Starting phenix.real_space_refine on Sun Sep 29 20:37:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/09_2024/7ng4_12307_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/09_2024/7ng4_12307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/09_2024/7ng4_12307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/09_2024/7ng4_12307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/09_2024/7ng4_12307_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng4_12307/09_2024/7ng4_12307_trim.cif" } resolution = 4.4 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= 0.004 sd= 0.051 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 162 5.16 5 C 23505 2.51 5 N 6447 2.21 5 O 7005 1.98 5 H 37485 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 225 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74624 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 12392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12392 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12369 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.23, per 1000 atoms: 0.38 Number of scatterers: 74624 At special positions: 0 Unit cell: (136.284, 143.763, 226.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 162 16.00 P 16 15.00 Mg 4 11.99 O 7005 8.00 N 6447 7.00 C 23505 6.00 H 37485 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.18 Conformation dependent library (CDL) restraints added in 4.6 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8778 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 52 sheets defined 52.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.553A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.591A pdb=" N ARG A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 354 through 408 removed outlier: 3.743A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.819A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.797A pdb=" N ALA A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.581A pdb=" N LYS A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.599A pdb=" N GLN A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.859A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.604A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 removed outlier: 3.615A pdb=" N SER A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 747 removed outlier: 4.253A pdb=" N GLN A 743 " --> pdb=" O PRO A 739 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASP A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 829 Processing helix chain 'A' and resid 849 through 855 Proline residue: A 854 - end of helix Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 924 through 929 removed outlier: 3.743A pdb=" N GLU A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 947 removed outlier: 4.197A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.606A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.548A pdb=" N GLU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.568A pdb=" N ARG B 323 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.727A pdb=" N LEU B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 removed outlier: 3.605A pdb=" N GLU B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 389 Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.680A pdb=" N LEU B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 removed outlier: 4.542A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.594A pdb=" N ASP B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 removed outlier: 3.689A pdb=" N THR B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.855A pdb=" N ALA B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'B' and resid 531 through 541 removed outlier: 4.259A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 580 removed outlier: 3.561A pdb=" N GLN B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 602 through 611 removed outlier: 4.369A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 646 through 653 removed outlier: 4.287A pdb=" N MET B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 710 through 729 removed outlier: 3.743A pdb=" N LEU B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 723 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 741 through 746 Processing helix chain 'B' and resid 787 through 791 removed outlier: 4.344A pdb=" N ASP B 791 " --> pdb=" O GLN B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 removed outlier: 3.621A pdb=" N GLU B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Proline residue: B 854 - end of helix Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.591A pdb=" N VAL B 861 " --> pdb=" O GLY B 857 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 removed outlier: 4.025A pdb=" N ILE B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 916 removed outlier: 3.636A pdb=" N ASN B 916 " --> pdb=" O PRO B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 916' Processing helix chain 'B' and resid 917 through 922 removed outlier: 3.821A pdb=" N ASP B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 removed outlier: 3.964A pdb=" N THR B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.690A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.560A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 290 through 307 removed outlier: 4.109A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 319 through 323 removed outlier: 3.649A pdb=" N GLN C 322 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG C 323 " --> pdb=" O ALA C 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 319 through 323' Processing helix chain 'C' and resid 327 through 337 Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 354 through 407 removed outlier: 3.643A pdb=" N LEU C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.653A pdb=" N GLU C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 removed outlier: 4.110A pdb=" N MET C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.893A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.679A pdb=" N VAL C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 removed outlier: 3.592A pdb=" N LYS C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.444A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 559 Processing helix chain 'C' and resid 571 through 580 removed outlier: 3.724A pdb=" N GLN C 575 " --> pdb=" O GLY C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 603 through 612 removed outlier: 3.542A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 646 through 653 removed outlier: 4.140A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 671 removed outlier: 3.932A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 704 removed outlier: 3.610A pdb=" N LEU C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS C 704 " --> pdb=" O ILE C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 738 through 747 removed outlier: 4.311A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 removed outlier: 3.926A pdb=" N LYS C 790 " --> pdb=" O PRO C 787 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP C 791 " --> pdb=" O GLN C 788 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA C 792 " --> pdb=" O ASP C 789 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 787 through 792' Processing helix chain 'C' and resid 808 through 829 Processing helix chain 'C' and resid 834 through 838 removed outlier: 4.183A pdb=" N SER C 838 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Proline residue: C 854 - end of helix Processing helix chain 'C' and resid 856 through 870 removed outlier: 4.016A pdb=" N ILE C 860 " --> pdb=" O ALA C 856 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.735A pdb=" N LYS C 898 " --> pdb=" O GLY C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 915 No H-bonds generated for 'chain 'C' and resid 913 through 915' Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 938 through 947 removed outlier: 4.459A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 158 removed outlier: 4.311A pdb=" N ARG D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 290 through 307 removed outlier: 3.503A pdb=" N ALA D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.979A pdb=" N GLN D 322 " --> pdb=" O GLN D 319 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 319 through 323' Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.584A pdb=" N LEU D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.751A pdb=" N GLU D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 389 Processing helix chain 'D' and resid 391 through 406 Processing helix chain 'D' and resid 413 through 426 removed outlier: 3.816A pdb=" N ILE D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 removed outlier: 3.715A pdb=" N ASP D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 438 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP D 439 " --> pdb=" O MET D 435 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 447 " --> pdb=" O SER D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 468 removed outlier: 4.075A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 489 Processing helix chain 'D' and resid 494 through 511 removed outlier: 3.746A pdb=" N LYS D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 511 " --> pdb=" O VAL D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 541 removed outlier: 3.993A pdb=" N ALA D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 removed outlier: 3.762A pdb=" N LYS D 559 " --> pdb=" O VAL D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 removed outlier: 3.650A pdb=" N GLN D 575 " --> pdb=" O GLY D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'D' and resid 603 through 612 removed outlier: 3.827A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.990A pdb=" N ALA D 617 " --> pdb=" O GLU D 614 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN D 618 " --> pdb=" O GLN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.662A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 674 removed outlier: 3.606A pdb=" N LYS D 666 " --> pdb=" O VAL D 662 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 674 " --> pdb=" O ALA D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 683 Processing helix chain 'D' and resid 692 through 703 removed outlier: 3.688A pdb=" N LEU D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 729 removed outlier: 3.893A pdb=" N SER D 729 " --> pdb=" O TYR D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 747 removed outlier: 4.249A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 745 " --> pdb=" O ASN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 removed outlier: 3.612A pdb=" N MET D 826 " --> pdb=" O ARG D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Proline residue: D 854 - end of helix Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.611A pdb=" N ILE D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 921 removed outlier: 3.745A pdb=" N TYR D 921 " --> pdb=" O LYS D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 929 Processing helix chain 'D' and resid 939 through 947 removed outlier: 3.555A pdb=" N PHE D 943 " --> pdb=" O TYR D 939 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 158 removed outlier: 3.716A pdb=" N GLU E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.662A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 307 Processing helix chain 'E' and resid 312 through 318 Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.587A pdb=" N GLN E 322 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 323 " --> pdb=" O ALA E 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 319 through 323' Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.757A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 352 removed outlier: 3.577A pdb=" N GLU E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 403 removed outlier: 3.523A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 393 " --> pdb=" O GLN E 389 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR E 394 " --> pdb=" O THR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 425 Processing helix chain 'E' and resid 431 through 446 removed outlier: 3.546A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 468 removed outlier: 3.624A pdb=" N ASN E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 489 removed outlier: 3.985A pdb=" N ALA E 485 " --> pdb=" O ALA E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 530 through 541 removed outlier: 3.651A pdb=" N ARG E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 580 Processing helix chain 'E' and resid 591 through 595 Processing helix chain 'E' and resid 602 through 612 removed outlier: 4.347A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 617 Processing helix chain 'E' and resid 641 through 645 removed outlier: 3.797A pdb=" N THR E 644 " --> pdb=" O VAL E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 664 through 674 removed outlier: 4.013A pdb=" N ALA E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 674 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 682 Processing helix chain 'E' and resid 692 through 702 removed outlier: 3.646A pdb=" N LEU E 696 " --> pdb=" O SER E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 729 removed outlier: 3.690A pdb=" N LYS E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER E 729 " --> pdb=" O TYR E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.576A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 855 Proline residue: E 854 - end of helix Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 921 removed outlier: 3.787A pdb=" N PHE E 920 " --> pdb=" O ASN E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 947 removed outlier: 4.242A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 943 " --> pdb=" O TYR E 939 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP E 944 " --> pdb=" O ARG E 940 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE E 945 " --> pdb=" O GLU E 941 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE E 947 " --> pdb=" O PHE E 943 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 290 through 307 Processing helix chain 'F' and resid 312 through 318 Processing helix chain 'F' and resid 319 through 323 removed outlier: 3.692A pdb=" N ARG F 323 " --> pdb=" O ALA F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 removed outlier: 4.020A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 Processing helix chain 'F' and resid 354 through 389 Processing helix chain 'F' and resid 391 through 405 removed outlier: 3.644A pdb=" N LEU F 395 " --> pdb=" O HIS F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 427 removed outlier: 3.875A pdb=" N ASP F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.632A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 Processing helix chain 'F' and resid 479 through 490 removed outlier: 3.794A pdb=" N ASP F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 528 through 541 Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.815A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.867A pdb=" N LYS F 594 " --> pdb=" O GLU F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 612 Processing helix chain 'F' and resid 612 through 617 Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 673 removed outlier: 4.043A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 683 removed outlier: 3.622A pdb=" N GLN F 677 " --> pdb=" O TYR F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 687 No H-bonds generated for 'chain 'F' and resid 685 through 687' Processing helix chain 'F' and resid 692 through 704 removed outlier: 3.886A pdb=" N CYS F 704 " --> pdb=" O ILE F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.934A pdb=" N GLN F 713 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 715 " --> pdb=" O ASN F 711 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER F 729 " --> pdb=" O TYR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 747 removed outlier: 4.211A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 removed outlier: 3.626A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 849 through 855 Proline residue: F 854 - end of helix Processing helix chain 'F' and resid 856 through 870 removed outlier: 3.839A pdb=" N ILE F 860 " --> pdb=" O ALA F 856 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 865 " --> pdb=" O VAL F 861 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 904 removed outlier: 3.575A pdb=" N LYS F 898 " --> pdb=" O GLY F 894 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG F 904 " --> pdb=" O ILE F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 921 removed outlier: 3.774A pdb=" N PHE F 920 " --> pdb=" O ASN F 916 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 929 removed outlier: 3.516A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 939 through 947 removed outlier: 3.596A pdb=" N ASP F 944 " --> pdb=" O ARG F 940 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE F 947 " --> pdb=" O PHE F 943 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 164 removed outlier: 5.513A pdb=" N LEU A 168 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.556A pdb=" N PHE A 521 " --> pdb=" O CYS A 637 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 548 Processing sheet with id=AA6, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.698A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.708A pdb=" N LEU A 842 " --> pdb=" O GLU A 801 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA9, first strand: chain 'A' and resid 912 through 913 removed outlier: 5.940A pdb=" N LEU A 912 " --> pdb=" O VAL A 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AB2, first strand: chain 'B' and resid 163 through 164 removed outlier: 4.848A pdb=" N LEU B 168 " --> pdb=" O TYR B 186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AB4, first strand: chain 'B' and resid 518 through 520 removed outlier: 3.639A pdb=" N LEU B 519 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 547 through 548 removed outlier: 7.439A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 765 through 770 removed outlier: 6.248A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.585A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 882 through 883 removed outlier: 4.581A pdb=" N GLU B 882 " --> pdb=" O LEU B 890 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 890 " --> pdb=" O GLU B 882 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AC1, first strand: chain 'C' and resid 163 through 164 removed outlier: 4.695A pdb=" N LEU C 168 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AC3, first strand: chain 'C' and resid 520 through 521 Processing sheet with id=AC4, first strand: chain 'C' and resid 544 through 548 removed outlier: 3.666A pdb=" N PHE C 545 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 547 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C 590 " --> pdb=" O PHE C 547 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 689 through 690 removed outlier: 6.935A pdb=" N VAL C 735 " --> pdb=" O LYS C 690 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 767 through 769 Processing sheet with id=AC7, first strand: chain 'C' and resid 781 through 784 removed outlier: 5.405A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 883 removed outlier: 4.042A pdb=" N GLU C 882 " --> pdb=" O LEU C 890 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AD1, first strand: chain 'D' and resid 163 through 169 removed outlier: 6.552A pdb=" N VAL D 164 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR D 190 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 166 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR D 188 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU D 168 " --> pdb=" O TYR D 186 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 638 through 639 removed outlier: 6.503A pdb=" N PHE D 521 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 522 " --> pdb=" O ILE D 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 544 through 548 removed outlier: 3.571A pdb=" N PHE D 545 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.562A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 764 through 766 removed outlier: 6.481A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 769 through 770 Processing sheet with id=AD7, first strand: chain 'D' and resid 912 through 913 removed outlier: 6.116A pdb=" N LEU D 912 " --> pdb=" O VAL D 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AD9, first strand: chain 'E' and resid 163 through 164 removed outlier: 5.453A pdb=" N LEU E 168 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 163 through 164 Processing sheet with id=AE2, first strand: chain 'E' and resid 521 through 522 Processing sheet with id=AE3, first strand: chain 'E' and resid 547 through 548 removed outlier: 7.200A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 619 through 620 removed outlier: 3.664A pdb=" N PHE E 619 " --> pdb=" O VAL E 628 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.285A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 764 through 769 removed outlier: 3.768A pdb=" N VAL E 765 " --> pdb=" O VAL E 780 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL E 780 " --> pdb=" O VAL E 765 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 882 through 883 removed outlier: 4.486A pdb=" N GLU E 882 " --> pdb=" O LEU E 890 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU E 890 " --> pdb=" O GLU E 882 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 911 through 913 removed outlier: 5.694A pdb=" N LEU E 912 " --> pdb=" O VAL E 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AF1, first strand: chain 'F' and resid 163 through 169 removed outlier: 6.315A pdb=" N VAL F 164 " --> pdb=" O THR F 190 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR F 190 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL F 166 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR F 188 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU F 168 " --> pdb=" O TYR F 186 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 637 through 639 removed outlier: 6.086A pdb=" N PHE F 521 " --> pdb=" O ALA F 639 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.573A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.776A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 764 through 766 removed outlier: 5.992A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 769 through 770 Processing sheet with id=AF7, first strand: chain 'F' and resid 909 through 913 removed outlier: 3.589A pdb=" N LEU F 912 " --> pdb=" O HIS F 934 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F 936 " --> pdb=" O LEU F 912 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4578 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: 26.37 Time building geometry restraints manager: 18.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 37443 1.02 - 1.22: 90 1.22 - 1.42: 14990 1.42 - 1.63: 22438 1.63 - 1.83: 282 Bond restraints: 75243 Sorted by residual: bond pdb=" C4 ATP F1001 " pdb=" C5 ATP F1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.67e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.13e+01 bond pdb=" C5 ATP F1001 " pdb=" C6 ATP F1001 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C4 ATP C1001 " pdb=" C5 ATP C1001 " ideal model delta sigma weight residual 1.388 1.450 -0.062 1.00e-02 1.00e+04 3.87e+01 bond pdb=" C5 ATP A1001 " pdb=" C6 ATP A1001 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.85e+01 ... (remaining 75238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.62: 136408 6.62 - 13.25: 163 13.25 - 19.87: 1 19.87 - 26.50: 17 26.50 - 33.12: 8 Bond angle restraints: 136597 Sorted by residual: angle pdb=" PA ATP C1001 " pdb=" O3A ATP C1001 " pdb=" PB ATP C1001 " ideal model delta sigma weight residual 136.83 110.91 25.92 1.00e+00 1.00e+00 6.72e+02 angle pdb=" PB ATP B1001 " pdb=" O3B ATP B1001 " pdb=" PG ATP B1001 " ideal model delta sigma weight residual 139.87 114.66 25.21 1.00e+00 1.00e+00 6.36e+02 angle pdb=" PA ATP B1001 " pdb=" O3A ATP B1001 " pdb=" PB ATP B1001 " ideal model delta sigma weight residual 136.83 112.06 24.77 1.00e+00 1.00e+00 6.14e+02 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 112.78 24.05 1.00e+00 1.00e+00 5.79e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 115.97 23.90 1.00e+00 1.00e+00 5.71e+02 ... (remaining 136592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 33389 27.34 - 54.68: 1427 54.68 - 82.02: 158 82.02 - 109.36: 20 109.36 - 136.70: 1 Dihedral angle restraints: 34995 sinusoidal: 19693 harmonic: 15302 Sorted by residual: dihedral pdb=" O2A ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PA ADP D1001 " pdb=" PB ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 76.70 -136.70 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" CA PRO E 762 " pdb=" C PRO E 762 " pdb=" N GLY E 763 " pdb=" CA GLY E 763 " ideal model delta harmonic sigma weight residual 180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS E 404 " pdb=" C LYS E 404 " pdb=" N LYS E 405 " pdb=" CA LYS E 405 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 34992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4921 0.090 - 0.181: 877 0.181 - 0.271: 50 0.271 - 0.362: 4 0.362 - 0.452: 1 Chirality restraints: 5853 Sorted by residual: chirality pdb=" CG LEU A 395 " pdb=" CB LEU A 395 " pdb=" CD1 LEU A 395 " pdb=" CD2 LEU A 395 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB THR F 299 " pdb=" CA THR F 299 " pdb=" OG1 THR F 299 " pdb=" CG2 THR F 299 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE E 402 " pdb=" CA ILE E 402 " pdb=" CG1 ILE E 402 " pdb=" CG2 ILE E 402 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 5850 not shown) Planarity restraints: 10966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 301 " -0.028 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C ARG E 301 " 0.097 2.00e-02 2.50e+03 pdb=" O ARG E 301 " -0.036 2.00e-02 2.50e+03 pdb=" N ASP E 302 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 803 " 0.027 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C THR E 803 " -0.095 2.00e-02 2.50e+03 pdb=" O THR E 803 " 0.036 2.00e-02 2.50e+03 pdb=" N GLY E 804 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 298 " 0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C LYS A 298 " -0.088 2.00e-02 2.50e+03 pdb=" O LYS A 298 " 0.033 2.00e-02 2.50e+03 pdb=" N THR A 299 " 0.030 2.00e-02 2.50e+03 ... (remaining 10963 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 6660 2.22 - 2.82: 160561 2.82 - 3.41: 194622 3.41 - 4.01: 243987 4.01 - 4.60: 384776 Nonbonded interactions: 990606 Sorted by model distance: nonbonded pdb=" H ILE A 889 " pdb=" O GLU A 937 " model vdw 1.628 2.450 nonbonded pdb=" O VAL E 166 " pdb=" H THR E 190 " model vdw 1.631 2.450 nonbonded pdb=" H CYS B 858 " pdb=" O GLY B 881 " model vdw 1.641 2.450 nonbonded pdb=" O ALA E 856 " pdb=" HG1 THR E 859 " model vdw 1.646 2.450 nonbonded pdb=" O VAL A 166 " pdb=" H THR A 190 " model vdw 1.653 2.450 ... (remaining 990601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 948)) selection = (chain 'B' and (resid 123 through 720 or (resid 721 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 t \ hrough 948)) selection = (chain 'C' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'D' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'E' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'F' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ } 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=0.00 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: 4.590 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: 0.990 Extract box with map and model: 2.510 Check model and map are aligned: 0.430 Set scattering table: 0.560 Process input model: 122.590 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.010 0.105 37758 Z= 0.684 Angle : 1.367 25.922 51016 Z= 0.809 Chirality : 0.065 0.452 5853 Planarity : 0.009 0.064 6542 Dihedral : 13.477 136.701 14572 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.12 % Allowed : 0.94 % Favored : 98.94 % 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: -2.19 (0.12), residues: 4632 helix: -1.86 (0.09), residues: 2065 sheet: -3.87 (0.18), residues: 537 loop : 0.06 (0.15), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 470 HIS 0.027 0.005 HIS B 839 PHE 0.046 0.005 PHE C 943 TYR 0.057 0.005 TYR A 673 ARG 0.018 0.002 ARG F 786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 4.611 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.0048 (mtp) cc_final: -0.0322 (tpp) REVERT: A 643 ASP cc_start: 0.9105 (m-30) cc_final: 0.8761 (p0) REVERT: A 756 MET cc_start: 0.8672 (tpp) cc_final: 0.8036 (tpp) REVERT: A 766 MET cc_start: 0.5411 (ptm) cc_final: 0.5194 (ppp) REVERT: B 494 MET cc_start: 0.8662 (mtm) cc_final: 0.8289 (mtt) REVERT: B 810 MET cc_start: 0.9317 (mtt) cc_final: 0.8790 (tpp) REVERT: C 272 MET cc_start: 0.3908 (ptm) cc_final: 0.1811 (ppp) REVERT: C 317 MET cc_start: -0.3901 (tmm) cc_final: -0.4164 (ttt) REVERT: C 773 MET cc_start: 0.9125 (mmp) cc_final: 0.8888 (tmm) REVERT: C 879 MET cc_start: 0.8324 (ptm) cc_final: 0.7516 (ppp) REVERT: D 197 MET cc_start: 0.1570 (mmt) cc_final: 0.1182 (pmm) REVERT: D 206 MET cc_start: -0.1635 (ppp) cc_final: -0.2248 (tpt) REVERT: D 569 MET cc_start: 0.9226 (ptp) cc_final: 0.8807 (pmm) REVERT: E 272 MET cc_start: 0.4485 (ppp) cc_final: 0.4165 (tmm) REVERT: F 318 MET cc_start: -0.3479 (ptt) cc_final: -0.4219 (ttt) outliers start: 5 outliers final: 2 residues processed: 154 average time/residue: 0.9401 time to fit residues: 239.2149 Evaluate side-chains 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 4.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 4.9990 chunk 351 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 363 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 421 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37758 Z= 0.223 Angle : 0.636 6.900 51016 Z= 0.345 Chirality : 0.040 0.161 5853 Planarity : 0.005 0.047 6542 Dihedral : 7.989 119.962 5236 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -1.26 (0.12), residues: 4632 helix: -0.22 (0.11), residues: 2096 sheet: -3.61 (0.18), residues: 576 loop : -0.39 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 470 HIS 0.013 0.001 HIS C 622 PHE 0.015 0.002 PHE C 370 TYR 0.017 0.001 TYR A 673 ARG 0.008 0.001 ARG C 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 4.640 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: 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 334 MET cc_start: 0.0028 (mtp) cc_final: -0.0293 (tpp) REVERT: A 643 ASP cc_start: 0.9124 (m-30) cc_final: 0.8744 (p0) REVERT: A 756 MET cc_start: 0.8591 (tpp) cc_final: 0.8084 (tpp) REVERT: B 494 MET cc_start: 0.8750 (mtm) cc_final: 0.8479 (mtt) REVERT: C 272 MET cc_start: 0.3699 (ptm) cc_final: 0.1584 (ppp) REVERT: C 317 MET cc_start: -0.3811 (tmm) cc_final: -0.4047 (ttt) REVERT: C 766 MET cc_start: 0.9481 (ptm) cc_final: 0.9217 (ptp) REVERT: C 773 MET cc_start: 0.9114 (mmp) cc_final: 0.8907 (tmm) REVERT: D 569 MET cc_start: 0.9216 (ptp) cc_final: 0.8753 (pmm) REVERT: D 869 MET cc_start: 0.8318 (mtm) cc_final: 0.8093 (mpp) REVERT: E 272 MET cc_start: 0.4527 (ppp) cc_final: 0.4259 (ppp) REVERT: E 879 MET cc_start: 0.9028 (ptp) cc_final: 0.8797 (ptp) REVERT: F 318 MET cc_start: -0.4143 (ptt) cc_final: -0.4826 (ttt) REVERT: F 879 MET cc_start: 0.9339 (ptt) cc_final: 0.9019 (ptt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.9538 time to fit residues: 227.4312 Evaluate side-chains 130 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 422 optimal weight: 9.9990 chunk 456 optimal weight: 7.9990 chunk 375 optimal weight: 6.9990 chunk 418 optimal weight: 8.9990 chunk 143 optimal weight: 30.0000 chunk 338 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS B 491 HIS ** C 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN E 491 HIS F 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 37758 Z= 0.281 Angle : 0.607 7.424 51016 Z= 0.325 Chirality : 0.039 0.142 5853 Planarity : 0.004 0.073 6542 Dihedral : 7.746 114.176 5236 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4632 helix: 0.18 (0.11), residues: 2111 sheet: -3.56 (0.18), residues: 577 loop : -0.69 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 470 HIS 0.007 0.001 HIS B 839 PHE 0.015 0.001 PHE D 920 TYR 0.015 0.001 TYR B 623 ARG 0.016 0.000 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 4.540 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: 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 209 MET cc_start: 0.5197 (mmm) cc_final: 0.4994 (mmt) REVERT: A 643 ASP cc_start: 0.9148 (m-30) cc_final: 0.8767 (p0) REVERT: A 756 MET cc_start: 0.8568 (tpp) cc_final: 0.8134 (tpp) REVERT: B 494 MET cc_start: 0.8871 (mtm) cc_final: 0.8655 (mtt) REVERT: C 206 MET cc_start: -0.5380 (ttt) cc_final: -0.5967 (ttt) REVERT: C 272 MET cc_start: 0.3953 (ptm) cc_final: 0.1694 (ppp) REVERT: C 317 MET cc_start: -0.4026 (tmm) cc_final: -0.4270 (ttt) REVERT: C 766 MET cc_start: 0.9509 (ptm) cc_final: 0.9261 (ptp) REVERT: C 773 MET cc_start: 0.9143 (mmp) cc_final: 0.8936 (tmm) REVERT: D 569 MET cc_start: 0.9223 (ptp) cc_final: 0.8871 (pmm) REVERT: E 197 MET cc_start: 0.2917 (mmt) cc_final: 0.2013 (mmm) REVERT: E 272 MET cc_start: 0.4641 (ppp) cc_final: 0.4273 (ppp) REVERT: E 494 MET cc_start: 0.8773 (mpp) cc_final: 0.8339 (mpp) REVERT: E 879 MET cc_start: 0.9052 (ptp) cc_final: 0.8822 (ptp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.8884 time to fit residues: 207.4114 Evaluate side-chains 129 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 9.9990 chunk 317 optimal weight: 30.0000 chunk 219 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 423 optimal weight: 20.0000 chunk 448 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 401 optimal weight: 50.0000 chunk 120 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 622 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 37758 Z= 0.189 Angle : 0.541 6.330 51016 Z= 0.287 Chirality : 0.038 0.141 5853 Planarity : 0.004 0.068 6542 Dihedral : 7.492 111.613 5236 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4632 helix: 0.48 (0.11), residues: 2120 sheet: -3.42 (0.19), residues: 570 loop : -0.79 (0.15), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 464 HIS 0.006 0.001 HIS B 839 PHE 0.021 0.001 PHE C 779 TYR 0.013 0.001 TYR E 394 ARG 0.004 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 4.540 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: 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 209 MET cc_start: 0.5211 (mmm) cc_final: 0.4998 (mmt) REVERT: A 643 ASP cc_start: 0.9169 (m-30) cc_final: 0.8789 (p0) REVERT: A 756 MET cc_start: 0.8541 (tpp) cc_final: 0.7878 (tpp) REVERT: B 494 MET cc_start: 0.8878 (mtm) cc_final: 0.8669 (mtt) REVERT: C 206 MET cc_start: -0.5349 (ttt) cc_final: -0.5932 (ttt) REVERT: C 272 MET cc_start: 0.3877 (ptm) cc_final: 0.1556 (ppp) REVERT: C 317 MET cc_start: -0.3991 (tmm) cc_final: -0.4232 (ttt) REVERT: C 766 MET cc_start: 0.9358 (ptm) cc_final: 0.8892 (mtm) REVERT: D 569 MET cc_start: 0.9202 (ptp) cc_final: 0.8858 (pmm) REVERT: E 272 MET cc_start: 0.4504 (ppp) cc_final: 0.4138 (ppp) REVERT: E 494 MET cc_start: 0.8613 (mpp) cc_final: 0.8156 (mpp) REVERT: F 879 MET cc_start: 0.9005 (ptt) cc_final: 0.8500 (ptt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.8882 time to fit residues: 205.6342 Evaluate side-chains 129 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 8.9990 chunk 254 optimal weight: 2.9990 chunk 6 optimal weight: 50.0000 chunk 333 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 382 optimal weight: 6.9990 chunk 310 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 229 optimal weight: 6.9990 chunk 402 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 HIS ** C 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37758 Z= 0.253 Angle : 0.563 6.408 51016 Z= 0.300 Chirality : 0.038 0.159 5853 Planarity : 0.004 0.063 6542 Dihedral : 7.410 111.912 5236 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.02 % Allowed : 1.14 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4632 helix: 0.53 (0.11), residues: 2120 sheet: -3.36 (0.19), residues: 564 loop : -0.95 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 770 HIS 0.007 0.001 HIS C 843 PHE 0.015 0.001 PHE D 824 TYR 0.016 0.001 TYR A 661 ARG 0.004 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 4.605 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: 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: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.5082 (mmm) cc_final: 0.4881 (mmt) REVERT: A 643 ASP cc_start: 0.9210 (m-30) cc_final: 0.8975 (p0) REVERT: A 756 MET cc_start: 0.8538 (tpp) cc_final: 0.7809 (mmm) REVERT: C 272 MET cc_start: 0.3925 (ptm) cc_final: 0.1610 (ppp) REVERT: C 317 MET cc_start: -0.3997 (tmm) cc_final: -0.4227 (ttt) REVERT: C 766 MET cc_start: 0.9411 (ptm) cc_final: 0.8886 (mtm) REVERT: C 869 MET cc_start: 0.9457 (mtm) cc_final: 0.9183 (ptp) REVERT: C 879 MET cc_start: 0.8076 (ptm) cc_final: 0.7602 (ptm) REVERT: D 569 MET cc_start: 0.9201 (ptp) cc_final: 0.8907 (pmm) REVERT: E 197 MET cc_start: 0.2970 (mmt) cc_final: 0.2228 (mmm) REVERT: E 494 MET cc_start: 0.8592 (mpp) cc_final: 0.8151 (mpp) REVERT: F 879 MET cc_start: 0.8989 (ptt) cc_final: 0.8778 (ptt) outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.8875 time to fit residues: 207.9312 Evaluate side-chains 130 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 4.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 30.0000 chunk 403 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 448 optimal weight: 2.9990 chunk 372 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN E 215 HIS E 347 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37758 Z= 0.241 Angle : 0.552 7.368 51016 Z= 0.294 Chirality : 0.038 0.148 5853 Planarity : 0.004 0.049 6542 Dihedral : 7.346 112.937 5236 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 4632 helix: 0.68 (0.11), residues: 2119 sheet: -3.28 (0.19), residues: 558 loop : -1.06 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 770 HIS 0.007 0.001 HIS C 843 PHE 0.016 0.001 PHE D 824 TYR 0.021 0.001 TYR A 703 ARG 0.006 0.000 ARG C 940 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 4.563 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: 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: symmetry clash REVERT: A 209 MET cc_start: 0.5176 (mmm) cc_final: 0.4976 (mmt) REVERT: A 643 ASP cc_start: 0.9239 (m-30) cc_final: 0.8974 (p0) REVERT: A 756 MET cc_start: 0.8507 (tpp) cc_final: 0.7923 (tpp) REVERT: C 206 MET cc_start: -0.5529 (ttt) cc_final: -0.6462 (ttt) REVERT: C 272 MET cc_start: 0.3770 (ptm) cc_final: 0.1460 (ppp) REVERT: C 766 MET cc_start: 0.9404 (ptm) cc_final: 0.8882 (mtm) REVERT: C 879 MET cc_start: 0.8083 (ptm) cc_final: 0.7564 (ptm) REVERT: D 569 MET cc_start: 0.9186 (ptp) cc_final: 0.8902 (pmm) REVERT: D 869 MET cc_start: 0.9265 (tpp) cc_final: 0.8926 (tpp) REVERT: E 494 MET cc_start: 0.8559 (mpp) cc_final: 0.8145 (mpp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.8773 time to fit residues: 201.5203 Evaluate side-chains 130 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 327 optimal weight: 40.0000 chunk 254 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 447 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37758 Z= 0.196 Angle : 0.524 8.374 51016 Z= 0.277 Chirality : 0.038 0.141 5853 Planarity : 0.004 0.044 6542 Dihedral : 7.235 112.177 5236 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4632 helix: 0.85 (0.11), residues: 2121 sheet: -3.16 (0.20), residues: 532 loop : -1.07 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 770 HIS 0.005 0.001 HIS B 839 PHE 0.018 0.001 PHE C 947 TYR 0.015 0.001 TYR B 703 ARG 0.003 0.000 ARG C 705 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 4.601 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: 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: symmetry clash REVERT: A 209 MET cc_start: 0.5336 (mmm) cc_final: 0.5111 (mmt) REVERT: A 756 MET cc_start: 0.8553 (tpp) cc_final: 0.7951 (tpp) REVERT: B 552 MET cc_start: 0.8302 (tpp) cc_final: 0.7664 (tpp) REVERT: C 272 MET cc_start: 0.3824 (ptm) cc_final: 0.1511 (ppp) REVERT: C 879 MET cc_start: 0.8091 (ptm) cc_final: 0.7584 (ptm) REVERT: D 569 MET cc_start: 0.9176 (ptp) cc_final: 0.8897 (pmm) REVERT: D 869 MET cc_start: 0.9250 (tpp) cc_final: 0.8914 (tpp) REVERT: E 494 MET cc_start: 0.8547 (mpp) cc_final: 0.8100 (mpp) REVERT: E 879 MET cc_start: 0.9064 (ptp) cc_final: 0.8796 (ptp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.9026 time to fit residues: 212.2833 Evaluate side-chains 130 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 351 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 839 HIS E 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37758 Z= 0.216 Angle : 0.531 8.031 51016 Z= 0.280 Chirality : 0.037 0.145 5853 Planarity : 0.003 0.040 6542 Dihedral : 7.186 113.019 5236 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4632 helix: 0.88 (0.11), residues: 2122 sheet: -3.15 (0.20), residues: 535 loop : -1.11 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 770 HIS 0.006 0.001 HIS C 843 PHE 0.014 0.001 PHE D 824 TYR 0.011 0.001 TYR D 492 ARG 0.004 0.000 ARG C 940 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 4.566 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: 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 209 MET cc_start: 0.5280 (mmm) cc_final: 0.5061 (mmt) REVERT: A 756 MET cc_start: 0.8558 (tpp) cc_final: 0.7968 (tpp) REVERT: C 272 MET cc_start: 0.3666 (ptm) cc_final: 0.1359 (ppp) REVERT: D 569 MET cc_start: 0.9174 (ptp) cc_final: 0.8899 (pmm) REVERT: D 869 MET cc_start: 0.9253 (tpp) cc_final: 0.8911 (tpp) REVERT: E 197 MET cc_start: 0.2850 (mmt) cc_final: 0.2502 (mmm) REVERT: E 494 MET cc_start: 0.8570 (mpp) cc_final: 0.8118 (mpp) REVERT: E 879 MET cc_start: 0.9059 (ptp) cc_final: 0.8786 (ptp) REVERT: F 879 MET cc_start: 0.8699 (ptt) cc_final: 0.8216 (ptt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.9516 time to fit residues: 218.4859 Evaluate side-chains 128 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 20.0000 chunk 428 optimal weight: 9.9990 chunk 390 optimal weight: 20.0000 chunk 416 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 327 optimal weight: 50.0000 chunk 127 optimal weight: 7.9990 chunk 376 optimal weight: 7.9990 chunk 394 optimal weight: 40.0000 chunk 415 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 37758 Z= 0.305 Angle : 0.589 10.765 51016 Z= 0.314 Chirality : 0.038 0.181 5853 Planarity : 0.004 0.092 6542 Dihedral : 7.231 115.729 5236 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 4632 helix: 0.64 (0.11), residues: 2125 sheet: -3.12 (0.20), residues: 534 loop : -1.28 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 464 HIS 0.010 0.001 HIS C 843 PHE 0.021 0.002 PHE D 824 TYR 0.025 0.002 TYR B 818 ARG 0.007 0.000 ARG B 822 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 4.689 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: 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 209 MET cc_start: 0.5353 (mmm) cc_final: 0.5123 (mmt) REVERT: A 756 MET cc_start: 0.8566 (tpp) cc_final: 0.7806 (mmm) REVERT: B 552 MET cc_start: 0.8404 (tpp) cc_final: 0.7813 (tpp) REVERT: C 272 MET cc_start: 0.3613 (ptm) cc_final: 0.2031 (ppp) REVERT: D 569 MET cc_start: 0.9194 (ptp) cc_final: 0.8818 (pmm) REVERT: D 869 MET cc_start: 0.9275 (tpp) cc_final: 0.8955 (tpp) REVERT: E 197 MET cc_start: 0.3053 (mmt) cc_final: 0.2424 (mmm) REVERT: E 494 MET cc_start: 0.8594 (mpp) cc_final: 0.8127 (mpp) REVERT: E 879 MET cc_start: 0.9035 (ptp) cc_final: 0.8769 (ptp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.9108 time to fit residues: 205.9968 Evaluate side-chains 128 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 20.0000 chunk 440 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 306 optimal weight: 9.9990 chunk 462 optimal weight: 50.0000 chunk 425 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37758 Z= 0.210 Angle : 0.538 11.186 51016 Z= 0.284 Chirality : 0.038 0.209 5853 Planarity : 0.004 0.067 6542 Dihedral : 7.134 114.403 5236 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4632 helix: 0.82 (0.11), residues: 2122 sheet: -3.08 (0.20), residues: 540 loop : -1.23 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 464 HIS 0.005 0.001 HIS C 843 PHE 0.016 0.001 PHE D 824 TYR 0.019 0.001 TYR E 522 ARG 0.004 0.000 ARG C 940 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 4.574 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: 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: symmetry clash REVERT: A 209 MET cc_start: 0.5347 (mmm) cc_final: 0.5126 (mmt) REVERT: A 756 MET cc_start: 0.8532 (tpp) cc_final: 0.7990 (tpp) REVERT: B 552 MET cc_start: 0.8437 (tpp) cc_final: 0.7855 (tpp) REVERT: C 272 MET cc_start: 0.3637 (ptm) cc_final: 0.1751 (ppp) REVERT: D 569 MET cc_start: 0.9177 (ptp) cc_final: 0.8811 (pmm) REVERT: E 197 MET cc_start: 0.2920 (mmt) cc_final: 0.2611 (mmm) REVERT: E 494 MET cc_start: 0.8534 (mpp) cc_final: 0.8128 (mpp) REVERT: E 879 MET cc_start: 0.9030 (ptp) cc_final: 0.8758 (ptp) REVERT: F 879 MET cc_start: 0.8692 (ptt) cc_final: 0.8192 (ptt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.9348 time to fit residues: 212.8905 Evaluate side-chains 130 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 6.9990 chunk 392 optimal weight: 30.0000 chunk 112 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 368 optimal weight: 3.9990 chunk 154 optimal weight: 50.0000 chunk 378 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.055400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.039713 restraints weight = 1226450.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.040255 restraints weight = 742142.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.040295 restraints weight = 471134.673| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37758 Z= 0.200 Angle : 0.528 7.089 51016 Z= 0.278 Chirality : 0.038 0.143 5853 Planarity : 0.004 0.043 6542 Dihedral : 7.048 113.854 5236 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4632 helix: 0.93 (0.11), residues: 2137 sheet: -3.00 (0.21), residues: 538 loop : -1.22 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 770 HIS 0.007 0.001 HIS E 622 PHE 0.018 0.001 PHE C 779 TYR 0.013 0.001 TYR E 623 ARG 0.004 0.000 ARG C 940 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8467.59 seconds wall clock time: 147 minutes 41.17 seconds (8861.17 seconds total)