEU cc_start: 0.8892 (mt) cc_final: 0.8264 (tp) REVERT: F 521 LEU cc_start: 0.8957 (mt) cc_final: 0.8691 (mt) REVERT: F 529 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.6069 (tt) REVERT: F 541 LEU cc_start: 0.4970 (mt) cc_final: 0.4642 (mt) REVERT: F 550 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8795 (mppt) REVERT: F 591 LEU cc_start: 0.7039 (mm) cc_final: 0.5393 (tp) REVERT: F 611 LEU cc_start: 0.7290 (mm) cc_final: 0.6677 (mm) REVERT: F 612 LEU cc_start: 0.7620 (mt) cc_final: 0.7363 (pp) REVERT: F 665 LEU cc_start: 0.8104 (tp) cc_final: 0.7893 (mt) REVERT: F 680 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.5150 (m-80) REVERT: F 687 TYR cc_start: 0.7147 (t80) cc_final: 0.6778 (t80) REVERT: F 688 LEU cc_start: 0.9374 (mt) cc_final: 0.9146 (mt) REVERT: F 701 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7563 (tp30) REVERT: F 704 VAL cc_start: 0.7170 (t) cc_final: 0.6388 (t) outliers start: 55 outliers final: 26 residues processed: 255 average time/residue: 0.2323 time to fit residues: 80.5783 Evaluate side-chains 208 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 680 PHE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 743 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 0.0980 chunk 109 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN F 606 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10071 Z= 0.189 Angle : 0.726 17.162 13642 Z= 0.350 Chirality : 0.045 0.225 1633 Planarity : 0.005 0.048 1715 Dihedral : 4.872 20.693 1303 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.66 % Allowed : 24.69 % Favored : 70.65 % 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: -2.53 (0.24), residues: 1212 helix: -2.19 (0.25), residues: 364 sheet: -2.24 (0.39), residues: 186 loop : -1.10 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 475 HIS 0.006 0.001 HIS A 694 PHE 0.017 0.002 PHE A 682 TYR 0.017 0.001 TYR B 653 ARG 0.008 0.001 ARG F 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 193 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 PHE cc_start: 0.8468 (t80) cc_final: 0.8225 (t80) REVERT: A 496 ARG cc_start: 0.8392 (mmt90) cc_final: 0.7969 (mmt-90) REVERT: A 595 GLU cc_start: 0.7846 (mp0) cc_final: 0.6746 (mp0) REVERT: A 710 LEU cc_start: 0.9013 (tp) cc_final: 0.8456 (mt) REVERT: A 734 ARG cc_start: 0.9172 (mmm-85) cc_final: 0.8881 (mmm-85) REVERT: A 736 LEU cc_start: 0.9142 (mt) cc_final: 0.8644 (mt) REVERT: A 737 HIS cc_start: 0.8519 (m170) cc_final: 0.8212 (m-70) REVERT: A 791 PHE cc_start: 0.7092 (t80) cc_final: 0.6878 (t80) REVERT: A 802 LEU cc_start: 0.8773 (tp) cc_final: 0.8551 (tp) REVERT: B 403 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.4484 (ptt-90) REVERT: B 434 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6407 (tmm) REVERT: B 454 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6132 (mt-10) REVERT: B 572 LEU cc_start: 0.6703 (tp) cc_final: 0.6459 (mt) REVERT: B 620 ASP cc_start: 0.7011 (t0) cc_final: 0.6147 (m-30) REVERT: B 621 LEU cc_start: 0.8416 (mt) cc_final: 0.7932 (mt) REVERT: B 687 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8231 (tp) REVERT: B 700 LEU cc_start: 0.5283 (tt) cc_final: 0.4217 (tp) REVERT: F 516 LEU cc_start: 0.8821 (mt) cc_final: 0.8078 (tp) REVERT: F 520 TYR cc_start: 0.8084 (m-80) cc_final: 0.7672 (m-80) REVERT: F 521 LEU cc_start: 0.8952 (mt) cc_final: 0.8657 (mt) REVERT: F 541 LEU cc_start: 0.4961 (mt) cc_final: 0.4515 (mt) REVERT: F 550 LYS cc_start: 0.9172 (tmtt) cc_final: 0.8775 (mppt) REVERT: F 588 MET cc_start: 0.8129 (mmm) cc_final: 0.7672 (mmm) REVERT: F 591 LEU cc_start: 0.6871 (mm) cc_final: 0.5310 (tp) REVERT: F 611 LEU cc_start: 0.7460 (mm) cc_final: 0.6789 (mm) REVERT: F 612 LEU cc_start: 0.7458 (mt) cc_final: 0.7217 (pp) REVERT: F 687 TYR cc_start: 0.7458 (t80) cc_final: 0.7132 (t80) REVERT: F 701 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7501 (tp30) REVERT: F 704 VAL cc_start: 0.7231 (t) cc_final: 0.6498 (t) outliers start: 53 outliers final: 29 residues processed: 227 average time/residue: 0.2181 time to fit residues: 69.5862 Evaluate side-chains 202 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10071 Z= 0.185 Angle : 0.704 12.409 13642 Z= 0.337 Chirality : 0.044 0.200 1633 Planarity : 0.005 0.063 1715 Dihedral : 4.771 18.980 1303 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.10 % Allowed : 23.99 % Favored : 70.91 % 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: -2.53 (0.24), residues: 1212 helix: -2.15 (0.25), residues: 377 sheet: -2.08 (0.41), residues: 188 loop : -1.13 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 475 HIS 0.005 0.001 HIS B 522 PHE 0.028 0.002 PHE B 635 TYR 0.015 0.001 TYR A 668 ARG 0.005 0.000 ARG F 603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 179 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8301 (tptp) REVERT: A 471 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8190 (tp) REVERT: A 496 ARG cc_start: 0.8467 (mmt90) cc_final: 0.8057 (mmt-90) REVERT: A 620 ASP cc_start: 0.8594 (t0) cc_final: 0.7984 (m-30) REVERT: A 710 LEU cc_start: 0.8976 (tp) cc_final: 0.8420 (mt) REVERT: A 734 ARG cc_start: 0.9210 (mmm-85) cc_final: 0.9003 (mmm-85) REVERT: A 737 HIS cc_start: 0.8841 (m170) cc_final: 0.8537 (m-70) REVERT: A 802 LEU cc_start: 0.8772 (tp) cc_final: 0.8571 (tp) REVERT: B 403 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.4152 (ptt-90) REVERT: B 434 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6359 (tmm) REVERT: B 454 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6251 (mt-10) REVERT: B 475 TRP cc_start: 0.7809 (m-10) cc_final: 0.7108 (m-10) REVERT: B 477 TYR cc_start: 0.7025 (m-10) cc_final: 0.6456 (m-10) REVERT: B 550 ARG cc_start: 0.8359 (ttt-90) cc_final: 0.8154 (tpt-90) REVERT: B 551 LEU cc_start: 0.7955 (tp) cc_final: 0.7595 (mm) REVERT: B 620 ASP cc_start: 0.7184 (t0) cc_final: 0.6493 (t70) REVERT: B 625 ASN cc_start: 0.8462 (t0) cc_final: 0.7691 (t0) REVERT: B 687 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8210 (tp) REVERT: B 700 LEU cc_start: 0.4828 (tt) cc_final: 0.3789 (tp) REVERT: B 749 ARG cc_start: 0.4551 (OUTLIER) cc_final: 0.4020 (ttp80) REVERT: F 521 LEU cc_start: 0.9011 (mt) cc_final: 0.8792 (mt) REVERT: F 550 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8800 (tptp) REVERT: F 593 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: F 611 LEU cc_start: 0.7635 (mm) cc_final: 0.6978 (mm) REVERT: F 612 LEU cc_start: 0.7421 (mt) cc_final: 0.7097 (pp) REVERT: F 701 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7486 (tp30) outliers start: 58 outliers final: 27 residues processed: 217 average time/residue: 0.2220 time to fit residues: 67.1311 Evaluate side-chains 193 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 1 optimal weight: 0.0670 chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS B 625 ASN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10071 Z= 0.176 Angle : 0.704 11.285 13642 Z= 0.334 Chirality : 0.045 0.240 1633 Planarity : 0.004 0.054 1715 Dihedral : 4.753 20.707 1303 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.48 % Allowed : 25.31 % Favored : 70.21 % 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: -2.40 (0.24), residues: 1212 helix: -1.95 (0.26), residues: 370 sheet: -1.96 (0.41), residues: 188 loop : -1.15 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 475 HIS 0.006 0.001 HIS B 522 PHE 0.020 0.002 PHE B 635 TYR 0.036 0.002 TYR F 687 ARG 0.004 0.000 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8289 (tptp) REVERT: A 471 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8248 (tp) REVERT: A 496 ARG cc_start: 0.8500 (mmt90) cc_final: 0.8042 (mmt-90) REVERT: A 571 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8586 (mmtm) REVERT: A 572 LEU cc_start: 0.8711 (mt) cc_final: 0.8510 (mt) REVERT: A 582 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 595 GLU cc_start: 0.8168 (mp0) cc_final: 0.7908 (mp0) REVERT: A 710 LEU cc_start: 0.8974 (tp) cc_final: 0.8211 (mt) REVERT: B 403 ARG cc_start: 0.5211 (OUTLIER) cc_final: 0.4465 (ptt-90) REVERT: B 434 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7247 (tmm) REVERT: B 454 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6311 (mt-10) REVERT: B 475 TRP cc_start: 0.7841 (m-10) cc_final: 0.7163 (m-10) REVERT: B 477 TYR cc_start: 0.7296 (m-10) cc_final: 0.6749 (m-10) REVERT: B 551 LEU cc_start: 0.8026 (tp) cc_final: 0.7648 (mm) REVERT: B 684 CYS cc_start: 0.5371 (OUTLIER) cc_final: 0.4287 (m) REVERT: B 687 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8223 (tp) REVERT: B 749 ARG cc_start: 0.4736 (OUTLIER) cc_final: 0.4104 (tmt170) REVERT: F 495 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7686 (t) REVERT: F 550 LYS cc_start: 0.9182 (tmtt) cc_final: 0.8785 (tptp) REVERT: F 588 MET cc_start: 0.8590 (mmp) cc_final: 0.8008 (mmm) REVERT: F 593 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: F 611 LEU cc_start: 0.7600 (mm) cc_final: 0.6805 (mm) REVERT: F 612 LEU cc_start: 0.7405 (mt) cc_final: 0.7069 (pp) REVERT: F 701 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7472 (tp30) outliers start: 51 outliers final: 30 residues processed: 205 average time/residue: 0.2330 time to fit residues: 66.2917 Evaluate side-chains 197 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.0270 chunk 104 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS B 625 ASN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10071 Z= 0.187 Angle : 0.687 10.799 13642 Z= 0.328 Chirality : 0.044 0.249 1633 Planarity : 0.004 0.052 1715 Dihedral : 4.705 20.530 1303 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.22 % Allowed : 26.63 % Favored : 69.16 % 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: -2.34 (0.25), residues: 1212 helix: -1.96 (0.26), residues: 371 sheet: -2.11 (0.39), residues: 209 loop : -0.94 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 475 HIS 0.022 0.001 HIS B 614 PHE 0.018 0.002 PHE B 635 TYR 0.038 0.002 TYR F 687 ARG 0.006 0.000 ARG B 550 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 161 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8236 (tp) REVERT: A 496 ARG cc_start: 0.8487 (mmt90) cc_final: 0.8051 (mmt-90) REVERT: A 571 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8594 (mmtm) REVERT: A 710 LEU cc_start: 0.8949 (tp) cc_final: 0.8410 (mt) REVERT: A 734 ARG cc_start: 0.9175 (mmm-85) cc_final: 0.8926 (mmm-85) REVERT: B 403 ARG cc_start: 0.5167 (OUTLIER) cc_final: 0.4124 (ptt-90) REVERT: B 434 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7058 (tmm) REVERT: B 453 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7709 (mm) REVERT: B 454 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6430 (mt-10) REVERT: B 477 TYR cc_start: 0.7380 (m-10) cc_final: 0.7020 (m-10) REVERT: B 684 CYS cc_start: 0.5287 (OUTLIER) cc_final: 0.4088 (m) REVERT: B 687 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8263 (tp) REVERT: B 749 ARG cc_start: 0.4783 (OUTLIER) cc_final: 0.4182 (tmt170) REVERT: F 495 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7580 (t) REVERT: F 550 LYS cc_start: 0.9217 (tmtt) cc_final: 0.8827 (tptp) REVERT: F 588 MET cc_start: 0.8550 (mmp) cc_final: 0.8282 (mmm) REVERT: F 593 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: F 611 LEU cc_start: 0.7633 (mm) cc_final: 0.6863 (mm) REVERT: F 612 LEU cc_start: 0.7335 (mt) cc_final: 0.6962 (pp) REVERT: F 701 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7481 (tp30) outliers start: 48 outliers final: 25 residues processed: 194 average time/residue: 0.2248 time to fit residues: 60.5603 Evaluate side-chains 189 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 636 GLN B 660 ASN B 696 ASN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10071 Z= 0.272 Angle : 0.749 12.085 13642 Z= 0.365 Chirality : 0.046 0.331 1633 Planarity : 0.006 0.080 1715 Dihedral : 4.927 20.984 1303 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 28.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.27 % Allowed : 26.71 % Favored : 68.01 % 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: -2.49 (0.24), residues: 1212 helix: -2.13 (0.25), residues: 373 sheet: -2.14 (0.37), residues: 220 loop : -0.99 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 475 HIS 0.007 0.001 HIS B 522 PHE 0.021 0.002 PHE B 635 TYR 0.024 0.002 TYR F 687 ARG 0.007 0.001 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 150 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8250 (tp) REVERT: A 496 ARG cc_start: 0.8589 (mmt90) cc_final: 0.8120 (mmt-90) REVERT: A 572 LEU cc_start: 0.8648 (mt) cc_final: 0.8372 (mt) REVERT: A 710 LEU cc_start: 0.8994 (tp) cc_final: 0.8413 (mt) REVERT: A 734 ARG cc_start: 0.9277 (mmm-85) cc_final: 0.8871 (mmm-85) REVERT: B 403 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.3698 (ptt-90) REVERT: B 434 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.6911 (tmm) REVERT: B 453 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8050 (mm) REVERT: B 454 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: B 596 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7828 (mt) REVERT: B 684 CYS cc_start: 0.5644 (OUTLIER) cc_final: 0.3622 (m) REVERT: B 687 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8575 (mm) REVERT: B 749 ARG cc_start: 0.4623 (OUTLIER) cc_final: 0.3848 (ttp80) REVERT: F 495 VAL cc_start: 0.7793 (OUTLIER) cc_final: 0.7395 (t) REVERT: F 529 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6326 (tt) REVERT: F 550 LYS cc_start: 0.9291 (tmtt) cc_final: 0.8918 (tptp) REVERT: F 588 MET cc_start: 0.8658 (mmp) cc_final: 0.8129 (mmm) REVERT: F 593 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: F 611 LEU cc_start: 0.7705 (mm) cc_final: 0.6954 (mp) REVERT: F 612 LEU cc_start: 0.7408 (mt) cc_final: 0.6987 (pp) REVERT: F 701 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7645 (tp30) outliers start: 60 outliers final: 33 residues processed: 195 average time/residue: 0.2157 time to fit residues: 59.4489 Evaluate side-chains 185 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 140 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 708 GLN Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 743 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN F 606 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10071 Z= 0.180 Angle : 0.712 10.814 13642 Z= 0.338 Chirality : 0.045 0.267 1633 Planarity : 0.005 0.055 1715 Dihedral : 4.787 18.736 1303 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.51 % Allowed : 29.70 % Favored : 66.78 % 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: -2.47 (0.24), residues: 1212 helix: -1.98 (0.26), residues: 374 sheet: -2.11 (0.38), residues: 211 loop : -1.11 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 475 HIS 0.006 0.001 HIS A 522 PHE 0.017 0.002 PHE B 635 TYR 0.040 0.002 TYR F 687 ARG 0.008 0.001 ARG B 533 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 496 ARG cc_start: 0.8593 (mmt90) cc_final: 0.8125 (mmt-90) REVERT: A 710 LEU cc_start: 0.8922 (tp) cc_final: 0.8367 (mt) REVERT: A 734 ARG cc_start: 0.9276 (mmm-85) cc_final: 0.8810 (mmm-85) REVERT: B 403 ARG cc_start: 0.5124 (OUTLIER) cc_final: 0.3736 (ptt-90) REVERT: B 434 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7148 (tmm) REVERT: B 453 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7729 (mm) REVERT: B 454 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6617 (mt-10) REVERT: B 596 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7754 (mt) REVERT: B 710 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8147 (mm) REVERT: F 495 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7446 (t) REVERT: F 550 LYS cc_start: 0.9281 (tmtt) cc_final: 0.8916 (tptp) REVERT: F 588 MET cc_start: 0.8609 (mmp) cc_final: 0.8058 (mmm) REVERT: F 593 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: F 611 LEU cc_start: 0.7702 (mm) cc_final: 0.6766 (mt) REVERT: F 612 LEU cc_start: 0.7345 (mt) cc_final: 0.6997 (pp) REVERT: F 701 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7598 (tp30) outliers start: 40 outliers final: 22 residues processed: 181 average time/residue: 0.2254 time to fit residues: 57.3038 Evaluate side-chains 174 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 chunk 84 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.0370 chunk 113 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10071 Z= 0.179 Angle : 0.712 11.266 13642 Z= 0.335 Chirality : 0.045 0.290 1633 Planarity : 0.005 0.052 1715 Dihedral : 4.763 19.641 1303 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.08 % Allowed : 30.23 % Favored : 66.70 % 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: -2.49 (0.24), residues: 1212 helix: -2.08 (0.25), residues: 382 sheet: -2.08 (0.37), residues: 216 loop : -1.05 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 475 HIS 0.008 0.001 HIS F 606 PHE 0.016 0.001 PHE B 635 TYR 0.032 0.002 TYR F 687 ARG 0.005 0.000 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ARG cc_start: 0.8587 (mmt90) cc_final: 0.8242 (mmt-90) REVERT: A 710 LEU cc_start: 0.8919 (tp) cc_final: 0.8367 (mt) REVERT: A 734 ARG cc_start: 0.9270 (mmm-85) cc_final: 0.8895 (mmm-85) REVERT: A 801 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7659 (tpt90) REVERT: B 403 ARG cc_start: 0.5204 (OUTLIER) cc_final: 0.3686 (ptt-90) REVERT: B 434 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6880 (ppp) REVERT: B 453 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8188 (mm) REVERT: B 454 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: B 596 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7754 (mt) REVERT: B 710 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8578 (mm) REVERT: F 495 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7402 (t) REVERT: F 550 LYS cc_start: 0.9281 (tmtt) cc_final: 0.8873 (mppt) REVERT: F 588 MET cc_start: 0.8601 (mmp) cc_final: 0.8029 (mmm) REVERT: F 611 LEU cc_start: 0.7683 (mm) cc_final: 0.6707 (mt) REVERT: F 612 LEU cc_start: 0.7310 (mt) cc_final: 0.6915 (pp) REVERT: F 701 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7594 (tp30) outliers start: 35 outliers final: 25 residues processed: 171 average time/residue: 0.2185 time to fit residues: 52.8388 Evaluate side-chains 176 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10071 Z= 0.241 Angle : 0.745 11.070 13642 Z= 0.353 Chirality : 0.046 0.273 1633 Planarity : 0.005 0.053 1715 Dihedral : 4.910 19.575 1303 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.90 % Allowed : 30.58 % Favored : 66.52 % 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: -2.48 (0.24), residues: 1212 helix: -2.05 (0.25), residues: 390 sheet: -2.06 (0.38), residues: 206 loop : -1.06 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 475 HIS 0.019 0.002 HIS F 606 PHE 0.018 0.002 PHE B 635 TYR 0.016 0.002 TYR F 710 ARG 0.009 0.001 ARG B 734 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ARG cc_start: 0.8623 (mmt90) cc_final: 0.8267 (mmt-90) REVERT: A 710 LEU cc_start: 0.9029 (tp) cc_final: 0.8436 (mt) REVERT: A 720 ILE cc_start: 0.9119 (mm) cc_final: 0.8874 (mm) REVERT: A 734 ARG cc_start: 0.9282 (mmm-85) cc_final: 0.8934 (mmm-85) REVERT: B 403 ARG cc_start: 0.5413 (OUTLIER) cc_final: 0.3774 (ptt-90) REVERT: B 434 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7094 (ppp) REVERT: B 453 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8279 (mm) REVERT: B 454 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: B 596 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7703 (mt) REVERT: B 762 ARG cc_start: 0.8379 (mmp-170) cc_final: 0.8017 (mmp-170) REVERT: F 495 VAL cc_start: 0.7718 (OUTLIER) cc_final: 0.7320 (t) REVERT: F 529 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6421 (tt) REVERT: F 588 MET cc_start: 0.8637 (mmp) cc_final: 0.7773 (mmm) REVERT: F 611 LEU cc_start: 0.7814 (mm) cc_final: 0.6929 (mt) REVERT: F 612 LEU cc_start: 0.7324 (mt) cc_final: 0.6917 (pp) REVERT: F 701 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7618 (tp30) REVERT: F 778 LYS cc_start: 0.8426 (tppt) cc_final: 0.7630 (tptt) outliers start: 33 outliers final: 25 residues processed: 170 average time/residue: 0.2155 time to fit residues: 52.2269 Evaluate side-chains 168 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 694 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.081608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.070308 restraints weight = 67932.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.070838 restraints weight = 49799.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.071401 restraints weight = 37305.450| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10071 Z= 0.181 Angle : 0.741 10.926 13642 Z= 0.345 Chirality : 0.045 0.271 1633 Planarity : 0.005 0.050 1715 Dihedral : 4.780 19.083 1303 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.16 % Allowed : 30.67 % Favored : 66.17 % 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: -2.59 (0.24), residues: 1212 helix: -2.04 (0.25), residues: 391 sheet: -2.03 (0.39), residues: 195 loop : -1.27 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 475 HIS 0.005 0.001 HIS A 522 PHE 0.016 0.001 PHE B 635 TYR 0.011 0.001 TYR B 653 ARG 0.008 0.001 ARG A 801 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.94 seconds wall clock time: 46 minutes 22.55 seconds (2782.55 seconds total)