Starting phenix.real_space_refine on Sun Sep 29 19:16:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/09_2024/7ng5_12308_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/09_2024/7ng5_12308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/09_2024/7ng5_12308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/09_2024/7ng5_12308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/09_2024/7ng5_12308_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ng5_12308/09_2024/7ng5_12308_trim.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 162 5.16 5 C 23475 2.51 5 N 6437 2.21 5 O 6998 1.98 5 H 37485 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 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: 74579 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 12392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12392 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12369 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.24, per 1000 atoms: 0.37 Number of scatterers: 74579 At special positions: 0 Unit cell: (137.946, 145.425, 230.187, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 162 16.00 P 17 15.00 Mg 5 11.99 O 6998 8.00 N 6437 7.00 C 23475 6.00 H 37485 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.51 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: 8758 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 46 sheets defined 52.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 147 through 157 removed outlier: 3.686A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.713A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.716A pdb=" N ARG A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 354 through 406 removed outlier: 4.401A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.704A pdb=" N LEU A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 467 Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.577A pdb=" N ALA A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.763A pdb=" N LYS A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.664A pdb=" N GLN A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.712A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.803A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 730 removed outlier: 3.682A pdb=" N SER A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 747 removed outlier: 4.296A pdb=" N GLN A 743 " --> pdb=" O PRO A 739 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 829 Processing helix chain 'A' and resid 849 through 855 Proline residue: A 854 - end of helix Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.584A pdb=" N PHE A 920 " --> pdb=" O ASN A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 929 removed outlier: 3.768A pdb=" N GLU A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 947 removed outlier: 3.593A pdb=" N PHE A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 944 " --> pdb=" O ARG A 940 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 157 removed outlier: 4.211A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.630A pdb=" N ALA B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.568A pdb=" N ARG B 323 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.907A pdb=" N LEU B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 removed outlier: 3.941A 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: 3.871A pdb=" N LEU B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 removed outlier: 4.071A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.920A pdb=" N ASP B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.863A pdb=" N ASN B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.903A pdb=" N ALA B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 512 removed outlier: 3.583A pdb=" N GLY B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.638A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 580 removed outlier: 3.610A pdb=" N GLN B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 602 through 611 removed outlier: 4.394A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.734A pdb=" N ALA B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 4.307A pdb=" N MET B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 703 removed outlier: 3.567A pdb=" N LEU B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 729 removed outlier: 3.909A pdb=" N LEU B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 723 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 729 " --> pdb=" O TYR B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 741 through 747 Processing helix chain 'B' and resid 807 through 829 removed outlier: 3.661A pdb=" N GLU B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Proline residue: B 854 - end of helix Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.532A pdb=" N THR B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.946A pdb=" N ILE B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 916 removed outlier: 3.675A pdb=" N ASN B 916 " --> pdb=" O PRO B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 916' Processing helix chain 'B' and resid 917 through 922 removed outlier: 4.038A pdb=" N ASP B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 removed outlier: 3.981A pdb=" N THR B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.830A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.860A pdb=" N GLU C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 290 through 307 removed outlier: 3.732A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 327 through 337 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 354 through 407 removed outlier: 3.585A pdb=" N ARG C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 394 " --> pdb=" O THR C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 425 Processing helix chain 'C' and resid 431 through 448 removed outlier: 4.150A pdb=" N MET C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.675A pdb=" N ASN C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.786A pdb=" N VAL C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 removed outlier: 3.636A pdb=" N LYS C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 540 removed outlier: 4.508A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 559 Processing helix chain 'C' and resid 571 through 580 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.672A pdb=" N ILE C 595 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 612 removed outlier: 4.872A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.990A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 671 removed outlier: 4.284A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 704 removed outlier: 3.648A pdb=" N LEU C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS C 704 " --> pdb=" O ILE C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 729 removed outlier: 3.744A pdb=" N SER C 729 " --> pdb=" O TYR C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 747 removed outlier: 4.465A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 removed outlier: 3.945A pdb=" N LYS C 790 " --> pdb=" O PRO C 787 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 791 " --> pdb=" O GLN C 788 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 792 " --> pdb=" O ASP C 789 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 787 through 792' Processing helix chain 'C' and resid 808 through 829 removed outlier: 3.656A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 838 removed outlier: 4.067A pdb=" N SER C 838 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Proline residue: C 854 - end of helix Processing helix chain 'C' and resid 856 through 870 removed outlier: 3.962A pdb=" N ILE C 860 " --> pdb=" O ALA C 856 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.669A pdb=" N LYS C 898 " --> pdb=" O GLY C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 915 No H-bonds generated for 'chain 'C' and resid 913 through 915' Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 939 through 947 removed outlier: 3.556A pdb=" N PHE C 943 " --> pdb=" O TYR C 939 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 157 removed outlier: 3.665A pdb=" N GLU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 288 through 307 removed outlier: 4.404A pdb=" N LEU D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 removed outlier: 3.578A pdb=" N MET D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.563A pdb=" N ARG D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.861A 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 407 removed outlier: 3.893A pdb=" N LEU D 395 " --> pdb=" O HIS D 391 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 426 removed outlier: 4.050A pdb=" N ILE D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 removed outlier: 3.801A pdb=" N ASP D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 438 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 439 " --> pdb=" O MET D 435 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU D 447 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 467 removed outlier: 3.685A pdb=" N ASN D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 489 Processing helix chain 'D' and resid 494 through 510 removed outlier: 3.677A pdb=" N LYS D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 510 " --> pdb=" O ALA D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 541 removed outlier: 3.811A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 removed outlier: 3.758A pdb=" N LYS D 559 " --> pdb=" O VAL D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 removed outlier: 3.504A pdb=" N GLN D 575 " --> pdb=" O GLY D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'D' and resid 602 through 606 Processing helix chain 'D' and resid 607 through 612 Processing helix chain 'D' and resid 614 through 619 removed outlier: 4.036A pdb=" N ALA D 617 " --> pdb=" O GLU D 614 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN D 618 " --> pdb=" O GLN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.683A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 674 removed outlier: 3.609A pdb=" N LYS D 666 " --> pdb=" O VAL D 662 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 674 " --> pdb=" O ALA D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 683 Processing helix chain 'D' and resid 692 through 703 removed outlier: 3.748A pdb=" N LEU D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 729 removed outlier: 3.970A pdb=" N SER D 729 " --> pdb=" O TYR D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 747 removed outlier: 4.347A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE D 745 " --> pdb=" O ASN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 removed outlier: 3.863A 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: 3.684A pdb=" N ILE D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 921 removed outlier: 3.648A pdb=" N TYR D 921 " --> pdb=" O LYS D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 929 removed outlier: 3.743A pdb=" N THR D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 947 removed outlier: 3.635A pdb=" N PHE D 943 " --> pdb=" O TYR D 939 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 157 removed outlier: 3.543A pdb=" N GLU E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.614A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 290 through 307 removed outlier: 3.643A pdb=" N GLU E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 318 removed outlier: 3.662A pdb=" N MET E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.666A pdb=" N ARG E 323 " --> pdb=" O ALA E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.786A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 352 removed outlier: 3.529A pdb=" N GLU E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 407 removed outlier: 3.617A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E 393 " --> pdb=" O GLN E 389 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR E 394 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 425 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.556A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 448 " --> pdb=" O LYS E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 468 removed outlier: 3.629A pdb=" N SER E 467 " --> pdb=" O ASP E 463 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 468 " --> pdb=" O TRP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 489 removed outlier: 3.912A pdb=" N ALA E 485 " --> pdb=" O ALA E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 530 through 541 removed outlier: 3.673A pdb=" N ARG E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 580 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.854A pdb=" N LYS E 594 " --> pdb=" O GLU E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 612 removed outlier: 4.384A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 617 Processing helix chain 'E' and resid 641 through 645 removed outlier: 3.919A pdb=" N THR E 644 " --> pdb=" O VAL E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 664 through 674 removed outlier: 3.986A pdb=" N ALA E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG E 672 " --> pdb=" O ALA E 668 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR E 673 " --> pdb=" O ILE E 669 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 674 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 682 Processing helix chain 'E' and resid 692 through 702 removed outlier: 3.701A pdb=" N LEU E 696 " --> pdb=" O SER E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 729 removed outlier: 3.862A pdb=" N LYS E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE E 727 " --> pdb=" O SER E 723 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER E 729 " --> pdb=" O TYR E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.730A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 855 Proline residue: E 854 - end of helix Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 921 removed outlier: 3.813A pdb=" N PHE E 920 " --> pdb=" O ASN E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 940 No H-bonds generated for 'chain 'E' and resid 938 through 940' Processing helix chain 'E' and resid 941 through 947 removed outlier: 3.649A pdb=" N ILE E 945 " --> pdb=" O GLU E 941 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 947 " --> pdb=" O PHE E 943 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 157 removed outlier: 3.599A pdb=" N GLU F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 290 through 307 removed outlier: 3.899A pdb=" N ALA F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 327 through 338 removed outlier: 3.681A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 removed outlier: 3.623A 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: 3.785A pdb=" N LEU F 395 " --> pdb=" O HIS F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 426 removed outlier: 4.321A pdb=" N ASP F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.848A pdb=" N MET F 435 " --> pdb=" O PRO F 431 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 Processing helix chain 'F' and resid 479 through 490 removed outlier: 3.538A pdb=" N LEU F 487 " --> pdb=" O ALA F 483 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 528 through 541 removed outlier: 3.610A pdb=" N ILE F 532 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 580 removed outlier: 3.754A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 595 removed outlier: 4.032A pdb=" N LYS F 594 " --> pdb=" O GLU F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 612 Processing helix chain 'F' and resid 612 through 617 Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 673 removed outlier: 4.489A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG F 672 " --> pdb=" O ALA F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 683 removed outlier: 3.837A pdb=" N GLN F 677 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.572A pdb=" N GLN F 713 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 715 " --> pdb=" O ASN F 711 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER F 729 " --> pdb=" O TYR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 747 removed outlier: 3.758A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 removed outlier: 3.663A 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: 3.754A pdb=" N ILE F 860 " --> pdb=" O ALA F 856 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU F 865 " --> pdb=" O VAL F 861 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 904 removed outlier: 3.569A pdb=" N LYS F 898 " --> pdb=" O GLY F 894 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG F 904 " --> pdb=" O ILE F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 921 removed outlier: 3.796A pdb=" N PHE F 920 " --> pdb=" O ASN F 916 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 929 removed outlier: 3.790A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 939 through 947 removed outlier: 3.522A pdb=" N PHE F 943 " --> pdb=" O TYR F 939 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP F 944 " --> pdb=" O ARG F 940 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE F 947 " --> pdb=" O PHE F 943 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA3, first strand: chain 'A' and resid 544 through 548 removed outlier: 3.800A pdb=" N PHE A 545 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 689 through 690 removed outlier: 4.009A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.556A pdb=" N GLU A 801 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 842 " --> pdb=" O GLU A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 912 through 913 removed outlier: 6.056A pdb=" N LEU A 912 " --> pdb=" O VAL A 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 164 removed outlier: 4.836A pdb=" N LEU B 168 " --> pdb=" O TYR B 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AB1, first strand: chain 'B' and resid 517 through 518 removed outlier: 6.343A pdb=" N LYS B 517 " --> pdb=" O PHE B 635 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 547 through 548 removed outlier: 7.226A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 765 through 770 removed outlier: 6.346A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 882 through 883 removed outlier: 4.091A pdb=" N GLU B 882 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'C' and resid 167 through 169 removed outlier: 5.275A pdb=" N LEU C 168 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 519 through 521 Processing sheet with id=AB8, first strand: chain 'C' and resid 544 through 548 removed outlier: 3.667A pdb=" N PHE C 545 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 547 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 590 " --> pdb=" O PHE C 547 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 689 through 690 removed outlier: 7.167A pdb=" N VAL C 735 " --> pdb=" O LYS C 690 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 767 through 769 Processing sheet with id=AC2, first strand: chain 'C' and resid 781 through 784 removed outlier: 5.657A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 882 through 883 removed outlier: 4.171A pdb=" N GLU C 882 " --> pdb=" O LEU C 890 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AC5, first strand: chain 'D' and resid 167 through 169 removed outlier: 4.831A pdb=" N LEU D 168 " --> pdb=" O TYR D 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 521 through 522 removed outlier: 6.517A pdb=" N PHE D 521 " --> pdb=" O ALA D 639 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 545 through 548 removed outlier: 7.089A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.753A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 764 through 766 removed outlier: 6.207A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 769 through 770 Processing sheet with id=AD2, first strand: chain 'D' and resid 910 through 913 removed outlier: 6.563A pdb=" N ILE D 910 " --> pdb=" O HIS D 934 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL D 936 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU D 912 " --> pdb=" O VAL D 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AD4, first strand: chain 'E' and resid 188 through 191 Processing sheet with id=AD5, first strand: chain 'E' and resid 521 through 522 removed outlier: 6.663A pdb=" N PHE E 521 " --> pdb=" O ALA E 639 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 544 through 548 removed outlier: 3.614A pdb=" N PHE E 545 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 547 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP E 590 " --> pdb=" O PHE E 547 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 619 through 620 removed outlier: 3.590A pdb=" N PHE E 619 " --> pdb=" O VAL E 628 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.162A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 764 through 769 removed outlier: 3.696A pdb=" N VAL E 765 " --> pdb=" O VAL E 780 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 780 " --> pdb=" O VAL E 765 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 882 through 883 removed outlier: 4.371A pdb=" N GLU E 882 " --> pdb=" O LEU E 890 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 890 " --> pdb=" O GLU E 882 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 911 through 913 removed outlier: 5.797A pdb=" N LEU E 912 " --> pdb=" O VAL E 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AE4, first strand: chain 'F' and resid 164 through 169 removed outlier: 4.433A pdb=" N LEU F 168 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR F 188 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 637 through 639 Processing sheet with id=AE6, first strand: chain 'F' and resid 544 through 548 removed outlier: 3.826A pdb=" N PHE F 545 " --> pdb=" O LEU F 586 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.038A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 764 through 766 removed outlier: 5.990A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 769 through 770 Processing sheet with id=AF1, first strand: chain 'F' and resid 909 through 913 removed outlier: 3.773A pdb=" N LEU F 912 " --> pdb=" O HIS F 934 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 936 " --> pdb=" O LEU F 912 " (cutoff:3.500A) 1535 hydrogen bonds defined for protein. 4392 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: 29.04 Time building geometry restraints manager: 18.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 37443 1.03 - 1.23: 371 1.23 - 1.42: 14781 1.42 - 1.62: 22320 1.62 - 1.82: 282 Bond restraints: 75197 Sorted by residual: bond pdb=" C4 ATP F1001 " pdb=" C5 ATP F1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 ATP B1001 " pdb=" N9 ATP B1001 " ideal model delta sigma weight residual 1.374 1.297 0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C5 ATP E1001 " pdb=" N7 ATP E1001 " ideal model delta sigma weight residual 1.387 1.310 0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" C5 ATP A1001 " pdb=" N7 ATP A1001 " ideal model delta sigma weight residual 1.387 1.316 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C4 ATP E1001 " pdb=" N9 ATP E1001 " ideal model delta sigma weight residual 1.374 1.304 0.070 1.00e-02 1.00e+04 4.90e+01 ... (remaining 75192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.68: 136379 6.68 - 13.37: 127 13.37 - 20.05: 0 20.05 - 26.74: 19 26.74 - 33.42: 9 Bond angle restraints: 136534 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 111.24 28.63 1.00e+00 1.00e+00 8.20e+02 angle pdb=" PB ATP F1001 " pdb=" O3B ATP F1001 " pdb=" PG ATP F1001 " ideal model delta sigma weight residual 139.87 113.74 26.13 1.00e+00 1.00e+00 6.83e+02 angle pdb=" PA ATP E1001 " pdb=" O3A ATP E1001 " pdb=" PB ATP E1001 " ideal model delta sigma weight residual 136.83 111.62 25.21 1.00e+00 1.00e+00 6.36e+02 angle pdb=" PA ATP C1001 " pdb=" O3A ATP C1001 " pdb=" PB ATP C1001 " ideal model delta sigma weight residual 136.83 112.19 24.64 1.00e+00 1.00e+00 6.07e+02 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 112.49 24.34 1.00e+00 1.00e+00 5.92e+02 ... (remaining 136529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.67: 32043 19.67 - 39.34: 2289 39.34 - 59.01: 573 59.01 - 78.68: 54 78.68 - 98.35: 29 Dihedral angle restraints: 34988 sinusoidal: 19716 harmonic: 15272 Sorted by residual: dihedral pdb=" CA PRO E 762 " pdb=" C PRO E 762 " pdb=" N GLY E 763 " pdb=" CA GLY E 763 " ideal model delta harmonic sigma weight residual -180.00 -149.45 -30.55 0 5.00e+00 4.00e-02 3.73e+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 -60.00 38.35 -98.35 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA ILE D 727 " pdb=" C ILE D 727 " pdb=" N VAL D 728 " pdb=" CA VAL D 728 " ideal model delta harmonic sigma weight residual 180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 34985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3697 0.056 - 0.113: 1638 0.113 - 0.169: 420 0.169 - 0.226: 75 0.226 - 0.282: 13 Chirality restraints: 5843 Sorted by residual: chirality pdb=" CB VAL C 907 " pdb=" CA VAL C 907 " pdb=" CG1 VAL C 907 " pdb=" CG2 VAL C 907 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' ATP A1001 " pdb=" C1' ATP A1001 " pdb=" C3' ATP A1001 " pdb=" O2' ATP A1001 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C2' ATP C1001 " pdb=" C1' ATP C1001 " pdb=" C3' ATP C1001 " pdb=" O2' ATP C1001 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 5840 not shown) Planarity restraints: 10956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 302 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" C ASP F 302 " -0.093 2.00e-02 2.50e+03 pdb=" O ASP F 302 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE F 303 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 608 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C LEU D 608 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU D 608 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU D 609 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 301 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C ARG A 301 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG A 301 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP A 302 " 0.030 2.00e-02 2.50e+03 ... (remaining 10953 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 8438 2.25 - 2.83: 163555 2.83 - 3.42: 184327 3.42 - 4.01: 235444 4.01 - 4.60: 368947 Nonbonded interactions: 960711 Sorted by model distance: nonbonded pdb="HH22 ARG C 822 " pdb=" O VAL C 836 " model vdw 1.657 2.450 nonbonded pdb=" OD1 ASP E 629 " pdb=" H SER E 631 " model vdw 1.660 2.450 nonbonded pdb=" H GLY E 471 " pdb=" OE1 GLU E 583 " model vdw 1.671 2.450 nonbonded pdb=" OE1 GLU E 557 " pdb=" H GLU E 557 " model vdw 1.679 2.450 nonbonded pdb=" O ALA A 336 " pdb=" HG1 THR A 339 " model vdw 1.681 2.450 ... (remaining 960706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 948)) selection = (chain 'B' and (resid 123 through 720 or (resid 721 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 t \ hrough 948)) selection = (chain 'C' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'D' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'E' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'F' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 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: 2.110 Check model and map are aligned: 0.430 Set scattering table: 0.520 Process input model: 125.500 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.250 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: 0.030 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 0.125 37712 Z= 0.822 Angle : 1.313 28.627 50953 Z= 0.784 Chirality : 0.066 0.282 5843 Planarity : 0.009 0.093 6532 Dihedral : 13.783 98.354 14585 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.56 % Favored : 92.42 % Rotamer: Outliers : 0.15 % Allowed : 0.62 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.18 (0.12), residues: 4632 helix: -1.97 (0.08), residues: 2034 sheet: -3.79 (0.19), residues: 493 loop : 0.05 (0.15), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 770 HIS 0.025 0.003 HIS B 839 PHE 0.039 0.004 PHE D 547 TYR 0.036 0.004 TYR E 703 ARG 0.038 0.002 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 4.368 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: A 766 MET cc_start: 0.7800 (ptm) cc_final: 0.7590 (ppp) REVERT: A 773 MET cc_start: 0.8618 (ppp) cc_final: 0.8411 (ppp) REVERT: A 810 MET cc_start: 0.8315 (mmm) cc_final: 0.8047 (mmm) REVERT: B 197 MET cc_start: -0.0461 (pmm) cc_final: -0.0797 (pmm) REVERT: B 209 MET cc_start: 0.5328 (mpp) cc_final: 0.5059 (mpp) REVERT: C 410 GLU cc_start: 0.4096 (OUTLIER) cc_final: 0.3632 (pt0) REVERT: C 411 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.5009 (tttt) REVERT: D 317 MET cc_start: -0.2376 (tmm) cc_final: -0.3320 (mtt) REVERT: E 334 MET cc_start: 0.0911 (mtm) cc_final: -0.0540 (tpt) REVERT: E 435 MET cc_start: 0.9338 (tpt) cc_final: 0.8899 (tpt) REVERT: F 655 MET cc_start: 0.8388 (mmt) cc_final: 0.8137 (mmt) outliers start: 6 outliers final: 0 residues processed: 197 average time/residue: 0.8673 time to fit residues: 288.8723 Evaluate side-chains 166 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 390 optimal weight: 7.9990 chunk 350 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 236 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 362 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 420 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 HIS B 541 ASN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37712 Z= 0.183 Angle : 0.617 7.820 50953 Z= 0.328 Chirality : 0.040 0.159 5843 Planarity : 0.005 0.052 6532 Dihedral : 8.360 94.161 5256 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.32 % Allowed : 4.05 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4632 helix: -0.24 (0.10), residues: 2061 sheet: -3.48 (0.19), residues: 513 loop : -0.29 (0.15), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 464 HIS 0.010 0.001 HIS B 839 PHE 0.016 0.001 PHE A 820 TYR 0.017 0.001 TYR A 394 ARG 0.006 0.000 ARG D 652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 MET cc_start: 0.8600 (ppp) cc_final: 0.8371 (ppp) REVERT: D 317 MET cc_start: -0.2410 (tmm) cc_final: -0.3343 (mtt) REVERT: D 433 HIS cc_start: 0.8129 (t-90) cc_final: 0.7902 (t70) REVERT: E 334 MET cc_start: 0.0993 (mtm) cc_final: -0.0501 (tpt) REVERT: E 435 MET cc_start: 0.9309 (tpt) cc_final: 0.8872 (tpt) REVERT: F 435 MET cc_start: 0.9326 (mmm) cc_final: 0.9111 (mmm) REVERT: F 655 MET cc_start: 0.8253 (mmt) cc_final: 0.7970 (mmt) outliers start: 13 outliers final: 7 residues processed: 175 average time/residue: 0.8890 time to fit residues: 266.8351 Evaluate side-chains 163 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 826 MET Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain F residue 403 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 233 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 421 optimal weight: 6.9990 chunk 455 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 417 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS B 433 HIS B 541 ASN B 788 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 37712 Z= 0.313 Angle : 0.588 6.700 50953 Z= 0.313 Chirality : 0.040 0.146 5843 Planarity : 0.004 0.049 6532 Dihedral : 7.837 89.437 5249 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.49 % Allowed : 5.46 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4632 helix: 0.29 (0.11), residues: 2069 sheet: -3.46 (0.20), residues: 520 loop : -0.65 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 470 HIS 0.012 0.001 HIS B 839 PHE 0.015 0.001 PHE A 547 TYR 0.016 0.001 TYR E 394 ARG 0.004 0.000 ARG F 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 MET cc_start: 0.8650 (ppp) cc_final: 0.8422 (ppp) REVERT: B 209 MET cc_start: 0.5787 (mpp) cc_final: 0.5434 (mpp) REVERT: D 317 MET cc_start: -0.2649 (tmm) cc_final: -0.3553 (mtt) REVERT: D 433 HIS cc_start: 0.8218 (t-90) cc_final: 0.8003 (t70) REVERT: D 756 MET cc_start: 0.8491 (ttm) cc_final: 0.8266 (ttm) REVERT: E 334 MET cc_start: 0.1003 (mtm) cc_final: -0.0487 (tpt) REVERT: E 435 MET cc_start: 0.9315 (tpt) cc_final: 0.8885 (tpt) REVERT: E 552 MET cc_start: 0.8912 (mmm) cc_final: 0.8604 (mmm) REVERT: F 435 MET cc_start: 0.9345 (mmm) cc_final: 0.9142 (mmm) REVERT: F 655 MET cc_start: 0.8285 (mmt) cc_final: 0.7924 (mmt) REVERT: F 941 GLU cc_start: 0.7815 (tp30) cc_final: 0.7569 (tp30) outliers start: 20 outliers final: 13 residues processed: 175 average time/residue: 0.8494 time to fit residues: 254.9485 Evaluate side-chains 168 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 621 ASP Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 945 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 416 optimal weight: 7.9990 chunk 316 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 422 optimal weight: 7.9990 chunk 447 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 400 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 37712 Z= 0.321 Angle : 0.575 8.083 50953 Z= 0.307 Chirality : 0.040 0.149 5843 Planarity : 0.004 0.050 6532 Dihedral : 7.694 88.900 5249 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.52 % Allowed : 6.62 % Favored : 92.86 % 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: -0.95 (0.12), residues: 4632 helix: 0.49 (0.11), residues: 2071 sheet: -3.30 (0.21), residues: 508 loop : -0.97 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 470 HIS 0.011 0.001 HIS B 839 PHE 0.016 0.001 PHE A 547 TYR 0.015 0.001 TYR F 461 ARG 0.007 0.000 ARG F 721 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 MET cc_start: 0.5938 (mpp) cc_final: 0.5659 (mpp) REVERT: D 317 MET cc_start: -0.2691 (tmm) cc_final: -0.3569 (mtt) REVERT: D 433 HIS cc_start: 0.8264 (t-90) cc_final: 0.8054 (t70) REVERT: D 773 MET cc_start: 0.8225 (ppp) cc_final: 0.7414 (ppp) REVERT: E 334 MET cc_start: 0.0981 (mtm) cc_final: -0.0493 (tpt) REVERT: E 435 MET cc_start: 0.9311 (tpt) cc_final: 0.8885 (tpt) REVERT: E 552 MET cc_start: 0.8930 (mmm) cc_final: 0.8650 (mmm) REVERT: F 435 MET cc_start: 0.9355 (mmm) cc_final: 0.9142 (mmm) REVERT: F 655 MET cc_start: 0.8246 (mmt) cc_final: 0.7841 (mmt) REVERT: F 941 GLU cc_start: 0.7864 (tp30) cc_final: 0.7477 (tp30) outliers start: 21 outliers final: 14 residues processed: 180 average time/residue: 0.9297 time to fit residues: 290.9641 Evaluate side-chains 170 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 621 ASP Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 477 ASN Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 945 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 372 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 333 optimal weight: 0.3980 chunk 184 optimal weight: 5.9990 chunk 381 optimal weight: 3.9990 chunk 309 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 chunk 401 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37712 Z= 0.261 Angle : 0.541 7.681 50953 Z= 0.287 Chirality : 0.039 0.149 5843 Planarity : 0.004 0.049 6532 Dihedral : 7.602 89.540 5249 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.54 % Allowed : 7.73 % Favored : 91.73 % 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: 0.70 (0.11), residues: 2073 sheet: -3.24 (0.21), residues: 521 loop : -0.99 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 464 HIS 0.009 0.001 HIS B 839 PHE 0.015 0.001 PHE A 820 TYR 0.014 0.001 TYR A 394 ARG 0.005 0.000 ARG F 721 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 MET cc_start: 0.5764 (mpp) cc_final: 0.5564 (mpp) REVERT: D 317 MET cc_start: -0.2673 (tmm) cc_final: -0.3550 (mtt) REVERT: D 773 MET cc_start: 0.8205 (ppp) cc_final: 0.7381 (ppp) REVERT: E 334 MET cc_start: 0.0889 (mtm) cc_final: -0.0577 (tpt) REVERT: E 435 MET cc_start: 0.9290 (tpt) cc_final: 0.8858 (tpt) REVERT: E 552 MET cc_start: 0.8954 (mmm) cc_final: 0.8689 (mmm) REVERT: F 435 MET cc_start: 0.9339 (mmm) cc_final: 0.9120 (mmm) REVERT: F 655 MET cc_start: 0.8232 (mmt) cc_final: 0.7895 (mmt) REVERT: F 941 GLU cc_start: 0.7900 (tp30) cc_final: 0.7484 (tp30) outliers start: 22 outliers final: 15 residues processed: 180 average time/residue: 0.9982 time to fit residues: 306.7836 Evaluate side-chains 170 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 621 ASP Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 945 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 150 optimal weight: 10.0000 chunk 403 optimal weight: 0.7980 chunk 88 optimal weight: 0.0770 chunk 262 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 447 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 399 GLN F 433 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37712 Z= 0.179 Angle : 0.507 7.213 50953 Z= 0.264 Chirality : 0.038 0.148 5843 Planarity : 0.003 0.048 6532 Dihedral : 7.409 85.624 5249 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.37 % Allowed : 8.32 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4632 helix: 0.98 (0.12), residues: 2077 sheet: -3.05 (0.21), residues: 512 loop : -0.92 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 464 HIS 0.007 0.001 HIS B 839 PHE 0.012 0.001 PHE A 820 TYR 0.013 0.001 TYR A 394 ARG 0.002 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 4.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 ASP cc_start: 0.8654 (p0) cc_final: 0.8387 (p0) REVERT: D 317 MET cc_start: -0.2749 (tmm) cc_final: -0.3604 (mtt) REVERT: D 773 MET cc_start: 0.8247 (ppp) cc_final: 0.7487 (ppp) REVERT: E 334 MET cc_start: 0.0874 (mtm) cc_final: -0.0577 (tpt) REVERT: E 435 MET cc_start: 0.9291 (tpt) cc_final: 0.8864 (tpt) REVERT: E 552 MET cc_start: 0.8942 (mmm) cc_final: 0.8683 (mmm) REVERT: F 435 MET cc_start: 0.9311 (mmm) cc_final: 0.9072 (mmm) REVERT: F 655 MET cc_start: 0.8228 (mmt) cc_final: 0.7963 (mmt) REVERT: F 941 GLU cc_start: 0.7873 (tp30) cc_final: 0.7396 (tp30) outliers start: 15 outliers final: 10 residues processed: 176 average time/residue: 0.9371 time to fit residues: 287.8632 Evaluate side-chains 168 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 735 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 431 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 255 optimal weight: 6.9990 chunk 327 optimal weight: 30.0000 chunk 253 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 250 optimal weight: 30.0000 chunk 446 optimal weight: 5.9990 chunk 279 optimal weight: 0.0670 chunk 272 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 overall best weight: 1.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37712 Z= 0.152 Angle : 0.486 7.773 50953 Z= 0.251 Chirality : 0.038 0.149 5843 Planarity : 0.003 0.045 6532 Dihedral : 7.168 82.572 5249 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.35 % Allowed : 8.40 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 4632 helix: 1.24 (0.12), residues: 2088 sheet: -2.93 (0.21), residues: 514 loop : -0.86 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 464 HIS 0.006 0.001 HIS B 839 PHE 0.011 0.001 PHE E 920 TYR 0.011 0.001 TYR A 394 ARG 0.003 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 4.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 ASP cc_start: 0.8567 (p0) cc_final: 0.8274 (p0) REVERT: B 655 MET cc_start: 0.8679 (mmm) cc_final: 0.8385 (mmt) REVERT: B 717 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 869 MET cc_start: 0.8221 (mpp) cc_final: 0.7963 (mpp) REVERT: D 317 MET cc_start: -0.2828 (tmm) cc_final: -0.3678 (mtt) REVERT: D 433 HIS cc_start: 0.8258 (t-90) cc_final: 0.8054 (t-90) REVERT: D 773 MET cc_start: 0.8251 (ppp) cc_final: 0.7500 (ppp) REVERT: E 334 MET cc_start: 0.0726 (mtm) cc_final: -0.0618 (tpt) REVERT: E 435 MET cc_start: 0.9288 (tpt) cc_final: 0.8861 (tpt) REVERT: F 435 MET cc_start: 0.9289 (mmm) cc_final: 0.9056 (mmm) REVERT: F 655 MET cc_start: 0.8214 (mmt) cc_final: 0.8003 (mmt) REVERT: F 941 GLU cc_start: 0.7887 (tp30) cc_final: 0.7420 (tp30) outliers start: 14 outliers final: 13 residues processed: 181 average time/residue: 0.8541 time to fit residues: 267.4349 Evaluate side-chains 172 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 477 ASN Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 945 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 276 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 350 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37712 Z= 0.244 Angle : 0.507 8.002 50953 Z= 0.265 Chirality : 0.038 0.169 5843 Planarity : 0.003 0.044 6532 Dihedral : 7.192 81.396 5249 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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: -0.32 (0.13), residues: 4632 helix: 1.22 (0.12), residues: 2091 sheet: -2.92 (0.22), residues: 524 loop : -0.93 (0.15), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 770 HIS 0.007 0.001 HIS B 839 PHE 0.012 0.001 PHE A 547 TYR 0.012 0.001 TYR F 461 ARG 0.003 0.000 ARG E 904 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 4.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 ASP cc_start: 0.8600 (p0) cc_final: 0.8309 (p0) REVERT: C 440 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: D 317 MET cc_start: -0.2803 (tmm) cc_final: -0.3635 (mtt) REVERT: D 433 HIS cc_start: 0.8319 (t-90) cc_final: 0.8086 (t-90) REVERT: D 773 MET cc_start: 0.8265 (ppp) cc_final: 0.7518 (ppp) REVERT: E 334 MET cc_start: 0.0731 (mtm) cc_final: -0.0614 (tpt) REVERT: E 435 MET cc_start: 0.9291 (tpt) cc_final: 0.8863 (tpt) REVERT: F 435 MET cc_start: 0.9305 (mmm) cc_final: 0.9086 (mmm) REVERT: F 655 MET cc_start: 0.8216 (mmt) cc_final: 0.7982 (mmt) REVERT: F 941 GLU cc_start: 0.7940 (tp30) cc_final: 0.7445 (tp30) outliers start: 14 outliers final: 13 residues processed: 170 average time/residue: 0.8579 time to fit residues: 251.0719 Evaluate side-chains 171 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 945 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 405 optimal weight: 9.9990 chunk 427 optimal weight: 0.9980 chunk 390 optimal weight: 20.0000 chunk 415 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 chunk 181 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 chunk 393 optimal weight: 20.0000 chunk 414 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS B 541 ASN ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37712 Z= 0.300 Angle : 0.543 8.304 50953 Z= 0.286 Chirality : 0.039 0.145 5843 Planarity : 0.004 0.044 6532 Dihedral : 7.268 80.697 5249 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.52 % Allowed : 8.84 % Favored : 90.64 % 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: -0.49 (0.13), residues: 4632 helix: 1.14 (0.12), residues: 2081 sheet: -2.93 (0.22), residues: 520 loop : -1.10 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 470 HIS 0.009 0.001 HIS B 839 PHE 0.016 0.001 PHE A 547 TYR 0.015 0.001 TYR F 461 ARG 0.005 0.000 ARG F 721 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 4.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 ASP cc_start: 0.8658 (p0) cc_final: 0.8382 (p0) REVERT: C 440 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: D 317 MET cc_start: -0.2703 (tmm) cc_final: -0.3520 (mtt) REVERT: D 433 HIS cc_start: 0.8302 (t-90) cc_final: 0.8052 (t70) REVERT: D 773 MET cc_start: 0.8197 (ppp) cc_final: 0.7461 (ppp) REVERT: E 334 MET cc_start: 0.1011 (mtm) cc_final: -0.0283 (tpt) REVERT: E 435 MET cc_start: 0.9280 (tpt) cc_final: 0.8831 (tpt) REVERT: F 435 MET cc_start: 0.9370 (mmm) cc_final: 0.9157 (mmm) REVERT: F 655 MET cc_start: 0.8235 (mmt) cc_final: 0.7927 (mmt) outliers start: 21 outliers final: 18 residues processed: 171 average time/residue: 0.8725 time to fit residues: 258.4413 Evaluate side-chains 172 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 828 HIS Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 945 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 273 optimal weight: 5.9990 chunk 439 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 461 optimal weight: 4.9990 chunk 424 optimal weight: 9.9990 chunk 367 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 283 optimal weight: 0.7980 chunk 225 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 37712 Z= 0.269 Angle : 0.634 59.197 50953 Z= 0.351 Chirality : 0.038 0.146 5843 Planarity : 0.004 0.044 6532 Dihedral : 7.269 80.747 5249 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.42 % Allowed : 8.94 % Favored : 90.64 % Cbeta Deviations : 0.02 % 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: -0.49 (0.13), residues: 4632 helix: 1.15 (0.12), residues: 2074 sheet: -2.97 (0.22), residues: 512 loop : -1.11 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 470 HIS 0.008 0.001 HIS B 839 PHE 0.016 0.001 PHE A 547 TYR 0.015 0.001 TYR F 461 ARG 0.014 0.000 ARG B 563 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 4.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 ASP cc_start: 0.8642 (p0) cc_final: 0.8370 (p0) REVERT: C 440 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: C 869 MET cc_start: 0.8311 (mpp) cc_final: 0.8070 (mpp) REVERT: D 317 MET cc_start: -0.2704 (tmm) cc_final: -0.3519 (mtt) REVERT: D 433 HIS cc_start: 0.8298 (t-90) cc_final: 0.8047 (t70) REVERT: D 773 MET cc_start: 0.8194 (ppp) cc_final: 0.7454 (ppp) REVERT: E 334 MET cc_start: 0.1010 (mtm) cc_final: -0.0284 (tpt) REVERT: E 435 MET cc_start: 0.9278 (tpt) cc_final: 0.8828 (tpt) REVERT: F 435 MET cc_start: 0.9367 (mmm) cc_final: 0.9154 (mmm) REVERT: F 655 MET cc_start: 0.8233 (mmt) cc_final: 0.7923 (mmt) outliers start: 17 outliers final: 16 residues processed: 167 average time/residue: 0.8845 time to fit residues: 254.0521 Evaluate side-chains 170 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 828 HIS Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 735 VAL Chi-restraints excluded: chain F residue 945 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 291 optimal weight: 3.9990 chunk 391 optimal weight: 20.0000 chunk 112 optimal weight: 0.1980 chunk 338 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 367 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.137106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088464 restraints weight = 272469.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092500 restraints weight = 127258.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.093752 restraints weight = 61914.817| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 37712 Z= 0.269 Angle : 0.634 59.197 50953 Z= 0.351 Chirality : 0.038 0.146 5843 Planarity : 0.004 0.044 6532 Dihedral : 7.269 80.747 5249 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.42 % Allowed : 8.94 % Favored : 90.64 % Cbeta Deviations : 0.02 % 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: -0.49 (0.13), residues: 4632 helix: 1.15 (0.12), residues: 2074 sheet: -2.97 (0.22), residues: 512 loop : -1.11 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 470 HIS 0.008 0.001 HIS B 839 PHE 0.016 0.001 PHE A 547 TYR 0.015 0.001 TYR F 461 ARG 0.014 0.000 ARG B 563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8721.93 seconds wall clock time: 151 minutes 33.59 seconds (9093.59 seconds total)