Starting phenix.real_space_refine on Sun Sep 29 19:04:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/09_2024/7oxo_13102_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/09_2024/7oxo_13102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/09_2024/7oxo_13102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/09_2024/7oxo_13102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/09_2024/7oxo_13102_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/09_2024/7oxo_13102_trim.cif" } resolution = 3.9 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= 0.060 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 162 5.16 5 C 23442 2.51 5 N 6426 2.21 5 O 6972 1.98 5 H 37715 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74729 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12427 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.54, per 1000 atoms: 0.36 Number of scatterers: 74729 At special positions: 0 Unit cell: (142.83, 144.946, 221.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 162 16.00 P 12 15.00 O 6972 8.00 N 6426 7.00 C 23442 6.00 H 37715 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.03 Conformation dependent library (CDL) restraints added in 4.4 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: 8736 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 39 sheets defined 51.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 4.120A pdb=" N GLU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.538A pdb=" N VAL A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 307 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.621A pdb=" N LEU A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 407 removed outlier: 3.761A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 428 removed outlier: 3.901A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.830A pdb=" N ASP A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.780A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.672A pdb=" N ALA A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.750A pdb=" N LYS A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 554 through 560 removed outlier: 4.059A pdb=" N ILE A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.875A pdb=" N GLN A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.621A pdb=" N LYS A 594 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.970A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.579A pdb=" N ALA A 617 " --> pdb=" O GLU A 614 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 618 " --> pdb=" O GLN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.678A pdb=" N ASP A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 674 removed outlier: 3.950A pdb=" N LEU A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 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 removed outlier: 3.671A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 729 removed outlier: 4.144A pdb=" N SER A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 747 removed outlier: 4.350A pdb=" N GLN A 743 " --> pdb=" O PRO A 739 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 removed outlier: 3.824A pdb=" N MET A 826 " --> pdb=" O ARG A 822 " (cutoff:3.500A) 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 removed outlier: 3.512A pdb=" N ILE A 860 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 861 " --> pdb=" O GLY A 857 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 862 " --> pdb=" O CYS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 removed outlier: 3.626A pdb=" N LYS A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.850A pdb=" N TYR A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 938 through 947 removed outlier: 4.238A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.085A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.541A pdb=" N VAL B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.571A pdb=" N ALA B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.778A 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 327 through 337 Processing helix chain 'B' and resid 342 through 352 removed outlier: 3.522A 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 406 removed outlier: 3.881A pdb=" N LEU B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 removed outlier: 3.838A pdb=" N ILE B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.669A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 494 through 511 removed outlier: 3.696A pdb=" N LYS B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 554 through 560 removed outlier: 3.980A pdb=" N ILE B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 removed outlier: 3.630A 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 612 removed outlier: 3.558A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.745A pdb=" N ASN B 618 " --> pdb=" O GLN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 removed outlier: 3.685A pdb=" N ASP B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 674 removed outlier: 3.860A pdb=" N LEU B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 692 through 703 removed outlier: 3.764A pdb=" N LEU B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 729 removed outlier: 4.002A pdb=" N SER B 729 " --> pdb=" O TYR B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 747 removed outlier: 4.423A pdb=" N GLN B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 removed outlier: 3.816A pdb=" N MET B 826 " --> pdb=" O ARG B 822 " (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: 3.707A pdb=" N THR B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.677A pdb=" N LYS B 898 " --> pdb=" O GLY B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 923 removed outlier: 3.777A pdb=" N TYR B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 923 " --> pdb=" O ASP B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 938 through 945 removed outlier: 4.299A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.727A pdb=" N GLU C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 290 through 307 removed outlier: 3.504A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.612A pdb=" N GLN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.643A pdb=" N LEU C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 354 through 407 Processing helix chain 'C' and resid 413 through 428 removed outlier: 4.216A pdb=" N ILE C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 Processing helix chain 'C' and resid 452 through 468 removed outlier: 4.087A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 489 removed outlier: 3.580A pdb=" N ALA C 483 " --> pdb=" O ASP C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 removed outlier: 3.771A pdb=" N LYS C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 541 removed outlier: 3.647A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.505A pdb=" N ILE C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 removed outlier: 3.580A pdb=" N GLN C 575 " --> pdb=" O GLY C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 595 Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.839A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.922A pdb=" N ASN C 618 " --> pdb=" O GLN C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 651 removed outlier: 3.526A pdb=" N ASP C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 674 removed outlier: 3.771A pdb=" N LEU C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 674 " --> pdb=" O ALA C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 692 through 703 removed outlier: 3.883A pdb=" N LEU C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 729 removed outlier: 3.720A pdb=" N SER C 729 " --> pdb=" O TYR C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 747 removed outlier: 4.519A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 removed outlier: 3.816A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (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: 3.755A pdb=" N THR C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 removed outlier: 3.603A pdb=" N LYS C 898 " --> pdb=" O GLY C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 923 removed outlier: 3.517A pdb=" N PHE C 920 " --> pdb=" O ASN C 916 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR C 921 " --> pdb=" O LYS C 917 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 922 " --> pdb=" O LYS C 918 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 923 " --> pdb=" O ASP C 919 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 916 through 923' Processing helix chain 'C' and resid 924 through 929 removed outlier: 3.595A pdb=" N THR C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 945 removed outlier: 4.229A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.146A pdb=" N GLU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 removed outlier: 3.641A pdb=" N VAL D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 307 removed outlier: 3.892A 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 327 through 339 removed outlier: 3.550A pdb=" N LEU D 331 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.607A 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 405 removed outlier: 3.807A pdb=" N LEU D 395 " --> pdb=" O HIS D 391 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 428 removed outlier: 4.111A pdb=" N ILE D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 479 through 491 removed outlier: 3.680A pdb=" N ALA D 483 " --> pdb=" O ASP D 479 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 511 Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 571 through 581 removed outlier: 3.735A pdb=" N GLN D 575 " --> pdb=" O GLY D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.595A pdb=" N LYS D 594 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.904A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 651 Processing helix chain 'D' and resid 662 through 674 removed outlier: 3.785A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 683 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 738 through 746 removed outlier: 3.885A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 removed outlier: 3.649A 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: 3.613A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 905 removed outlier: 3.854A pdb=" N LYS D 898 " --> pdb=" O GLY D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 923 removed outlier: 3.779A pdb=" N TYR D 921 " --> pdb=" O LYS D 917 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 922 " --> pdb=" O LYS D 918 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 923 " --> pdb=" O ASP D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 929 Processing helix chain 'D' and resid 939 through 947 removed outlier: 3.610A pdb=" N PHE D 943 " --> pdb=" O TYR D 939 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 removed outlier: 4.212A pdb=" N GLU E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.103A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 307 removed outlier: 3.544A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 318 Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.533A pdb=" N LEU E 331 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 352 Processing helix chain 'E' and resid 354 through 404 removed outlier: 3.740A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS E 393 " --> pdb=" O GLN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 428 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.522A pdb=" N GLY E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 468 removed outlier: 3.703A pdb=" N ASN E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE E 468 " --> pdb=" O TRP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 491 removed outlier: 3.800A pdb=" N ALA E 483 " --> pdb=" O ASP E 479 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 512 removed outlier: 3.771A pdb=" N ARG E 511 " --> pdb=" O VAL E 507 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 512 " --> pdb=" O SER E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 581 Processing helix chain 'E' and resid 591 through 595 Processing helix chain 'E' and resid 602 through 612 removed outlier: 3.800A pdb=" N LEU E 608 " --> pdb=" O SER E 604 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 662 through 674 removed outlier: 3.715A pdb=" N LEU E 667 " --> pdb=" O ALA E 663 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG E 672 " --> pdb=" O ALA E 668 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU E 674 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 683 Processing helix chain 'E' and resid 692 through 703 removed outlier: 3.693A pdb=" N LEU E 696 " --> pdb=" O SER E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 729 removed outlier: 3.894A pdb=" N SER E 729 " --> pdb=" O TYR E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 747 removed outlier: 4.254A pdb=" N PHE E 745 " --> pdb=" O ASN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.747A 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 removed outlier: 3.635A pdb=" N ILE E 860 " --> pdb=" O ALA E 856 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL E 861 " --> pdb=" O GLY E 857 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR E 862 " --> pdb=" O CYS E 858 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 905 removed outlier: 3.552A pdb=" N LYS E 898 " --> pdb=" O GLY E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 915 No H-bonds generated for 'chain 'E' and resid 913 through 915' Processing helix chain 'E' and resid 916 through 923 removed outlier: 3.851A pdb=" N TYR E 921 " --> pdb=" O LYS E 917 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU E 923 " --> pdb=" O ASP E 919 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 939 through 947 removed outlier: 3.628A pdb=" N PHE E 943 " --> pdb=" O TYR E 939 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 removed outlier: 3.718A pdb=" N GLU F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 290 through 307 removed outlier: 3.776A pdb=" N ALA F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.520A pdb=" N GLN F 316 " --> pdb=" O GLU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 removed outlier: 3.522A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 removed outlier: 3.529A pdb=" N GLU F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 389 Processing helix chain 'F' and resid 391 through 405 removed outlier: 3.982A pdb=" N LEU F 395 " --> pdb=" O HIS F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 428 removed outlier: 3.961A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.729A pdb=" N GLY F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 removed outlier: 4.018A pdb=" N ILE F 468 " --> pdb=" O TRP F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 489 removed outlier: 3.577A pdb=" N ALA F 483 " --> pdb=" O ASP F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 511 removed outlier: 3.557A pdb=" N LYS F 498 " --> pdb=" O MET F 494 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 510 " --> pdb=" O ALA F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 541 Processing helix chain 'F' and resid 554 through 560 removed outlier: 3.808A pdb=" N ILE F 558 " --> pdb=" O ASP F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.585A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 595 Processing helix chain 'F' and resid 602 through 612 removed outlier: 3.737A pdb=" N ALA F 606 " --> pdb=" O ASP F 602 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU F 608 " --> pdb=" O SER F 604 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.507A pdb=" N ASN F 618 " --> pdb=" O GLN F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 651 removed outlier: 3.672A pdb=" N ASP F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 674 removed outlier: 3.633A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG F 672 " --> pdb=" O ALA F 668 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU F 674 " --> pdb=" O ALA F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 682 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 703 removed outlier: 3.818A pdb=" N LEU F 696 " --> pdb=" O SER F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.774A pdb=" N SER F 729 " --> pdb=" O TYR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 747 removed outlier: 4.558A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 removed outlier: 3.825A 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: 3.510A pdb=" N ILE F 860 " --> pdb=" O ALA F 856 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 861 " --> pdb=" O GLY F 857 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR F 862 " --> pdb=" O CYS F 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 905 removed outlier: 3.586A pdb=" N LYS F 898 " --> pdb=" O GLY F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 923 removed outlier: 3.763A pdb=" N TYR F 921 " --> pdb=" O LYS F 917 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 923 " --> pdb=" O ASP F 919 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 929 removed outlier: 3.615A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 938 through 947 removed outlier: 4.236A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) removed outlier: 3.573A 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 164 through 167 Processing sheet with id=AA3, first strand: chain 'A' and resid 637 through 639 removed outlier: 5.979A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.851A pdb=" N PHE A 545 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP A 590 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 547 " --> pdb=" O ASP A 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.848A pdb=" N LYS A 690 " --> pdb=" O VAL A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 766 removed outlier: 6.102A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 910 through 913 removed outlier: 6.762A pdb=" N ILE A 910 " --> pdb=" O HIS A 934 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 936 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 912 " --> pdb=" O VAL A 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 140 through 143 Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 169 removed outlier: 7.623A pdb=" N VAL B 164 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR B 190 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL B 166 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR B 188 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU B 168 " --> pdb=" O TYR B 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 637 through 639 Processing sheet with id=AB2, first strand: chain 'B' and resid 544 through 548 removed outlier: 3.683A pdb=" N PHE B 545 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 689 through 691 removed outlier: 6.798A pdb=" N LYS B 690 " --> pdb=" O VAL B 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 764 through 766 removed outlier: 6.157A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 910 through 913 removed outlier: 6.843A pdb=" N ILE B 910 " --> pdb=" O HIS B 934 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL B 936 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU B 912 " --> pdb=" O VAL B 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB7, first strand: chain 'C' and resid 164 through 167 Processing sheet with id=AB8, first strand: chain 'C' and resid 520 through 522 removed outlier: 8.830A pdb=" N THR C 638 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE C 589 " --> pdb=" O THR C 638 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 689 through 691 removed outlier: 6.938A pdb=" N LYS C 690 " --> pdb=" O VAL C 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 764 through 766 removed outlier: 6.204A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 910 through 913 removed outlier: 6.627A pdb=" N ILE C 910 " --> pdb=" O HIS C 934 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL C 936 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU C 912 " --> pdb=" O VAL C 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AC4, first strand: chain 'D' and resid 163 through 169 removed outlier: 6.916A pdb=" N VAL D 164 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR D 190 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL D 166 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR D 188 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU D 168 " --> pdb=" O TYR D 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.318A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 638 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU D 519 " --> pdb=" O CYS D 637 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 690 through 691 removed outlier: 5.839A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 764 through 766 removed outlier: 6.006A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 878 through 879 removed outlier: 7.414A pdb=" N ALA D 878 " --> pdb=" O VAL D 911 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 910 " --> pdb=" O HIS D 934 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL D 936 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 912 " --> pdb=" O VAL D 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AD1, first strand: chain 'E' and resid 163 through 169 removed outlier: 6.589A pdb=" N VAL E 164 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR E 190 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL E 166 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR E 188 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU E 168 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 637 through 638 removed outlier: 5.985A pdb=" N LEU E 519 " --> pdb=" O CYS E 637 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 543 through 548 removed outlier: 6.289A pdb=" N GLU E 543 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU E 588 " --> pdb=" O GLU E 543 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.254A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 764 through 765 removed outlier: 3.553A pdb=" N VAL E 765 " --> pdb=" O VAL E 780 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AD7, first strand: chain 'F' and resid 188 through 191 Processing sheet with id=AD8, first strand: chain 'F' and resid 637 through 639 removed outlier: 6.130A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 544 through 548 removed outlier: 7.069A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.773A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'F' and resid 764 through 769 removed outlier: 6.085A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 910 through 913 removed outlier: 6.824A pdb=" N ILE F 910 " --> pdb=" O HIS F 934 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL F 936 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU F 912 " --> pdb=" O VAL F 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 1543 hydrogen bonds defined for protein. 4467 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: 27.39 Time building geometry restraints manager: 18.56 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: 37673 1.02 - 1.22: 109 1.22 - 1.42: 14913 1.42 - 1.62: 22375 1.62 - 1.81: 283 Bond restraints: 75353 Sorted by residual: bond pdb=" CB MET F 879 " pdb=" CG MET F 879 " ideal model delta sigma weight residual 1.520 1.416 0.104 3.00e-02 1.11e+03 1.20e+01 bond pdb=" CA SER F 838 " pdb=" CB SER F 838 " ideal model delta sigma weight residual 1.534 1.475 0.059 1.78e-02 3.16e+03 1.08e+01 bond pdb=" C5 ADP A1001 " pdb=" C6 ADP A1001 " ideal model delta sigma weight residual 1.490 1.425 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" CG1 ILE F 900 " pdb=" CD1 ILE F 900 " ideal model delta sigma weight residual 1.513 1.387 0.126 3.90e-02 6.57e+02 1.05e+01 bond pdb=" CG GLU A 665 " pdb=" CD GLU A 665 " ideal model delta sigma weight residual 1.516 1.438 0.078 2.50e-02 1.60e+03 9.65e+00 ... (remaining 75348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 133739 3.15 - 6.29: 3044 6.29 - 9.44: 156 9.44 - 12.58: 17 12.58 - 15.73: 3 Bond angle restraints: 136959 Sorted by residual: angle pdb=" N GLY E 601 " pdb=" CA GLY E 601 " pdb=" C GLY E 601 " ideal model delta sigma weight residual 113.18 98.68 14.50 2.37e+00 1.78e-01 3.74e+01 angle pdb=" N GLY D 601 " pdb=" CA GLY D 601 " pdb=" C GLY D 601 " ideal model delta sigma weight residual 113.18 100.00 13.18 2.37e+00 1.78e-01 3.09e+01 angle pdb=" N GLN D 515 " pdb=" CA GLN D 515 " pdb=" C GLN D 515 " ideal model delta sigma weight residual 109.23 100.62 8.61 1.55e+00 4.16e-01 3.09e+01 angle pdb=" CB MET E 435 " pdb=" CG MET E 435 " pdb=" SD MET E 435 " ideal model delta sigma weight residual 112.70 128.43 -15.73 3.00e+00 1.11e-01 2.75e+01 angle pdb=" N MET E 435 " pdb=" CA MET E 435 " pdb=" CB MET E 435 " ideal model delta sigma weight residual 109.94 117.38 -7.44 1.49e+00 4.50e-01 2.49e+01 ... (remaining 136954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 33928 32.13 - 64.26: 912 64.26 - 96.39: 57 96.39 - 128.52: 1 128.52 - 160.65: 4 Dihedral angle restraints: 34902 sinusoidal: 19662 harmonic: 15240 Sorted by residual: dihedral pdb=" O1B ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PB ADP C1001 " pdb=" PA ADP C1001 " ideal model delta sinusoidal sigma weight residual -60.00 100.65 -160.65 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O1B ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PB ADP D1001 " pdb=" PA ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 144.33 155.66 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O1B ADP B1001 " pdb=" O3A ADP B1001 " pdb=" PB ADP B1001 " pdb=" PA ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 80.89 -140.90 1 2.00e+01 2.50e-03 4.26e+01 ... (remaining 34899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4765 0.089 - 0.178: 979 0.178 - 0.267: 80 0.267 - 0.357: 7 0.357 - 0.446: 1 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CB ILE B 532 " pdb=" CA ILE B 532 " pdb=" CG1 ILE B 532 " pdb=" CG2 ILE B 532 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CB ILE D 558 " pdb=" CA ILE D 558 " pdb=" CG1 ILE D 558 " pdb=" CG2 ILE D 558 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB VAL A 802 " pdb=" CA VAL A 802 " pdb=" CG1 VAL A 802 " pdb=" CG2 VAL A 802 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 5829 not shown) Planarity restraints: 10974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 421 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PHE E 421 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE E 421 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG E 422 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 615 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C GLN E 615 " -0.068 2.00e-02 2.50e+03 pdb=" O GLN E 615 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN E 616 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 464 " 0.025 2.00e-02 2.50e+03 1.93e-02 1.49e+01 pdb=" CG TRP D 464 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP D 464 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 464 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 464 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 464 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 464 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 464 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 464 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 464 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP D 464 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 TRP D 464 " 0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP D 464 " -0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 464 " -0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 464 " 0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP D 464 " 0.001 2.00e-02 2.50e+03 ... (remaining 10971 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 3156 2.17 - 2.77: 151128 2.77 - 3.38: 205088 3.38 - 3.99: 250474 3.99 - 4.60: 397695 Nonbonded interactions: 1007541 Sorted by model distance: nonbonded pdb=" O PHE F 619 " pdb=" H VAL F 628 " model vdw 1.556 2.450 nonbonded pdb=" O VAL F 166 " pdb=" H THR F 190 " model vdw 1.589 2.450 nonbonded pdb=" O ALA B 856 " pdb=" HG1 THR B 859 " model vdw 1.596 2.450 nonbonded pdb=" O ASP B 852 " pdb=" HG SER B 855 " model vdw 1.597 2.450 nonbonded pdb=" O ASP D 852 " pdb=" HG SER D 855 " model vdw 1.601 2.450 ... (remaining 1007536 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 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'B' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'C' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'D' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = chain 'E' selection = (chain 'F' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.990 Extract box with map and model: 2.080 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 121.330 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.290 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: 0.020 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: 133.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.013 0.136 37638 Z= 0.870 Angle : 1.336 15.727 50844 Z= 0.737 Chirality : 0.069 0.446 5832 Planarity : 0.008 0.056 6522 Dihedral : 13.053 160.653 14460 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.30 % Favored : 90.67 % Rotamer: Outliers : 0.02 % Allowed : 0.69 % Favored : 99.28 % 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: -2.64 (0.12), residues: 4632 helix: -2.04 (0.09), residues: 1956 sheet: -3.77 (0.18), residues: 585 loop : -0.54 (0.15), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.006 TRP D 464 HIS 0.027 0.003 HIS B 491 PHE 0.039 0.004 PHE F 545 TYR 0.033 0.004 TYR C 725 ARG 0.017 0.001 ARG E 137 *********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 4.344 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: B 569 MET cc_start: 0.9292 (pmm) cc_final: 0.8989 (pmm) REVERT: B 773 MET cc_start: 0.8551 (ppp) cc_final: 0.8204 (ppp) REVERT: C 317 MET cc_start: -0.2757 (tpp) cc_final: -0.2982 (mtm) REVERT: C 334 MET cc_start: 0.3561 (tpt) cc_final: 0.3276 (ttm) REVERT: C 432 LYS cc_start: 0.9507 (tmtt) cc_final: 0.9092 (mmmt) REVERT: C 552 MET cc_start: 0.9309 (tpp) cc_final: 0.8835 (tpp) REVERT: D 272 MET cc_start: 0.0916 (ptt) cc_final: -0.0516 (ttp) REVERT: D 334 MET cc_start: -0.2549 (mmt) cc_final: -0.3026 (tpt) REVERT: D 810 MET cc_start: 0.9525 (mmp) cc_final: 0.9295 (mmp) REVERT: E 206 MET cc_start: -0.1388 (ptp) cc_final: -0.1840 (tpp) REVERT: F 209 MET cc_start: 0.2666 (ptt) cc_final: 0.1420 (mtt) REVERT: F 451 HIS cc_start: 0.8213 (m90) cc_final: 0.7387 (m-70) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.8836 time to fit residues: 235.6595 Evaluate side-chains 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 4.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 0.8980 chunk 350 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 236 optimal weight: 30.0000 chunk 187 optimal weight: 0.9990 chunk 362 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 269 optimal weight: 8.9990 chunk 419 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN B 219 GLN C 219 GLN C 307 ASN C 916 ASN E 477 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37638 Z= 0.198 Angle : 0.684 8.575 50844 Z= 0.355 Chirality : 0.041 0.160 5832 Planarity : 0.005 0.044 6522 Dihedral : 7.684 179.132 5124 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % 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: -1.92 (0.12), residues: 4632 helix: -0.65 (0.11), residues: 2032 sheet: -3.42 (0.19), residues: 577 loop : -1.07 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 464 HIS 0.008 0.001 HIS B 195 PHE 0.016 0.001 PHE F 947 TYR 0.018 0.002 TYR E 360 ARG 0.006 0.001 ARG B 381 *********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 4.340 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: B 569 MET cc_start: 0.9284 (pmm) cc_final: 0.8997 (pmm) REVERT: B 773 MET cc_start: 0.8443 (ppp) cc_final: 0.8122 (ppp) REVERT: C 552 MET cc_start: 0.9284 (tpp) cc_final: 0.8649 (tpp) REVERT: D 334 MET cc_start: -0.2829 (mmt) cc_final: -0.3325 (tpt) REVERT: D 810 MET cc_start: 0.9464 (mmp) cc_final: 0.9195 (mmp) REVERT: F 209 MET cc_start: 0.2770 (ptt) cc_final: 0.1465 (mtt) REVERT: F 451 HIS cc_start: 0.8180 (m90) cc_final: 0.7337 (m-70) outliers start: 7 outliers final: 6 residues processed: 152 average time/residue: 0.8861 time to fit residues: 231.7533 Evaluate side-chains 141 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 569 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 349 optimal weight: 7.9990 chunk 285 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 420 optimal weight: 1.9990 chunk 454 optimal weight: 1.9990 chunk 374 optimal weight: 4.9990 chunk 416 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 GLN E 132 ASN E 916 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37638 Z= 0.272 Angle : 0.624 7.333 50844 Z= 0.319 Chirality : 0.039 0.146 5832 Planarity : 0.004 0.045 6522 Dihedral : 7.354 175.551 5124 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.22 % Allowed : 5.65 % Favored : 94.12 % 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: -1.52 (0.12), residues: 4632 helix: -0.06 (0.11), residues: 2038 sheet: -3.28 (0.19), residues: 588 loop : -1.14 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 770 HIS 0.004 0.001 HIS B 195 PHE 0.014 0.001 PHE F 947 TYR 0.015 0.001 TYR A 360 ARG 0.005 0.000 ARG D 822 *********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 4.328 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: B 569 MET cc_start: 0.9271 (pmm) cc_final: 0.8991 (pmm) REVERT: B 773 MET cc_start: 0.8539 (ppp) cc_final: 0.8145 (ppp) REVERT: C 334 MET cc_start: 0.3574 (tpt) cc_final: 0.3362 (ttm) REVERT: C 552 MET cc_start: 0.9246 (tpp) cc_final: 0.8624 (tpp) REVERT: D 334 MET cc_start: -0.2790 (mmt) cc_final: -0.3217 (tpt) REVERT: D 810 MET cc_start: 0.9437 (mmp) cc_final: 0.9205 (mmp) REVERT: F 209 MET cc_start: 0.2870 (ptt) cc_final: 0.1551 (mtt) REVERT: F 435 MET cc_start: 0.9237 (tpt) cc_final: 0.8977 (tpt) REVERT: F 451 HIS cc_start: 0.8167 (m90) cc_final: 0.7317 (m-70) outliers start: 9 outliers final: 9 residues processed: 143 average time/residue: 0.8869 time to fit residues: 217.2309 Evaluate side-chains 142 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain D residue 687 SER Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 7.9990 chunk 316 optimal weight: 30.0000 chunk 218 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 282 optimal weight: 20.0000 chunk 421 optimal weight: 2.9990 chunk 446 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 399 optimal weight: 30.0000 chunk 120 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 916 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 37638 Z= 0.162 Angle : 0.563 6.834 50844 Z= 0.281 Chirality : 0.039 0.150 5832 Planarity : 0.003 0.042 6522 Dihedral : 7.121 165.876 5124 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.30 % Allowed : 6.54 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4632 helix: 0.38 (0.11), residues: 2047 sheet: -3.05 (0.20), residues: 561 loop : -1.16 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 470 HIS 0.003 0.001 HIS B 195 PHE 0.010 0.001 PHE C 619 TYR 0.012 0.001 TYR A 360 ARG 0.005 0.000 ARG D 822 *********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 4.285 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: B 569 MET cc_start: 0.9273 (pmm) cc_final: 0.8990 (pmm) REVERT: B 773 MET cc_start: 0.8527 (ppp) cc_final: 0.8133 (ppp) REVERT: C 552 MET cc_start: 0.9224 (tpp) cc_final: 0.8870 (tpp) REVERT: D 209 MET cc_start: -0.0085 (tpt) cc_final: -0.0315 (tpt) REVERT: D 334 MET cc_start: -0.3141 (mmt) cc_final: -0.3574 (tpt) REVERT: D 810 MET cc_start: 0.9394 (mmp) cc_final: 0.9176 (mmp) REVERT: F 209 MET cc_start: 0.2629 (ptt) cc_final: 0.1386 (mtt) REVERT: F 435 MET cc_start: 0.9203 (tpt) cc_final: 0.8942 (tpt) REVERT: F 451 HIS cc_start: 0.8177 (m90) cc_final: 0.7348 (m-70) outliers start: 12 outliers final: 10 residues processed: 146 average time/residue: 0.9450 time to fit residues: 236.4205 Evaluate side-chains 144 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 4.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 2.9990 chunk 253 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 332 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 381 optimal weight: 3.9990 chunk 308 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 228 optimal weight: 0.9990 chunk 400 optimal weight: 0.0980 chunk 112 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37638 Z= 0.248 Angle : 0.573 6.987 50844 Z= 0.289 Chirality : 0.038 0.144 5832 Planarity : 0.003 0.037 6522 Dihedral : 6.916 163.252 5124 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.30 % Allowed : 7.38 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4632 helix: 0.52 (0.12), residues: 2052 sheet: -3.00 (0.20), residues: 587 loop : -1.16 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 770 HIS 0.003 0.001 HIS F 491 PHE 0.014 0.001 PHE F 947 TYR 0.015 0.001 TYR B 599 ARG 0.004 0.000 ARG D 822 *********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 4.299 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: B 569 MET cc_start: 0.9256 (pmm) cc_final: 0.8974 (pmm) REVERT: B 773 MET cc_start: 0.8563 (ppp) cc_final: 0.8152 (ppp) REVERT: C 552 MET cc_start: 0.9220 (tpp) cc_final: 0.8607 (tpp) REVERT: D 209 MET cc_start: -0.0038 (tpt) cc_final: -0.0281 (tpt) REVERT: D 272 MET cc_start: 0.1168 (ptt) cc_final: -0.0392 (ttp) REVERT: D 334 MET cc_start: -0.3347 (mmt) cc_final: -0.3798 (tpt) REVERT: D 810 MET cc_start: 0.9403 (mmp) cc_final: 0.9191 (mmp) REVERT: F 209 MET cc_start: 0.2621 (ptt) cc_final: 0.1377 (mtt) REVERT: F 435 MET cc_start: 0.9208 (tpt) cc_final: 0.8934 (tpt) REVERT: F 451 HIS cc_start: 0.8185 (m90) cc_final: 0.7407 (m-70) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.9012 time to fit residues: 221.8926 Evaluate side-chains 144 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 1.9990 chunk 402 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 262 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 447 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 234 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37638 Z= 0.190 Angle : 0.548 7.320 50844 Z= 0.272 Chirality : 0.038 0.149 5832 Planarity : 0.003 0.033 6522 Dihedral : 6.702 154.692 5124 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.35 % Allowed : 7.85 % Favored : 91.80 % 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: -0.86 (0.13), residues: 4632 helix: 0.74 (0.12), residues: 2053 sheet: -2.92 (0.20), residues: 580 loop : -1.15 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 770 HIS 0.003 0.001 HIS A 938 PHE 0.011 0.001 PHE C 619 TYR 0.012 0.001 TYR A 360 ARG 0.004 0.000 ARG D 822 *********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 4.384 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: B 569 MET cc_start: 0.9250 (pmm) cc_final: 0.8963 (pmm) REVERT: B 773 MET cc_start: 0.8540 (ppp) cc_final: 0.8115 (ppp) REVERT: C 552 MET cc_start: 0.9223 (tpp) cc_final: 0.8616 (tpp) REVERT: D 209 MET cc_start: -0.0108 (tpt) cc_final: -0.0400 (tpt) REVERT: D 272 MET cc_start: 0.1145 (ptt) cc_final: -0.0428 (ttp) REVERT: D 334 MET cc_start: -0.3395 (mmt) cc_final: -0.3863 (tpt) REVERT: F 209 MET cc_start: 0.2604 (ptt) cc_final: 0.1354 (mtt) REVERT: F 435 MET cc_start: 0.9198 (tpt) cc_final: 0.8918 (tpt) REVERT: F 451 HIS cc_start: 0.8241 (m90) cc_final: 0.7622 (t-90) outliers start: 14 outliers final: 10 residues processed: 150 average time/residue: 0.9257 time to fit residues: 238.0878 Evaluate side-chains 146 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 4.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 326 optimal weight: 40.0000 chunk 252 optimal weight: 30.0000 chunk 376 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 445 optimal weight: 0.3980 chunk 278 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37638 Z= 0.234 Angle : 0.557 9.433 50844 Z= 0.277 Chirality : 0.038 0.146 5832 Planarity : 0.003 0.034 6522 Dihedral : 6.520 151.366 5124 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.32 % Allowed : 8.30 % Favored : 91.38 % 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 (0.13), residues: 4632 helix: 0.83 (0.12), residues: 2054 sheet: -2.91 (0.20), residues: 601 loop : -1.14 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 770 HIS 0.004 0.001 HIS F 491 PHE 0.015 0.001 PHE F 947 TYR 0.018 0.001 TYR B 599 ARG 0.004 0.000 ARG D 822 *********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.6962 (mp) REVERT: B 569 MET cc_start: 0.9211 (pmm) cc_final: 0.8918 (pmm) REVERT: B 773 MET cc_start: 0.8540 (ppp) cc_final: 0.8113 (ppp) REVERT: C 552 MET cc_start: 0.9208 (tpp) cc_final: 0.8617 (tpp) REVERT: D 209 MET cc_start: -0.0159 (tpt) cc_final: -0.0439 (tpt) REVERT: D 272 MET cc_start: 0.1362 (ptt) cc_final: -0.0181 (ttp) REVERT: D 334 MET cc_start: -0.3515 (mmt) cc_final: -0.3966 (tpt) REVERT: F 209 MET cc_start: 0.2744 (ptt) cc_final: 0.1598 (mtt) REVERT: F 435 MET cc_start: 0.9201 (tpt) cc_final: 0.8912 (tpt) REVERT: F 451 HIS cc_start: 0.8258 (m90) cc_final: 0.7598 (t-90) outliers start: 13 outliers final: 10 residues processed: 150 average time/residue: 0.9018 time to fit residues: 232.3646 Evaluate side-chains 147 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 886 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 10.0000 chunk 177 optimal weight: 0.0030 chunk 265 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 87 optimal weight: 40.0000 chunk 86 optimal weight: 30.0000 chunk 283 optimal weight: 9.9990 chunk 303 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 350 optimal weight: 10.0000 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 37638 Z= 0.191 Angle : 0.538 7.725 50844 Z= 0.266 Chirality : 0.038 0.150 5832 Planarity : 0.003 0.032 6522 Dihedral : 6.323 146.363 5124 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.40 % Allowed : 8.49 % Favored : 91.11 % 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: -0.68 (0.13), residues: 4632 helix: 0.96 (0.12), residues: 2068 sheet: -2.76 (0.21), residues: 566 loop : -1.20 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 770 HIS 0.003 0.001 HIS B 195 PHE 0.010 0.001 PHE F 947 TYR 0.011 0.001 TYR A 360 ARG 0.004 0.000 ARG D 822 *********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 4.286 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: A 448 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.6989 (mp) REVERT: B 569 MET cc_start: 0.9206 (pmm) cc_final: 0.8913 (pmm) REVERT: B 773 MET cc_start: 0.8537 (ppp) cc_final: 0.8121 (ppp) REVERT: C 552 MET cc_start: 0.9251 (tpp) cc_final: 0.8638 (tpp) REVERT: C 835 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7603 (mm) REVERT: D 209 MET cc_start: -0.0109 (tpt) cc_final: -0.0392 (tpt) REVERT: D 272 MET cc_start: 0.1361 (ptt) cc_final: -0.0187 (ttp) REVERT: D 334 MET cc_start: -0.3507 (mmt) cc_final: -0.3982 (tpt) REVERT: F 209 MET cc_start: 0.2709 (ptt) cc_final: 0.1571 (mtt) REVERT: F 435 MET cc_start: 0.9207 (tpt) cc_final: 0.8912 (tpt) REVERT: F 451 HIS cc_start: 0.8263 (m90) cc_final: 0.7599 (t-90) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 0.8956 time to fit residues: 229.8971 Evaluate side-chains 150 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 886 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 20.0000 chunk 426 optimal weight: 1.9990 chunk 389 optimal weight: 9.9990 chunk 414 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 325 optimal weight: 40.0000 chunk 127 optimal weight: 0.1980 chunk 374 optimal weight: 0.3980 chunk 392 optimal weight: 20.0000 chunk 413 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37638 Z= 0.153 Angle : 0.525 8.385 50844 Z= 0.257 Chirality : 0.038 0.151 5832 Planarity : 0.003 0.031 6522 Dihedral : 6.149 143.101 5124 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.35 % Allowed : 8.72 % Favored : 90.94 % 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: -0.51 (0.13), residues: 4632 helix: 1.12 (0.12), residues: 2069 sheet: -2.67 (0.21), residues: 566 loop : -1.13 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 770 HIS 0.002 0.000 HIS D 841 PHE 0.008 0.001 PHE B 920 TYR 0.021 0.001 TYR B 599 ARG 0.003 0.000 ARG D 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.6956 (mp) REVERT: B 569 MET cc_start: 0.9201 (pmm) cc_final: 0.8908 (pmm) REVERT: B 773 MET cc_start: 0.8501 (ppp) cc_final: 0.8069 (ppp) REVERT: C 552 MET cc_start: 0.9264 (tpp) cc_final: 0.8648 (tpp) REVERT: C 835 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7596 (mm) REVERT: D 209 MET cc_start: -0.0073 (tpt) cc_final: -0.0359 (tpt) REVERT: D 272 MET cc_start: 0.1334 (ptt) cc_final: -0.0213 (ttp) REVERT: D 334 MET cc_start: -0.3501 (mmt) cc_final: -0.4011 (tpt) REVERT: F 209 MET cc_start: 0.2704 (ptt) cc_final: 0.1570 (mtt) REVERT: F 435 MET cc_start: 0.9211 (tpt) cc_final: 0.8915 (tpt) REVERT: F 451 HIS cc_start: 0.8265 (m90) cc_final: 0.7626 (t-90) outliers start: 14 outliers final: 12 residues processed: 149 average time/residue: 0.8867 time to fit residues: 225.3906 Evaluate side-chains 151 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 886 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 1.9990 chunk 438 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 460 optimal weight: 3.9990 chunk 423 optimal weight: 7.9990 chunk 366 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 224 optimal weight: 0.3980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** A 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37638 Z= 0.216 Angle : 0.542 9.258 50844 Z= 0.267 Chirality : 0.038 0.149 5832 Planarity : 0.003 0.032 6522 Dihedral : 6.075 141.660 5124 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.35 % Allowed : 8.77 % Favored : 90.89 % 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: -0.56 (0.13), residues: 4632 helix: 1.11 (0.12), residues: 2067 sheet: -2.70 (0.21), residues: 587 loop : -1.16 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 770 HIS 0.005 0.001 HIS F 491 PHE 0.017 0.001 PHE F 947 TYR 0.016 0.001 TYR B 599 ARG 0.004 0.000 ARG D 822 ********************** 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 LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.6714 (mp) REVERT: B 569 MET cc_start: 0.9185 (pmm) cc_final: 0.8889 (pmm) REVERT: B 773 MET cc_start: 0.8518 (ppp) cc_final: 0.8081 (ppp) REVERT: C 552 MET cc_start: 0.9253 (tpp) cc_final: 0.8641 (tpp) REVERT: C 835 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7628 (mm) REVERT: D 272 MET cc_start: 0.1251 (ptt) cc_final: -0.0299 (ttp) REVERT: D 334 MET cc_start: -0.3497 (mmt) cc_final: -0.4013 (tpt) REVERT: F 209 MET cc_start: 0.2680 (ptt) cc_final: 0.1554 (mtt) REVERT: F 435 MET cc_start: 0.9210 (tpt) cc_final: 0.8914 (tpt) REVERT: F 451 HIS cc_start: 0.8270 (m90) cc_final: 0.7589 (t-90) REVERT: F 653 MET cc_start: 0.8587 (mpp) cc_final: 0.8223 (mpp) outliers start: 14 outliers final: 12 residues processed: 150 average time/residue: 0.9173 time to fit residues: 235.0755 Evaluate side-chains 151 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain D residue 756 MET Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 886 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 9.9990 chunk 390 optimal weight: 40.0000 chunk 112 optimal weight: 0.7980 chunk 337 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 367 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 376 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** A 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.156870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.110662 restraints weight = 432573.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.110725 restraints weight = 222629.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.110158 restraints weight = 210152.785| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37638 Z= 0.150 Angle : 0.525 8.966 50844 Z= 0.255 Chirality : 0.038 0.151 5832 Planarity : 0.003 0.031 6522 Dihedral : 5.949 136.647 5124 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.35 % Allowed : 8.79 % Favored : 90.86 % 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: -0.40 (0.13), residues: 4632 helix: 1.26 (0.12), residues: 2069 sheet: -2.65 (0.21), residues: 558 loop : -1.13 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 770 HIS 0.002 0.000 HIS D 841 PHE 0.008 0.001 PHE F 947 TYR 0.017 0.001 TYR B 599 ARG 0.003 0.000 ARG D 822 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8433.37 seconds wall clock time: 146 minutes 53.25 seconds (8813.25 seconds total)