Starting phenix.real_space_refine on Fri Mar 6 19:47:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lxd_63474/03_2026/9lxd_63474_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lxd_63474/03_2026/9lxd_63474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lxd_63474/03_2026/9lxd_63474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lxd_63474/03_2026/9lxd_63474.map" model { file = "/net/cci-nas-00/data/ceres_data/9lxd_63474/03_2026/9lxd_63474_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lxd_63474/03_2026/9lxd_63474_neut.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 185 5.16 5 C 20629 2.51 5 N 5836 2.21 5 O 6266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32927 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 5628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5628 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 677} Chain breaks: 4 Chain: "3" Number of atoms: 4922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4922 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Chain: "4" Number of atoms: 5753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5753 Classifications: {'peptide': 724} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 694} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 5183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5183 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 5586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5586 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 21, 'TRANS': 671} Chain breaks: 3 Chain: "7" Number of atoms: 5141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5141 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 29, 'TRANS': 619} Chain: "B" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 575 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.73, per 1000 atoms: 0.20 Number of scatterers: 32927 At special positions: 0 Unit cell: (156.208, 174.523, 169.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 185 16.00 P 11 15.00 O 6266 8.00 N 5836 7.00 C 20629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7850 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 46 sheets defined 41.3% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain '2' and resid 188 through 205 Processing helix chain '2' and resid 213 through 226 removed outlier: 4.176A pdb=" N GLU 2 225 " --> pdb=" O ASP 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 234 through 241 Processing helix chain '2' and resid 242 through 246 removed outlier: 3.557A pdb=" N TYR 2 246 " --> pdb=" O VAL 2 243 " (cutoff:3.500A) Processing helix chain '2' and resid 251 through 271 removed outlier: 3.985A pdb=" N GLN 2 257 " --> pdb=" O ALA 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 277 removed outlier: 4.142A pdb=" N ASP 2 275 " --> pdb=" O PRO 2 272 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG 2 276 " --> pdb=" O LYS 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 297 removed outlier: 4.025A pdb=" N LEU 2 297 " --> pdb=" O LEU 2 294 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 Processing helix chain '2' and resid 459 through 470 removed outlier: 4.281A pdb=" N MET 2 463 " --> pdb=" O GLU 2 459 " (cutoff:3.500A) Processing helix chain '2' and resid 472 through 479 Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 529 through 540 Processing helix chain '2' and resid 574 through 579 removed outlier: 3.720A pdb=" N LEU 2 578 " --> pdb=" O GLY 2 574 " (cutoff:3.500A) Processing helix chain '2' and resid 593 through 604 removed outlier: 3.907A pdb=" N GLU 2 602 " --> pdb=" O THR 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 636 removed outlier: 4.346A pdb=" N ARG 2 636 " --> pdb=" O ILE 2 633 " (cutoff:3.500A) Processing helix chain '2' and resid 642 through 648 removed outlier: 4.070A pdb=" N ASP 2 648 " --> pdb=" O SER 2 644 " (cutoff:3.500A) Processing helix chain '2' and resid 650 through 656 Processing helix chain '2' and resid 670 through 686 removed outlier: 3.523A pdb=" N MET 2 674 " --> pdb=" O VAL 2 670 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS 2 686 " --> pdb=" O SER 2 682 " (cutoff:3.500A) Processing helix chain '2' and resid 716 through 731 removed outlier: 3.827A pdb=" N GLU 2 729 " --> pdb=" O ILE 2 725 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL 2 731 " --> pdb=" O ALA 2 727 " (cutoff:3.500A) Processing helix chain '2' and resid 740 through 754 removed outlier: 3.941A pdb=" N ALA 2 744 " --> pdb=" O GLN 2 740 " (cutoff:3.500A) Processing helix chain '2' and resid 764 through 781 Processing helix chain '2' and resid 787 through 804 removed outlier: 4.073A pdb=" N ASP 2 804 " --> pdb=" O GLU 2 800 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 818 Processing helix chain '2' and resid 828 through 852 removed outlier: 3.579A pdb=" N LEU 2 832 " --> pdb=" O ASN 2 828 " (cutoff:3.500A) Processing helix chain '2' and resid 862 through 873 removed outlier: 3.676A pdb=" N GLN 2 871 " --> pdb=" O ASP 2 867 " (cutoff:3.500A) Processing helix chain '2' and resid 877 through 883 removed outlier: 3.753A pdb=" N SER 2 883 " --> pdb=" O ALA 2 879 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 23 Processing helix chain '3' and resid 31 through 43 removed outlier: 3.522A pdb=" N SER 3 41 " --> pdb=" O ARG 3 37 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 61 through 68 removed outlier: 3.696A pdb=" N LEU 3 66 " --> pdb=" O ALA 3 62 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN 3 67 " --> pdb=" O ASN 3 63 " (cutoff:3.500A) Processing helix chain '3' and resid 73 through 83 removed outlier: 3.513A pdb=" N ALA 3 79 " --> pdb=" O ALA 3 75 " (cutoff:3.500A) Processing helix chain '3' and resid 280 through 289 Processing helix chain '3' and resid 295 through 302 removed outlier: 3.595A pdb=" N SER 3 302 " --> pdb=" O GLN 3 298 " (cutoff:3.500A) Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 351 through 362 Processing helix chain '3' and resid 415 through 428 removed outlier: 3.527A pdb=" N HIS 3 423 " --> pdb=" O ARG 3 419 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN 3 428 " --> pdb=" O GLU 3 424 " (cutoff:3.500A) Processing helix chain '3' and resid 472 through 479 removed outlier: 3.856A pdb=" N ARG 3 478 " --> pdb=" O SER 3 474 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE 3 479 " --> pdb=" O LEU 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 490 through 505 Processing helix chain '3' and resid 566 through 576 Processing helix chain '3' and resid 583 through 598 Processing helix chain '3' and resid 599 through 604 removed outlier: 3.563A pdb=" N MET 3 603 " --> pdb=" O SER 3 599 " (cutoff:3.500A) Processing helix chain '3' and resid 614 through 632 Processing helix chain '3' and resid 638 through 654 Processing helix chain '4' and resid 161 through 172 removed outlier: 3.688A pdb=" N ASN 4 165 " --> pdb=" O ALA 4 161 " (cutoff:3.500A) Processing helix chain '4' and resid 191 through 202 Processing helix chain '4' and resid 213 through 219 Processing helix chain '4' and resid 219 through 229 Processing helix chain '4' and resid 229 through 249 Proline residue: 4 235 - end of helix removed outlier: 3.722A pdb=" N ASP 4 247 " --> pdb=" O GLU 4 243 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 279 removed outlier: 3.713A pdb=" N ILE 4 279 " --> pdb=" O PRO 4 276 " (cutoff:3.500A) Processing helix chain '4' and resid 433 through 442 Processing helix chain '4' and resid 444 through 454 Processing helix chain '4' and resid 457 through 466 removed outlier: 3.603A pdb=" N ARG 4 461 " --> pdb=" O ASP 4 457 " (cutoff:3.500A) Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 516 through 527 Processing helix chain '4' and resid 561 through 567 removed outlier: 3.506A pdb=" N SER 4 566 " --> pdb=" O ALA 4 562 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP 4 567 " --> pdb=" O LEU 4 563 " (cutoff:3.500A) Processing helix chain '4' and resid 580 through 594 removed outlier: 3.631A pdb=" N SER 4 585 " --> pdb=" O GLU 4 581 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL 4 586 " --> pdb=" O SER 4 582 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 623 removed outlier: 3.819A pdb=" N SER 4 622 " --> pdb=" O PRO 4 619 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN 4 623 " --> pdb=" O ILE 4 620 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 619 through 623' Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 642 Processing helix chain '4' and resid 655 through 672 removed outlier: 3.884A pdb=" N TYR 4 670 " --> pdb=" O LEU 4 666 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR 4 671 " --> pdb=" O VAL 4 667 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN 4 672 " --> pdb=" O ALA 4 668 " (cutoff:3.500A) Processing helix chain '4' and resid 683 through 698 Processing helix chain '4' and resid 703 through 720 Processing helix chain '4' and resid 730 through 748 removed outlier: 3.720A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG 4 748 " --> pdb=" O HIS 4 744 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 773 removed outlier: 3.745A pdb=" N GLN 4 771 " --> pdb=" O GLU 4 767 " (cutoff:3.500A) Processing helix chain '4' and resid 783 through 788 removed outlier: 3.696A pdb=" N THR 4 788 " --> pdb=" O SER 4 784 " (cutoff:3.500A) Processing helix chain '4' and resid 793 through 813 removed outlier: 3.838A pdb=" N LYS 4 798 " --> pdb=" O SER 4 794 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU 4 799 " --> pdb=" O ARG 4 795 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU 4 800 " --> pdb=" O LYS 4 796 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER 4 811 " --> pdb=" O LYS 4 807 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 831 Processing helix chain '4' and resid 836 through 850 Processing helix chain '5' and resid 28 through 42 Processing helix chain '5' and resid 54 through 66 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 81 through 91 Processing helix chain '5' and resid 91 through 112 removed outlier: 4.521A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU 5 98 " --> pdb=" O GLU 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 140 Processing helix chain '5' and resid 141 through 145 Processing helix chain '5' and resid 232 through 236 Processing helix chain '5' and resid 306 through 311 Processing helix chain '5' and resid 315 through 326 Processing helix chain '5' and resid 327 through 329 No H-bonds generated for 'chain '5' and resid 327 through 329' Processing helix chain '5' and resid 330 through 335 removed outlier: 3.656A pdb=" N ILE 5 335 " --> pdb=" O VAL 5 331 " (cutoff:3.500A) Processing helix chain '5' and resid 349 through 357 removed outlier: 3.812A pdb=" N CYS 5 355 " --> pdb=" O LYS 5 351 " (cutoff:3.500A) Processing helix chain '5' and resid 366 through 370 removed outlier: 3.869A pdb=" N LEU 5 369 " --> pdb=" O PRO 5 366 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR 5 370 " --> pdb=" O ASP 5 367 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 366 through 370' Processing helix chain '5' and resid 387 through 398 Processing helix chain '5' and resid 432 through 437 Processing helix chain '5' and resid 447 through 450 Processing helix chain '5' and resid 456 through 464 removed outlier: 4.604A pdb=" N GLU 5 460 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) Processing helix chain '5' and resid 470 through 474 Processing helix chain '5' and resid 555 through 568 removed outlier: 3.834A pdb=" N VAL 5 568 " --> pdb=" O ALA 5 564 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 596 removed outlier: 3.525A pdb=" N ARG 5 594 " --> pdb=" O ARG 5 590 " (cutoff:3.500A) Processing helix chain '5' and resid 609 through 627 removed outlier: 3.723A pdb=" N MET 5 626 " --> pdb=" O ALA 5 622 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 648 Processing helix chain '5' and resid 668 through 683 removed outlier: 3.878A pdb=" N ILE 5 675 " --> pdb=" O MET 5 671 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU 5 676 " --> pdb=" O LEU 5 672 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS 5 677 " --> pdb=" O SER 5 673 " (cutoff:3.500A) Processing helix chain '5' and resid 691 through 701 removed outlier: 3.549A pdb=" N LYS 5 700 " --> pdb=" O LYS 5 696 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN 5 701 " --> pdb=" O ASP 5 697 " (cutoff:3.500A) Processing helix chain '5' and resid 704 through 719 removed outlier: 3.524A pdb=" N ILE 5 708 " --> pdb=" O PRO 5 704 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 37 Processing helix chain '6' and resid 44 through 53 Processing helix chain '6' and resid 65 through 72 Processing helix chain '6' and resid 72 through 82 Processing helix chain '6' and resid 82 through 99 Proline residue: 6 88 - end of helix Processing helix chain '6' and resid 100 through 102 No H-bonds generated for 'chain '6' and resid 100 through 102' Processing helix chain '6' and resid 122 through 126 Processing helix chain '6' and resid 127 through 131 removed outlier: 3.617A pdb=" N ARG 6 130 " --> pdb=" O THR 6 127 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE 6 131 " --> pdb=" O SER 6 128 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 127 through 131' Processing helix chain '6' and resid 321 through 328 Processing helix chain '6' and resid 330 through 343 Processing helix chain '6' and resid 345 through 355 Processing helix chain '6' and resid 361 through 374 Processing helix chain '6' and resid 401 through 413 removed outlier: 3.993A pdb=" N PHE 6 405 " --> pdb=" O ALA 6 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) Processing helix chain '6' and resid 462 through 465 removed outlier: 4.096A pdb=" N MET 6 465 " --> pdb=" O PHE 6 462 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 462 through 465' Processing helix chain '6' and resid 466 through 480 removed outlier: 4.196A pdb=" N VAL 6 471 " --> pdb=" O VAL 6 467 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA 6 472 " --> pdb=" O ARG 6 468 " (cutoff:3.500A) Processing helix chain '6' and resid 515 through 520 Processing helix chain '6' and resid 523 through 528 Processing helix chain '6' and resid 541 through 558 Processing helix chain '6' and resid 568 through 580 Processing helix chain '6' and resid 587 through 605 removed outlier: 3.823A pdb=" N ASP 6 605 " --> pdb=" O LEU 6 601 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 635 removed outlier: 3.709A pdb=" N GLU 6 622 " --> pdb=" O VAL 6 618 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET 6 624 " --> pdb=" O GLN 6 620 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 656 removed outlier: 3.530A pdb=" N VAL 6 645 " --> pdb=" O GLN 6 641 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 734 removed outlier: 3.934A pdb=" N SER 6 724 " --> pdb=" O TYR 6 720 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG 6 732 " --> pdb=" O VAL 6 728 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS 6 733 " --> pdb=" O LEU 6 729 " (cutoff:3.500A) Processing helix chain '6' and resid 735 through 739 removed outlier: 3.704A pdb=" N GLU 6 738 " --> pdb=" O GLU 6 735 " (cutoff:3.500A) Processing helix chain '6' and resid 744 through 756 removed outlier: 3.584A pdb=" N VAL 6 749 " --> pdb=" O ARG 6 745 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN 6 750 " --> pdb=" O SER 6 746 " (cutoff:3.500A) Processing helix chain '6' and resid 757 through 759 No H-bonds generated for 'chain '6' and resid 757 through 759' Processing helix chain '6' and resid 762 through 782 removed outlier: 3.586A pdb=" N HIS 6 782 " --> pdb=" O HIS 6 778 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 19 removed outlier: 3.724A pdb=" N GLU 7 9 " --> pdb=" O ASP 7 5 " (cutoff:3.500A) Processing helix chain '7' and resid 33 through 42 removed outlier: 3.622A pdb=" N HIS 7 42 " --> pdb=" O VAL 7 38 " (cutoff:3.500A) Processing helix chain '7' and resid 52 through 59 removed outlier: 3.973A pdb=" N ASP 7 58 " --> pdb=" O ASP 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 69 Processing helix chain '7' and resid 69 through 85 Processing helix chain '7' and resid 86 through 89 Processing helix chain '7' and resid 97 through 113 Processing helix chain '7' and resid 148 through 152 removed outlier: 3.524A pdb=" N VAL 7 152 " --> pdb=" O ILE 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 153 through 157 removed outlier: 3.774A pdb=" N VAL 7 157 " --> pdb=" O ALA 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 214 Processing helix chain '7' and resid 260 through 262 No H-bonds generated for 'chain '7' and resid 260 through 262' Processing helix chain '7' and resid 320 through 327 Processing helix chain '7' and resid 331 through 339 Processing helix chain '7' and resid 347 through 360 Processing helix chain '7' and resid 390 through 398 Processing helix chain '7' and resid 433 through 437 Processing helix chain '7' and resid 446 through 450 Processing helix chain '7' and resid 451 through 465 Processing helix chain '7' and resid 508 through 514 Processing helix chain '7' and resid 530 through 544 removed outlier: 3.631A pdb=" N HIS 7 536 " --> pdb=" O ARG 7 532 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN 7 542 " --> pdb=" O THR 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 567 Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 577 through 595 Processing helix chain '7' and resid 602 through 620 removed outlier: 3.572A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 645 Processing helix chain 'B' and resid 740 through 758 removed outlier: 3.578A pdb=" N LEU B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 757 " --> pdb=" O ASP B 753 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA B 758 " --> pdb=" O VAL B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 774 Processing helix chain 'B' and resid 781 through 795 removed outlier: 3.772A pdb=" N ALA B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 233 Processing sheet with id=AA2, first strand: chain '2' and resid 291 through 292 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 291 through 292 current: chain '2' and resid 393 through 398 removed outlier: 6.712A pdb=" N THR 2 415 " --> pdb=" O ASN 2 442 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL 2 444 " --> pdb=" O GLU 2 413 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU 2 413 " --> pdb=" O VAL 2 444 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 544 through 547 removed outlier: 6.547A pdb=" N ILE 2 544 " --> pdb=" O LEU 2 585 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASP 2 587 " --> pdb=" O ILE 2 544 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR 2 546 " --> pdb=" O ASP 2 587 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N CYS 2 584 " --> pdb=" O ILE 2 627 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA 2 629 " --> pdb=" O CYS 2 584 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE 2 586 " --> pdb=" O ALA 2 629 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 2 519 " --> pdb=" O ALA 2 628 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA 2 630 " --> pdb=" O VAL 2 519 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU 2 521 " --> pdb=" O ALA 2 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 608 through 612 Processing sheet with id=AA5, first strand: chain '2' and resid 858 through 861 Processing sheet with id=AA6, first strand: chain '3' and resid 46 through 50 removed outlier: 6.579A pdb=" N LEU 3 47 " --> pdb=" O GLY 3 101 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLU 3 103 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL 3 49 " --> pdb=" O GLU 3 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '3' and resid 110 through 111 removed outlier: 3.544A pdb=" N GLY 3 129 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 200 through 201 removed outlier: 6.641A pdb=" N THR 3 200 " --> pdb=" O THR 3 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 156 through 158 removed outlier: 6.669A pdb=" N VAL 3 192 " --> pdb=" O VAL 3 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 156 through 158 removed outlier: 4.593A pdb=" N ARG 7 286 " --> pdb=" O LEU 7 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 327 through 328 Processing sheet with id=AB3, first strand: chain '3' and resid 365 through 369 removed outlier: 6.860A pdb=" N ILE 3 366 " --> pdb=" O CYS 3 407 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASP 3 409 " --> pdb=" O ILE 3 366 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR 3 368 " --> pdb=" O ASP 3 409 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL 3 406 " --> pdb=" O LEU 3 449 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA 3 451 " --> pdb=" O VAL 3 406 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE 3 408 " --> pdb=" O ALA 3 451 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA 3 452 " --> pdb=" O ILE 3 341 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU 3 343 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE 3 344 " --> pdb=" O MET 3 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain '3' and resid 430 through 434 Processing sheet with id=AB5, first strand: chain '3' and resid 581 through 582 removed outlier: 6.764A pdb=" N VAL 3 581 " --> pdb=" O VAL 3 637 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 207 through 208 Processing sheet with id=AB7, first strand: chain '4' and resid 282 through 288 removed outlier: 6.846A pdb=" N ASN 4 389 " --> pdb=" O TYR 4 421 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR 4 421 " --> pdb=" O ASN 4 389 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE 4 371 " --> pdb=" O THR 4 414 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 298 through 299 Processing sheet with id=AB9, first strand: chain '4' and resid 312 through 316 Processing sheet with id=AC1, first strand: chain '4' and resid 408 through 409 Processing sheet with id=AC2, first strand: chain '4' and resid 531 through 534 removed outlier: 6.489A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU 4 650 " --> pdb=" O LEU 4 507 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS 4 509 " --> pdb=" O LEU 4 650 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 545 through 549 Processing sheet with id=AC4, first strand: chain '4' and resid 595 through 599 Processing sheet with id=AC5, first strand: chain '4' and resid 701 through 702 removed outlier: 6.460A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '4' and resid 854 through 856 removed outlier: 4.377A pdb=" N THR 4 859 " --> pdb=" O THR 4 856 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 43 through 44 removed outlier: 3.756A pdb=" N VAL 5 44 " --> pdb=" O THR 5 52 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR 5 52 " --> pdb=" O VAL 5 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '5' and resid 69 through 73 Processing sheet with id=AC9, first strand: chain '5' and resid 417 through 420 removed outlier: 8.746A pdb=" N SER 5 292 " --> pdb=" O HIS 5 244 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN 5 246 " --> pdb=" O SER 5 292 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU 5 247 " --> pdb=" O LEU 5 227 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR 5 226 " --> pdb=" O ALA 5 158 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA 5 158 " --> pdb=" O THR 5 226 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS 5 228 " --> pdb=" O ILE 5 156 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 178 through 183 removed outlier: 6.638A pdb=" N THR 5 178 " --> pdb=" O CYS 5 172 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N CYS 5 172 " --> pdb=" O THR 5 178 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR 5 180 " --> pdb=" O ILE 5 170 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE 5 170 " --> pdb=" O THR 5 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS 5 220 " --> pdb=" O THR 5 166 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE 5 168 " --> pdb=" O LYS 5 218 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N LYS 5 218 " --> pdb=" O ILE 5 168 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N ILE 5 170 " --> pdb=" O PRO 5 216 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N CYS 5 172 " --> pdb=" O ILE 5 214 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ILE 5 214 " --> pdb=" O CYS 5 172 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '5' and resid 378 through 379 removed outlier: 3.630A pdb=" N ALA 5 486 " --> pdb=" O MET 5 379 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL 5 442 " --> pdb=" O LEU 5 485 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA 5 487 " --> pdb=" O VAL 5 442 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE 5 444 " --> pdb=" O ALA 5 487 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL 5 402 " --> pdb=" O CYS 5 443 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP 5 445 " --> pdb=" O VAL 5 402 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR 5 404 " --> pdb=" O ASP 5 445 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '5' and resid 466 through 467 Processing sheet with id=AD4, first strand: chain '5' and resid 573 through 574 removed outlier: 7.220A pdb=" N ARG 5 573 " --> pdb=" O ALA 5 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '5' and resid 689 through 690 removed outlier: 3.713A pdb=" N VAL 5 689 " --> pdb=" O LEU 5 730 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '6' and resid 60 through 64 removed outlier: 5.970A pdb=" N LEU 6 61 " --> pdb=" O ALA 6 113 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN 6 115 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '6' and resid 134 through 136 removed outlier: 7.187A pdb=" N THR 6 245 " --> pdb=" O CYS 6 301 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N SER 6 223 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N PHE 6 298 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU 6 225 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA 6 300 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE 6 227 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N CYS 6 302 " --> pdb=" O ILE 6 227 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '6' and resid 134 through 136 removed outlier: 7.187A pdb=" N THR 6 245 " --> pdb=" O CYS 6 301 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N SER 6 223 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N PHE 6 298 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU 6 225 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA 6 300 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE 6 227 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N CYS 6 302 " --> pdb=" O ILE 6 227 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL 6 142 " --> pdb=" O ALA 6 446 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE 6 444 " --> pdb=" O THR 6 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 164 through 169 removed outlier: 3.778A pdb=" N PHE 6 156 " --> pdb=" O ILE 6 165 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP 6 167 " --> pdb=" O GLY 6 154 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY 6 154 " --> pdb=" O ASP 6 167 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '6' and resid 378 through 379 removed outlier: 3.508A pdb=" N LYS 6 378 " --> pdb=" O LEU 6 386 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '6' and resid 416 through 420 removed outlier: 6.219A pdb=" N VAL 6 417 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP 6 460 " --> pdb=" O VAL 6 417 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR 6 419 " --> pdb=" O ASP 6 460 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY 6 396 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N CYS 6 393 " --> pdb=" O PHE 6 534 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU 6 536 " --> pdb=" O CYS 6 393 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL 6 395 " --> pdb=" O LEU 6 536 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '6' and resid 481 through 485 Processing sheet with id=AE4, first strand: chain '6' and resid 585 through 586 removed outlier: 6.913A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain '7' and resid 47 through 51 Processing sheet with id=AE6, first strand: chain '7' and resid 191 through 194 removed outlier: 6.835A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA 7 180 " --> pdb=" O GLY 7 226 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N GLY 7 226 " --> pdb=" O ALA 7 180 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N TYR 7 182 " --> pdb=" O THR 7 224 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N THR 7 224 " --> pdb=" O TYR 7 182 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N CYS 7 184 " --> pdb=" O LEU 7 222 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU 7 222 " --> pdb=" O CYS 7 184 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N SER 7 252 " --> pdb=" O THR 7 296 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N LEU 7 298 " --> pdb=" O SER 7 252 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR 7 254 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA 7 300 " --> pdb=" O THR 7 254 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU 7 256 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ARG 7 302 " --> pdb=" O LEU 7 256 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N GLU 7 258 " --> pdb=" O ARG 7 302 " (cutoff:3.500A) removed outlier: 12.130A pdb=" N VAL 7 304 " --> pdb=" O GLU 7 258 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE 7 303 " --> pdb=" O SER 7 272 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LYS 7 305 " --> pdb=" O HIS 7 270 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N HIS 7 270 " --> pdb=" O LYS 7 305 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS 7 236 " --> pdb=" O THR 7 168 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL 7 170 " --> pdb=" O GLU 7 234 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU 7 234 " --> pdb=" O VAL 7 170 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '7' and resid 401 through 404 removed outlier: 6.524A pdb=" N CYS 7 378 " --> pdb=" O TRP 7 519 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE 7 521 " --> pdb=" O CYS 7 378 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET 7 380 " --> pdb=" O ILE 7 521 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '7' and resid 416 through 421 Processing sheet with id=AE9, first strand: chain '7' and resid 466 through 471 Processing sheet with id=AF1, first strand: chain 'B' and resid 762 through 764 1313 hydrogen bonds defined for protein. 3780 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: 7.18 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8335 1.33 - 1.45: 5708 1.45 - 1.57: 19108 1.57 - 1.69: 17 1.69 - 1.81: 297 Bond restraints: 33465 Sorted by residual: bond pdb=" N GLY 7 646 " pdb=" CA GLY 7 646 " ideal model delta sigma weight residual 1.449 1.494 -0.044 1.45e-02 4.76e+03 9.37e+00 bond pdb=" N LEU 7 645 " pdb=" CA LEU 7 645 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.07e+00 bond pdb=" N LEU 2 319 " pdb=" CA LEU 2 319 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.18e-02 7.18e+03 8.47e+00 bond pdb=" N GLU 4 181 " pdb=" CA GLU 4 181 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.22e-02 6.72e+03 8.23e+00 bond pdb=" N GLN 2 345 " pdb=" CA GLN 2 345 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.74e+00 ... (remaining 33460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 44710 2.83 - 5.67: 418 5.67 - 8.50: 29 8.50 - 11.33: 3 11.33 - 14.17: 2 Bond angle restraints: 45162 Sorted by residual: angle pdb=" PB ATP 21001 " pdb=" O3B ATP 21001 " pdb=" PG ATP 21001 " ideal model delta sigma weight residual 139.87 125.70 14.17 1.00e+00 1.00e+00 2.01e+02 angle pdb=" N PRO 2 320 " pdb=" CA PRO 2 320 " pdb=" CB PRO 2 320 " ideal model delta sigma weight residual 103.25 95.53 7.72 1.05e+00 9.07e-01 5.40e+01 angle pdb=" PA ATP 21001 " pdb=" O3A ATP 21001 " pdb=" PB ATP 21001 " ideal model delta sigma weight residual 136.83 130.40 6.43 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ARG 2 825 " pdb=" C ARG 2 825 " pdb=" O ARG 2 825 " ideal model delta sigma weight residual 121.87 115.05 6.82 1.16e+00 7.43e-01 3.46e+01 angle pdb=" N ASP 2 741 " pdb=" CA ASP 2 741 " pdb=" C ASP 2 741 " ideal model delta sigma weight residual 112.89 105.62 7.27 1.24e+00 6.50e-01 3.43e+01 ... (remaining 45157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 18930 22.64 - 45.28: 1557 45.28 - 67.91: 197 67.91 - 90.55: 42 90.55 - 113.19: 2 Dihedral angle restraints: 20728 sinusoidal: 8638 harmonic: 12090 Sorted by residual: dihedral pdb=" CA ASP 3 531 " pdb=" C ASP 3 531 " pdb=" N PRO 3 532 " pdb=" CA PRO 3 532 " ideal model delta harmonic sigma weight residual -180.00 -66.81 -113.19 0 5.00e+00 4.00e-02 5.12e+02 dihedral pdb=" CA PHE 3 83 " pdb=" C PHE 3 83 " pdb=" N VAL 3 84 " pdb=" CA VAL 3 84 " ideal model delta harmonic sigma weight residual -180.00 -140.21 -39.79 0 5.00e+00 4.00e-02 6.33e+01 dihedral pdb=" CA ALA 3 69 " pdb=" C ALA 3 69 " pdb=" N PHE 3 70 " pdb=" CA PHE 3 70 " ideal model delta harmonic sigma weight residual 180.00 -141.31 -38.69 0 5.00e+00 4.00e-02 5.99e+01 ... (remaining 20725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3900 0.046 - 0.093: 911 0.093 - 0.139: 271 0.139 - 0.185: 22 0.185 - 0.232: 8 Chirality restraints: 5112 Sorted by residual: chirality pdb=" CB VAL 3 376 " pdb=" CA VAL 3 376 " pdb=" CG1 VAL 3 376 " pdb=" CG2 VAL 3 376 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL 2 347 " pdb=" N VAL 2 347 " pdb=" C VAL 2 347 " pdb=" CB VAL 2 347 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE 2 760 " pdb=" N ILE 2 760 " pdb=" C ILE 2 760 " pdb=" CB ILE 2 760 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5109 not shown) Planarity restraints: 5853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 825 " 0.949 9.50e-02 1.11e+02 4.25e-01 1.10e+02 pdb=" NE ARG 2 825 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG 2 825 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 825 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 825 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 208 " -0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO 3 209 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO 3 209 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 3 209 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET 2 738 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C MET 2 738 " -0.052 2.00e-02 2.50e+03 pdb=" O MET 2 738 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP 2 739 " 0.017 2.00e-02 2.50e+03 ... (remaining 5850 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 535 2.65 - 3.21: 30684 3.21 - 3.77: 48771 3.77 - 4.34: 66237 4.34 - 4.90: 109815 Nonbonded interactions: 256042 Sorted by model distance: nonbonded pdb=" OH TYR 2 726 " pdb=" CD ARG 2 730 " model vdw 2.082 3.440 nonbonded pdb=" O ASP 3 82 " pdb=" OG SER 3 86 " model vdw 2.136 3.040 nonbonded pdb=" OD2 ASP 6 343 " pdb=" OH TYR 6 567 " model vdw 2.147 3.040 nonbonded pdb=" OG SER 6 39 " pdb=" O GLY 6 42 " model vdw 2.174 3.040 nonbonded pdb=" NH1 ARG 3 327 " pdb=" O ILE 7 537 " model vdw 2.192 3.120 ... (remaining 256037 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.250 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.003 0.046 33465 Z= 0.171 Angle : 0.663 14.165 45162 Z= 0.375 Chirality : 0.044 0.232 5112 Planarity : 0.007 0.425 5853 Dihedral : 15.856 113.188 12878 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.20 % Favored : 90.36 % Rotamer: Outliers : 1.77 % Allowed : 14.72 % Favored : 83.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4096 helix: 1.00 (0.14), residues: 1516 sheet: -0.97 (0.21), residues: 677 loop : -2.09 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 7 169 TYR 0.020 0.001 TYR 2 373 PHE 0.018 0.001 PHE B 806 TRP 0.033 0.002 TRP 2 185 HIS 0.009 0.001 HIS 2 180 Details of bonding type rmsd covalent geometry : bond 0.00321 (33465) covalent geometry : angle 0.66277 (45162) hydrogen bonds : bond 0.17939 ( 1296) hydrogen bonds : angle 6.80065 ( 3780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 326 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: 2 410 ASP cc_start: 0.7346 (m-30) cc_final: 0.6882 (m-30) REVERT: 2 755 MET cc_start: 0.7952 (tmm) cc_final: 0.7500 (ptp) REVERT: 2 789 ASP cc_start: 0.7058 (t70) cc_final: 0.6627 (t0) REVERT: 2 899 MET cc_start: 0.7037 (tpp) cc_final: 0.6821 (tpp) REVERT: 3 47 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8414 (pt) REVERT: 3 388 THR cc_start: 0.8846 (m) cc_final: 0.8585 (p) REVERT: 3 473 ASP cc_start: 0.8150 (m-30) cc_final: 0.7838 (m-30) REVERT: 3 491 PRO cc_start: 0.8249 (Cg_exo) cc_final: 0.7992 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8635 (tp) REVERT: 4 361 MET cc_start: 0.6739 (tmm) cc_final: 0.6188 (tmm) REVERT: 4 379 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7720 (t) REVERT: 4 390 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8561 (m) REVERT: 5 74 MET cc_start: 0.6950 (ppp) cc_final: 0.6125 (ppp) REVERT: 5 434 MET cc_start: 0.9038 (tpp) cc_final: 0.8705 (mtp) REVERT: 5 715 MET cc_start: 0.7767 (tpp) cc_final: 0.7437 (tpp) REVERT: 6 57 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: 6 237 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7924 (pt0) REVERT: 6 415 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7100 (ptt-90) REVERT: 6 450 MET cc_start: 0.8179 (tpp) cc_final: 0.7974 (tpp) REVERT: 6 780 LEU cc_start: 0.4815 (OUTLIER) cc_final: 0.4101 (mt) REVERT: 7 83 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7130 (mm-30) REVERT: 7 364 GLN cc_start: 0.6214 (mp10) cc_final: 0.5980 (tt0) REVERT: 7 588 MET cc_start: 0.8329 (ttm) cc_final: 0.8015 (mtp) REVERT: B 741 GLU cc_start: 0.8261 (tp30) cc_final: 0.7911 (tp30) outliers start: 64 outliers final: 49 residues processed: 371 average time/residue: 0.1906 time to fit residues: 117.9235 Evaluate side-chains 350 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 294 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 47 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 115 THR Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 198 THR Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 498 SER Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 139 ILE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 327 VAL Chi-restraints excluded: chain 4 residue 379 VAL Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 611 THR Chi-restraints excluded: chain 4 residue 785 ILE Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 5 residue 245 MET Chi-restraints excluded: chain 5 residue 289 ILE Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 310 PHE Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 636 ASP Chi-restraints excluded: chain 5 residue 708 ILE Chi-restraints excluded: chain 6 residue 26 CYS Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 237 GLN Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 566 VAL Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 780 LEU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 478 LEU Chi-restraints excluded: chain 7 residue 482 CYS Chi-restraints excluded: chain 7 residue 537 ILE Chi-restraints excluded: chain 7 residue 555 ASP Chi-restraints excluded: chain 7 residue 645 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.1980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 242 HIS 2 549 GLN ** 2 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 847 GLN ** 3 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 18 GLN 7 374 ASN ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN B 761 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.149359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.117847 restraints weight = 53852.264| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.01 r_work: 0.3259 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33465 Z= 0.127 Angle : 0.604 12.949 45162 Z= 0.309 Chirality : 0.043 0.199 5112 Planarity : 0.004 0.108 5853 Dihedral : 6.853 96.000 4710 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.06 % Favored : 90.82 % Rotamer: Outliers : 2.60 % Allowed : 15.91 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 4096 helix: 1.03 (0.14), residues: 1579 sheet: -0.85 (0.20), residues: 689 loop : -2.10 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 5 724 TYR 0.013 0.001 TYR 7 562 PHE 0.015 0.001 PHE 2 851 TRP 0.027 0.002 TRP 2 185 HIS 0.007 0.001 HIS 5 596 Details of bonding type rmsd covalent geometry : bond 0.00279 (33465) covalent geometry : angle 0.60442 (45162) hydrogen bonds : bond 0.04232 ( 1296) hydrogen bonds : angle 5.12721 ( 3780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 321 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: 2 222 MET cc_start: 0.6419 (tmm) cc_final: 0.5940 (tmm) REVERT: 2 410 ASP cc_start: 0.7740 (m-30) cc_final: 0.7464 (m-30) REVERT: 2 746 MET cc_start: 0.6957 (mmt) cc_final: 0.6735 (mmt) REVERT: 2 789 ASP cc_start: 0.7516 (t70) cc_final: 0.7057 (t0) REVERT: 2 899 MET cc_start: 0.7131 (tpp) cc_final: 0.6865 (tpp) REVERT: 3 320 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8758 (tp) REVERT: 3 473 ASP cc_start: 0.8149 (m-30) cc_final: 0.7899 (m-30) REVERT: 3 482 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8505 (tp) REVERT: 3 491 PRO cc_start: 0.8208 (Cg_exo) cc_final: 0.7959 (Cg_endo) REVERT: 4 283 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7927 (tp) REVERT: 4 361 MET cc_start: 0.6649 (tmm) cc_final: 0.6143 (tmm) REVERT: 4 390 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8280 (m) REVERT: 4 839 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6337 (tmm) REVERT: 5 74 MET cc_start: 0.7003 (ppp) cc_final: 0.4488 (ppp) REVERT: 5 89 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.6162 (m-80) REVERT: 5 434 MET cc_start: 0.8927 (tpp) cc_final: 0.8717 (mtp) REVERT: 5 516 MET cc_start: 0.7353 (mtt) cc_final: 0.7103 (mtt) REVERT: 5 676 GLU cc_start: 0.8007 (mp0) cc_final: 0.6624 (tt0) REVERT: 5 722 GLN cc_start: 0.7505 (pp30) cc_final: 0.7272 (pp30) REVERT: 5 724 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7452 (ptm-80) REVERT: 6 57 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: 6 104 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7874 (mp) REVERT: 6 237 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: 6 415 ARG cc_start: 0.7488 (mtm110) cc_final: 0.6823 (ptt-90) REVERT: 6 780 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.3925 (mt) REVERT: 7 364 GLN cc_start: 0.6136 (mp10) cc_final: 0.5766 (tt0) REVERT: 7 588 MET cc_start: 0.8275 (ttm) cc_final: 0.8036 (mtp) REVERT: B 741 GLU cc_start: 0.7929 (tp30) cc_final: 0.7612 (tp30) outliers start: 94 outliers final: 41 residues processed: 393 average time/residue: 0.1885 time to fit residues: 125.6005 Evaluate side-chains 344 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 641 LEU Chi-restraints excluded: chain 2 residue 760 ILE Chi-restraints excluded: chain 2 residue 831 LEU Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 785 ILE Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 712 LEU Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 237 GLN Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 715 LEU Chi-restraints excluded: chain 6 residue 780 LEU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain B residue 740 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 371 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 376 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 339 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 370 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 242 HIS 2 549 GLN ** 2 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 792 ASN 3 58 ASN ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 723 HIS 7 389 GLN B 793 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.146356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114095 restraints weight = 53616.654| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.11 r_work: 0.3210 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33465 Z= 0.197 Angle : 0.634 11.117 45162 Z= 0.323 Chirality : 0.044 0.222 5112 Planarity : 0.004 0.085 5853 Dihedral : 6.839 110.681 4662 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.45 % Favored : 90.45 % Rotamer: Outliers : 3.51 % Allowed : 16.85 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 4096 helix: 1.01 (0.14), residues: 1583 sheet: -1.01 (0.20), residues: 698 loop : -2.10 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 850 TYR 0.016 0.002 TYR 7 73 PHE 0.016 0.002 PHE 2 339 TRP 0.027 0.002 TRP 6 614 HIS 0.007 0.001 HIS 2 419 Details of bonding type rmsd covalent geometry : bond 0.00469 (33465) covalent geometry : angle 0.63405 (45162) hydrogen bonds : bond 0.04112 ( 1296) hydrogen bonds : angle 4.92494 ( 3780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 293 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: 2 242 HIS cc_start: 0.7783 (t70) cc_final: 0.7303 (t-170) REVERT: 2 246 TYR cc_start: 0.7525 (m-80) cc_final: 0.7265 (m-80) REVERT: 2 746 MET cc_start: 0.7094 (mmt) cc_final: 0.6748 (mmt) REVERT: 2 789 ASP cc_start: 0.7573 (t70) cc_final: 0.7099 (t0) REVERT: 3 482 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8530 (tt) REVERT: 3 491 PRO cc_start: 0.8211 (Cg_exo) cc_final: 0.7974 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8312 (tt) REVERT: 4 283 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8038 (tp) REVERT: 4 361 MET cc_start: 0.6740 (tmm) cc_final: 0.6213 (tmm) REVERT: 4 390 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8447 (m) REVERT: 4 839 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6492 (tmm) REVERT: 5 74 MET cc_start: 0.7035 (ppp) cc_final: 0.4604 (ppp) REVERT: 5 89 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6267 (m-80) REVERT: 5 698 PHE cc_start: 0.8735 (m-80) cc_final: 0.8473 (m-80) REVERT: 5 715 MET cc_start: 0.7871 (tpp) cc_final: 0.7486 (tpp) REVERT: 5 723 HIS cc_start: 0.7559 (m170) cc_final: 0.7267 (m-70) REVERT: 6 57 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7295 (pm20) REVERT: 6 104 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7897 (mp) REVERT: 6 415 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7055 (ptt-90) REVERT: 7 364 GLN cc_start: 0.6215 (mp10) cc_final: 0.5848 (tt0) REVERT: 7 511 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8702 (tt) outliers start: 127 outliers final: 77 residues processed: 390 average time/residue: 0.1864 time to fit residues: 123.2145 Evaluate side-chains 368 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 282 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 554 VAL Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 641 LEU Chi-restraints excluded: chain 2 residue 760 ILE Chi-restraints excluded: chain 2 residue 831 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 127 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 260 LEU Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 524 VAL Chi-restraints excluded: chain 3 residue 617 THR Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 139 ILE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 546 TYR Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 684 MET Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 4 residue 737 LEU Chi-restraints excluded: chain 4 residue 785 ILE Chi-restraints excluded: chain 4 residue 787 THR Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 4 residue 856 THR Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 151 ILE Chi-restraints excluded: chain 5 residue 245 MET Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 357 LEU Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 643 LEU Chi-restraints excluded: chain 5 residue 712 LEU Chi-restraints excluded: chain 6 residue 26 CYS Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 135 THR Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 237 GLN Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 481 THR Chi-restraints excluded: chain 6 residue 543 VAL Chi-restraints excluded: chain 6 residue 566 VAL Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 622 GLU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 340 ILE Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 87 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 351 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 644 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.145595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113335 restraints weight = 53611.110| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.08 r_work: 0.3196 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33465 Z= 0.207 Angle : 0.638 11.276 45162 Z= 0.324 Chirality : 0.044 0.208 5112 Planarity : 0.004 0.067 5853 Dihedral : 6.862 109.745 4658 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.84 % Favored : 90.04 % Rotamer: Outliers : 3.93 % Allowed : 17.93 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 4096 helix: 0.97 (0.13), residues: 1586 sheet: -0.98 (0.20), residues: 684 loop : -2.15 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 6 188 TYR 0.018 0.002 TYR 3 45 PHE 0.024 0.002 PHE 3 256 TRP 0.027 0.002 TRP 6 614 HIS 0.008 0.001 HIS 2 419 Details of bonding type rmsd covalent geometry : bond 0.00497 (33465) covalent geometry : angle 0.63785 (45162) hydrogen bonds : bond 0.03943 ( 1296) hydrogen bonds : angle 4.85403 ( 3780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 294 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: 2 746 MET cc_start: 0.7100 (mmt) cc_final: 0.6781 (mmt) REVERT: 2 775 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: 2 789 ASP cc_start: 0.7594 (t70) cc_final: 0.7131 (t0) REVERT: 3 47 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8412 (pt) REVERT: 3 393 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8631 (pt) REVERT: 3 482 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8545 (tt) REVERT: 3 491 PRO cc_start: 0.8234 (Cg_exo) cc_final: 0.7970 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8309 (tt) REVERT: 4 361 MET cc_start: 0.6754 (tmm) cc_final: 0.6242 (tmm) REVERT: 4 379 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7928 (t) REVERT: 4 390 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8458 (m) REVERT: 4 839 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6532 (tmm) REVERT: 5 74 MET cc_start: 0.7104 (ppp) cc_final: 0.4739 (ppp) REVERT: 5 89 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6245 (m-80) REVERT: 5 196 LYS cc_start: 0.6968 (tmtt) cc_final: 0.6699 (tmtt) REVERT: 5 485 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8609 (tp) REVERT: 5 724 ARG cc_start: 0.7893 (ptm-80) cc_final: 0.7657 (ptm-80) REVERT: 6 104 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7876 (mp) REVERT: 6 415 ARG cc_start: 0.7603 (mtm110) cc_final: 0.6936 (ptt-90) REVERT: 7 364 GLN cc_start: 0.6309 (mp10) cc_final: 0.5976 (tt0) REVERT: 7 511 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8700 (tt) outliers start: 142 outliers final: 88 residues processed: 402 average time/residue: 0.1834 time to fit residues: 125.2889 Evaluate side-chains 381 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 281 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 319 LEU Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 554 VAL Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 641 LEU Chi-restraints excluded: chain 2 residue 760 ILE Chi-restraints excluded: chain 2 residue 775 GLU Chi-restraints excluded: chain 2 residue 831 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 47 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 127 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 469 ILE Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 524 VAL Chi-restraints excluded: chain 3 residue 617 THR Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 139 ILE Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 327 VAL Chi-restraints excluded: chain 4 residue 379 VAL Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 546 TYR Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 607 LEU Chi-restraints excluded: chain 4 residue 684 MET Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 4 residue 785 ILE Chi-restraints excluded: chain 4 residue 787 THR Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 151 ILE Chi-restraints excluded: chain 5 residue 245 MET Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 310 PHE Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 357 LEU Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 485 LEU Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 643 LEU Chi-restraints excluded: chain 5 residue 712 LEU Chi-restraints excluded: chain 6 residue 26 CYS Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 135 THR Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 237 GLN Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 481 THR Chi-restraints excluded: chain 6 residue 543 VAL Chi-restraints excluded: chain 6 residue 566 VAL Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 610 THR Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 622 GLU Chi-restraints excluded: chain 6 residue 715 LEU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 340 ILE Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 482 CYS Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 783 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 209 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 329 optimal weight: 0.9980 chunk 320 optimal weight: 0.8980 chunk 323 optimal weight: 1.9990 chunk 293 optimal weight: 0.3980 chunk 394 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 242 HIS ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 722 GLN 5 723 HIS B 761 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113450 restraints weight = 53888.517| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.12 r_work: 0.3223 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33465 Z= 0.151 Angle : 0.601 11.290 45162 Z= 0.305 Chirality : 0.043 0.212 5112 Planarity : 0.004 0.061 5853 Dihedral : 6.725 109.022 4658 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.35 % Favored : 90.53 % Rotamer: Outliers : 3.68 % Allowed : 18.95 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4096 helix: 1.09 (0.14), residues: 1584 sheet: -1.02 (0.20), residues: 694 loop : -2.08 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 169 TYR 0.014 0.001 TYR 7 562 PHE 0.018 0.001 PHE 3 120 TRP 0.025 0.002 TRP 6 614 HIS 0.007 0.001 HIS 5 596 Details of bonding type rmsd covalent geometry : bond 0.00355 (33465) covalent geometry : angle 0.60142 (45162) hydrogen bonds : bond 0.03538 ( 1296) hydrogen bonds : angle 4.69824 ( 3780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 293 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 738 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.5216 (tmm) REVERT: 2 746 MET cc_start: 0.7074 (mmt) cc_final: 0.6749 (mmt) REVERT: 2 775 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: 2 789 ASP cc_start: 0.7527 (t70) cc_final: 0.7088 (t0) REVERT: 3 47 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8392 (pt) REVERT: 3 473 ASP cc_start: 0.8207 (m-30) cc_final: 0.7925 (m-30) REVERT: 3 482 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8511 (tt) REVERT: 3 491 PRO cc_start: 0.8189 (Cg_exo) cc_final: 0.7942 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8296 (tt) REVERT: 4 283 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8019 (tp) REVERT: 4 361 MET cc_start: 0.6657 (tmm) cc_final: 0.6218 (tmm) REVERT: 4 379 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7884 (t) REVERT: 4 839 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6254 (tmm) REVERT: 5 74 MET cc_start: 0.7044 (ppp) cc_final: 0.4782 (ppp) REVERT: 5 89 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: 5 676 GLU cc_start: 0.7779 (mp0) cc_final: 0.7414 (pm20) REVERT: 5 715 MET cc_start: 0.7785 (tpp) cc_final: 0.7478 (tpp) REVERT: 5 722 GLN cc_start: 0.8532 (pt0) cc_final: 0.8031 (pp30) REVERT: 5 723 HIS cc_start: 0.7971 (m170) cc_final: 0.7381 (m-70) REVERT: 6 104 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7888 (mp) REVERT: 6 415 ARG cc_start: 0.7522 (mtm110) cc_final: 0.6879 (ptt-90) REVERT: 6 780 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4029 (mt) REVERT: 7 364 GLN cc_start: 0.6208 (mp10) cc_final: 0.5839 (tt0) outliers start: 133 outliers final: 87 residues processed: 395 average time/residue: 0.1809 time to fit residues: 122.0832 Evaluate side-chains 381 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 283 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 VAL Chi-restraints excluded: chain 2 residue 188 MET Chi-restraints excluded: chain 2 residue 319 LEU Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 641 LEU Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 2 residue 760 ILE Chi-restraints excluded: chain 2 residue 775 GLU Chi-restraints excluded: chain 2 residue 831 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 47 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 127 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 469 ILE Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 524 VAL Chi-restraints excluded: chain 3 residue 617 THR Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 139 ILE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 327 VAL Chi-restraints excluded: chain 4 residue 375 HIS Chi-restraints excluded: chain 4 residue 379 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 607 LEU Chi-restraints excluded: chain 4 residue 684 MET Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 151 ILE Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 287 VAL Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 310 PHE Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 357 LEU Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 643 LEU Chi-restraints excluded: chain 6 residue 26 CYS Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 135 THR Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 543 VAL Chi-restraints excluded: chain 6 residue 566 VAL Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 610 THR Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 622 GLU Chi-restraints excluded: chain 6 residue 715 LEU Chi-restraints excluded: chain 6 residue 780 LEU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 340 ILE Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 482 CYS Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 521 ILE Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain B residue 761 GLN Chi-restraints excluded: chain B residue 801 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 76 optimal weight: 0.6980 chunk 377 optimal weight: 0.5980 chunk 354 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 112 optimal weight: 0.0070 chunk 230 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 242 HIS ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 376 ASN ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.148384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116202 restraints weight = 53489.326| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.93 r_work: 0.3263 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33465 Z= 0.112 Angle : 0.573 12.006 45162 Z= 0.290 Chirality : 0.042 0.187 5112 Planarity : 0.004 0.056 5853 Dihedral : 6.470 105.903 4652 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.91 % Favored : 90.97 % Rotamer: Outliers : 3.43 % Allowed : 19.47 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4096 helix: 1.22 (0.14), residues: 1581 sheet: -0.96 (0.20), residues: 688 loop : -2.01 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 169 TYR 0.013 0.001 TYR 2 535 PHE 0.017 0.001 PHE 3 120 TRP 0.022 0.001 TRP 6 614 HIS 0.008 0.001 HIS 5 596 Details of bonding type rmsd covalent geometry : bond 0.00253 (33465) covalent geometry : angle 0.57269 (45162) hydrogen bonds : bond 0.03152 ( 1296) hydrogen bonds : angle 4.53169 ( 3780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 315 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.5949 (tmm) REVERT: 2 389 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6727 (mmp80) REVERT: 2 495 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8937 (mp) REVERT: 2 738 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5481 (tmm) REVERT: 2 746 MET cc_start: 0.7016 (mmt) cc_final: 0.6672 (mmt) REVERT: 2 770 MET cc_start: 0.8839 (mmt) cc_final: 0.8291 (mmm) REVERT: 2 775 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: 2 789 ASP cc_start: 0.7461 (t70) cc_final: 0.7031 (t0) REVERT: 3 47 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8415 (pt) REVERT: 3 473 ASP cc_start: 0.8120 (m-30) cc_final: 0.7855 (m-30) REVERT: 3 482 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8486 (tt) REVERT: 3 491 PRO cc_start: 0.8164 (Cg_exo) cc_final: 0.7935 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8246 (tt) REVERT: 4 283 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7973 (tp) REVERT: 4 361 MET cc_start: 0.6587 (tmm) cc_final: 0.6234 (tmm) REVERT: 4 379 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7723 (t) REVERT: 4 733 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: 4 839 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6425 (tmm) REVERT: 5 74 MET cc_start: 0.7043 (ppp) cc_final: 0.4853 (ppp) REVERT: 5 89 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6162 (m-80) REVERT: 5 676 GLU cc_start: 0.7683 (mp0) cc_final: 0.7442 (pm20) REVERT: 6 104 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7909 (mp) REVERT: 6 415 ARG cc_start: 0.7417 (mtm110) cc_final: 0.6796 (ptt-90) REVERT: 6 780 LEU cc_start: 0.4826 (OUTLIER) cc_final: 0.4158 (mt) REVERT: 7 364 GLN cc_start: 0.6102 (mp10) cc_final: 0.5798 (tt0) outliers start: 124 outliers final: 82 residues processed: 408 average time/residue: 0.1816 time to fit residues: 126.6698 Evaluate side-chains 392 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 295 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 VAL Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 319 LEU Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 361 PHE Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 2 residue 389 ARG Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 641 LEU Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 2 residue 775 GLU Chi-restraints excluded: chain 2 residue 831 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 47 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 524 VAL Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 327 VAL Chi-restraints excluded: chain 4 residue 375 HIS Chi-restraints excluded: chain 4 residue 379 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 607 LEU Chi-restraints excluded: chain 4 residue 684 MET Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 4 residue 733 GLN Chi-restraints excluded: chain 4 residue 747 VAL Chi-restraints excluded: chain 4 residue 787 THR Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 643 LEU Chi-restraints excluded: chain 5 residue 665 SER Chi-restraints excluded: chain 5 residue 708 ILE Chi-restraints excluded: chain 5 residue 712 LEU Chi-restraints excluded: chain 6 residue 26 CYS Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 135 THR Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 469 ASP Chi-restraints excluded: chain 6 residue 543 VAL Chi-restraints excluded: chain 6 residue 566 VAL Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 610 THR Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 622 GLU Chi-restraints excluded: chain 6 residue 715 LEU Chi-restraints excluded: chain 6 residue 780 LEU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 222 LEU Chi-restraints excluded: chain 7 residue 235 MET Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 482 CYS Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 521 ILE Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 537 ILE Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 801 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 210 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 402 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 378 optimal weight: 10.0000 chunk 387 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 242 HIS 2 344 ASN 2 419 HIS 4 420 HIS ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 722 GLN 5 723 HIS 6 140 GLN 6 162 GLN B 761 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.144210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112193 restraints weight = 54089.468| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.24 r_work: 0.3167 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 33465 Z= 0.271 Angle : 0.680 11.619 45162 Z= 0.345 Chirality : 0.046 0.258 5112 Planarity : 0.005 0.067 5853 Dihedral : 6.861 110.609 4652 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.23 % Favored : 89.62 % Rotamer: Outliers : 3.96 % Allowed : 20.17 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 4096 helix: 1.01 (0.13), residues: 1585 sheet: -1.03 (0.20), residues: 684 loop : -2.10 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 169 TYR 0.020 0.002 TYR 3 45 PHE 0.021 0.002 PHE 2 339 TRP 0.030 0.002 TRP 6 614 HIS 0.010 0.001 HIS 5 596 Details of bonding type rmsd covalent geometry : bond 0.00657 (33465) covalent geometry : angle 0.68042 (45162) hydrogen bonds : bond 0.04079 ( 1296) hydrogen bonds : angle 4.80717 ( 3780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 287 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: 2 389 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.5517 (mmp-170) REVERT: 2 738 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5411 (tmm) REVERT: 2 775 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: 2 789 ASP cc_start: 0.7622 (t70) cc_final: 0.7182 (t0) REVERT: 3 47 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8417 (pt) REVERT: 3 482 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8535 (tp) REVERT: 3 491 PRO cc_start: 0.8209 (Cg_exo) cc_final: 0.7952 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8321 (tt) REVERT: 4 361 MET cc_start: 0.6734 (tmm) cc_final: 0.6256 (tmm) REVERT: 4 379 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8153 (t) REVERT: 4 733 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: 4 839 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6293 (tmm) REVERT: 5 74 MET cc_start: 0.7067 (ppp) cc_final: 0.4964 (ppp) REVERT: 5 89 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: 5 196 LYS cc_start: 0.7121 (tmtt) cc_final: 0.6781 (tmtt) REVERT: 5 485 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8589 (tp) REVERT: 5 676 GLU cc_start: 0.7593 (mp0) cc_final: 0.7372 (pm20) REVERT: 6 104 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7993 (mp) REVERT: 6 162 GLN cc_start: 0.8315 (mm110) cc_final: 0.8020 (mp10) REVERT: 6 237 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7901 (pt0) REVERT: 6 415 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7169 (ptt-90) REVERT: 6 780 LEU cc_start: 0.4369 (OUTLIER) cc_final: 0.3790 (mt) REVERT: 7 364 GLN cc_start: 0.6116 (mp10) cc_final: 0.5772 (tt0) outliers start: 143 outliers final: 104 residues processed: 397 average time/residue: 0.1825 time to fit residues: 123.9245 Evaluate side-chains 395 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 277 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 VAL Chi-restraints excluded: chain 2 residue 318 VAL Chi-restraints excluded: chain 2 residue 319 LEU Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 2 residue 389 ARG Chi-restraints excluded: chain 2 residue 410 ASP Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 554 VAL Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 2 residue 760 ILE Chi-restraints excluded: chain 2 residue 775 GLU Chi-restraints excluded: chain 2 residue 831 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 47 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 127 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 366 ILE Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 524 VAL Chi-restraints excluded: chain 3 residue 617 THR Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 139 ILE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 333 THR Chi-restraints excluded: chain 4 residue 379 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 607 LEU Chi-restraints excluded: chain 4 residue 684 MET Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 4 residue 733 GLN Chi-restraints excluded: chain 4 residue 747 VAL Chi-restraints excluded: chain 4 residue 787 THR Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 151 ILE Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 245 MET Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 310 PHE Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 357 LEU Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 485 LEU Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 643 LEU Chi-restraints excluded: chain 5 residue 665 SER Chi-restraints excluded: chain 5 residue 708 ILE Chi-restraints excluded: chain 5 residue 712 LEU Chi-restraints excluded: chain 6 residue 26 CYS Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 135 THR Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 237 GLN Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 302 CYS Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 469 ASP Chi-restraints excluded: chain 6 residue 543 VAL Chi-restraints excluded: chain 6 residue 566 VAL Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 610 THR Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 622 GLU Chi-restraints excluded: chain 6 residue 715 LEU Chi-restraints excluded: chain 6 residue 780 LEU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 235 MET Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 340 ILE Chi-restraints excluded: chain 7 residue 428 THR Chi-restraints excluded: chain 7 residue 434 LEU Chi-restraints excluded: chain 7 residue 482 CYS Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 521 ILE Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 537 ILE Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 799 MET Chi-restraints excluded: chain B residue 801 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 297 optimal weight: 0.9980 chunk 287 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 339 optimal weight: 0.6980 chunk 245 optimal weight: 0.7980 chunk 329 optimal weight: 0.9990 chunk 400 optimal weight: 0.6980 chunk 385 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 288 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 419 HIS 4 259 GLN ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 822 GLN ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 596 HIS B 761 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116553 restraints weight = 53822.178| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.92 r_work: 0.3253 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33465 Z= 0.117 Angle : 0.595 12.822 45162 Z= 0.300 Chirality : 0.042 0.171 5112 Planarity : 0.004 0.057 5853 Dihedral : 6.556 107.627 4652 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.79 % Favored : 91.09 % Rotamer: Outliers : 3.10 % Allowed : 21.19 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 4096 helix: 1.28 (0.14), residues: 1565 sheet: -1.00 (0.20), residues: 692 loop : -2.00 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 169 TYR 0.012 0.001 TYR 2 535 PHE 0.019 0.001 PHE 3 120 TRP 0.023 0.002 TRP 6 614 HIS 0.008 0.001 HIS 5 596 Details of bonding type rmsd covalent geometry : bond 0.00265 (33465) covalent geometry : angle 0.59451 (45162) hydrogen bonds : bond 0.03135 ( 1296) hydrogen bonds : angle 4.51197 ( 3780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 301 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 202 PHE cc_start: 0.5781 (t80) cc_final: 0.4867 (t80) REVERT: 2 389 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6771 (mmp80) REVERT: 2 738 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5362 (tmm) REVERT: 2 746 MET cc_start: 0.7034 (mmt) cc_final: 0.6703 (mmt) REVERT: 2 770 MET cc_start: 0.8863 (mmt) cc_final: 0.7923 (mmm) REVERT: 2 775 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: 2 789 ASP cc_start: 0.7440 (t70) cc_final: 0.7017 (t0) REVERT: 3 47 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8394 (pt) REVERT: 3 473 ASP cc_start: 0.8114 (m-30) cc_final: 0.7869 (m-30) REVERT: 3 482 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8482 (tt) REVERT: 3 491 PRO cc_start: 0.8174 (Cg_exo) cc_final: 0.7961 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8253 (tt) REVERT: 4 283 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7983 (tp) REVERT: 4 361 MET cc_start: 0.6665 (tmm) cc_final: 0.6289 (tmm) REVERT: 4 379 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7801 (t) REVERT: 4 733 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: 4 839 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6515 (tmm) REVERT: 5 74 MET cc_start: 0.6991 (ppp) cc_final: 0.4861 (ppp) REVERT: 5 89 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: 5 485 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8574 (tp) REVERT: 5 636 ASP cc_start: 0.6947 (m-30) cc_final: 0.6588 (m-30) REVERT: 6 104 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.8008 (mp) REVERT: 6 162 GLN cc_start: 0.8296 (mm110) cc_final: 0.8006 (mp10) REVERT: 6 415 ARG cc_start: 0.7455 (mtm110) cc_final: 0.6852 (ptt-90) REVERT: 7 364 GLN cc_start: 0.5947 (mp10) cc_final: 0.5692 (tt0) outliers start: 112 outliers final: 77 residues processed: 389 average time/residue: 0.1822 time to fit residues: 121.4521 Evaluate side-chains 372 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 282 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 VAL Chi-restraints excluded: chain 2 residue 319 LEU Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 361 PHE Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 2 residue 389 ARG Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 2 residue 775 GLU Chi-restraints excluded: chain 2 residue 831 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 47 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 617 THR Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 139 ILE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 333 THR Chi-restraints excluded: chain 4 residue 379 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 607 LEU Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 4 residue 733 GLN Chi-restraints excluded: chain 4 residue 747 VAL Chi-restraints excluded: chain 4 residue 787 THR Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 151 ILE Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 357 LEU Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 485 LEU Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 643 LEU Chi-restraints excluded: chain 5 residue 708 ILE Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 469 ASP Chi-restraints excluded: chain 6 residue 543 VAL Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 610 THR Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 622 GLU Chi-restraints excluded: chain 6 residue 715 LEU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 235 MET Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 428 THR Chi-restraints excluded: chain 7 residue 482 CYS Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 521 ILE Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 537 ILE Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 761 GLN Chi-restraints excluded: chain B residue 783 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 311 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 325 optimal weight: 0.0980 chunk 341 optimal weight: 4.9990 chunk 154 optimal weight: 0.2980 chunk 347 optimal weight: 0.0970 chunk 346 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 242 HIS 2 419 HIS 4 335 HIS ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 389 GLN B 761 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.148906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117224 restraints weight = 53413.188| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.96 r_work: 0.3263 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33465 Z= 0.106 Angle : 0.593 13.207 45162 Z= 0.296 Chirality : 0.042 0.194 5112 Planarity : 0.004 0.075 5853 Dihedral : 6.442 110.127 4651 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.81 % Favored : 91.04 % Rotamer: Outliers : 2.88 % Allowed : 21.52 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.13), residues: 4096 helix: 1.36 (0.14), residues: 1565 sheet: -0.94 (0.20), residues: 708 loop : -1.97 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 169 TYR 0.017 0.001 TYR 4 671 PHE 0.023 0.001 PHE 5 447 TRP 0.023 0.002 TRP 6 751 HIS 0.011 0.001 HIS 4 335 Details of bonding type rmsd covalent geometry : bond 0.00234 (33465) covalent geometry : angle 0.59347 (45162) hydrogen bonds : bond 0.03008 ( 1296) hydrogen bonds : angle 4.43429 ( 3780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 308 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 202 PHE cc_start: 0.5773 (t80) cc_final: 0.4866 (t80) REVERT: 2 389 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6783 (mmp80) REVERT: 2 495 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8940 (mp) REVERT: 2 738 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.5396 (tmm) REVERT: 2 746 MET cc_start: 0.6937 (mmt) cc_final: 0.6609 (mmt) REVERT: 2 770 MET cc_start: 0.8852 (mmt) cc_final: 0.8304 (mmm) REVERT: 2 775 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: 2 789 ASP cc_start: 0.7465 (t70) cc_final: 0.7028 (t0) REVERT: 3 47 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8364 (pt) REVERT: 3 473 ASP cc_start: 0.8071 (m-30) cc_final: 0.7817 (m-30) REVERT: 3 482 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8475 (tt) REVERT: 3 491 PRO cc_start: 0.8169 (Cg_exo) cc_final: 0.7946 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8204 (tt) REVERT: 4 283 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7963 (tp) REVERT: 4 361 MET cc_start: 0.6639 (tmm) cc_final: 0.6248 (tmm) REVERT: 4 379 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7741 (t) REVERT: 4 733 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: 4 839 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6491 (tmm) REVERT: 5 74 MET cc_start: 0.7020 (ppp) cc_final: 0.4934 (ppp) REVERT: 5 89 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6105 (m-80) REVERT: 5 636 ASP cc_start: 0.7015 (m-30) cc_final: 0.6675 (m-30) REVERT: 6 104 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7952 (mp) REVERT: 6 162 GLN cc_start: 0.8355 (mm110) cc_final: 0.8073 (mp10) REVERT: 6 415 ARG cc_start: 0.7570 (mtm110) cc_final: 0.6850 (ptt-90) REVERT: 6 780 LEU cc_start: 0.4771 (OUTLIER) cc_final: 0.4063 (mt) REVERT: 7 364 GLN cc_start: 0.6025 (mp10) cc_final: 0.5803 (tt0) outliers start: 104 outliers final: 76 residues processed: 390 average time/residue: 0.1764 time to fit residues: 117.8322 Evaluate side-chains 379 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 289 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 VAL Chi-restraints excluded: chain 2 residue 319 LEU Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 2 residue 389 ARG Chi-restraints excluded: chain 2 residue 410 ASP Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 641 LEU Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 2 residue 775 GLU Chi-restraints excluded: chain 2 residue 831 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 47 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 617 THR Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 152 ILE Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 333 THR Chi-restraints excluded: chain 4 residue 379 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 607 LEU Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 4 residue 733 GLN Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 289 ILE Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 643 LEU Chi-restraints excluded: chain 5 residue 708 ILE Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 135 THR Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 302 CYS Chi-restraints excluded: chain 6 residue 469 ASP Chi-restraints excluded: chain 6 residue 543 VAL Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 610 THR Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 622 GLU Chi-restraints excluded: chain 6 residue 715 LEU Chi-restraints excluded: chain 6 residue 780 LEU Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 235 MET Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 428 THR Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 482 CYS Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 521 ILE Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 537 ILE Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 131 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 118 optimal weight: 0.0010 chunk 245 optimal weight: 0.3980 chunk 307 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 355 optimal weight: 0.0470 chunk 190 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 197 optimal weight: 0.9990 overall best weight: 0.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 242 HIS 2 419 HIS 4 335 HIS 4 415 HIS ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 246 GLN ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 644 HIS 6 730 HIS B 761 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.119392 restraints weight = 54141.847| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.96 r_work: 0.3295 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33465 Z= 0.101 Angle : 0.588 13.677 45162 Z= 0.293 Chirality : 0.042 0.177 5112 Planarity : 0.004 0.079 5853 Dihedral : 6.199 103.473 4651 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.01 % Favored : 91.85 % Rotamer: Outliers : 2.54 % Allowed : 21.88 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 4096 helix: 1.44 (0.14), residues: 1566 sheet: -0.80 (0.19), residues: 724 loop : -1.95 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 169 TYR 0.024 0.001 TYR 4 671 PHE 0.026 0.001 PHE 5 447 TRP 0.039 0.002 TRP 6 751 HIS 0.012 0.001 HIS 4 335 Details of bonding type rmsd covalent geometry : bond 0.00218 (33465) covalent geometry : angle 0.58814 (45162) hydrogen bonds : bond 0.02820 ( 1296) hydrogen bonds : angle 4.32497 ( 3780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 317 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: 2 202 PHE cc_start: 0.5897 (t80) cc_final: 0.5027 (t80) REVERT: 2 222 MET cc_start: 0.6566 (tmm) cc_final: 0.5833 (tmm) REVERT: 2 389 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6832 (mmp80) REVERT: 2 738 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5415 (tmm) REVERT: 2 746 MET cc_start: 0.6836 (mmt) cc_final: 0.6504 (mmt) REVERT: 2 770 MET cc_start: 0.8834 (mmt) cc_final: 0.7936 (mmm) REVERT: 2 775 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: 2 789 ASP cc_start: 0.7388 (t70) cc_final: 0.6949 (t0) REVERT: 2 890 LYS cc_start: 0.8732 (mttt) cc_final: 0.8175 (ptpt) REVERT: 3 47 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8363 (pt) REVERT: 3 482 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8467 (tp) REVERT: 3 491 PRO cc_start: 0.8131 (Cg_exo) cc_final: 0.7898 (Cg_endo) REVERT: 3 648 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8160 (tt) REVERT: 4 283 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7865 (tp) REVERT: 4 361 MET cc_start: 0.6478 (tmm) cc_final: 0.6134 (tmm) REVERT: 4 733 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: 4 839 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6617 (tmm) REVERT: 5 74 MET cc_start: 0.6941 (ppp) cc_final: 0.4923 (ppp) REVERT: 5 89 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: 5 636 ASP cc_start: 0.6946 (m-30) cc_final: 0.6576 (m-30) REVERT: 6 104 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7917 (mp) REVERT: 6 162 GLN cc_start: 0.8350 (mm110) cc_final: 0.8067 (mp10) REVERT: 6 390 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7512 (tp) REVERT: 6 415 ARG cc_start: 0.7507 (mtm110) cc_final: 0.6862 (ptt-90) REVERT: 7 645 LEU cc_start: 0.7740 (pp) cc_final: 0.7533 (pp) outliers start: 92 outliers final: 70 residues processed: 386 average time/residue: 0.1818 time to fit residues: 120.1544 Evaluate side-chains 383 residues out of total 3617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 301 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 VAL Chi-restraints excluded: chain 2 residue 319 LEU Chi-restraints excluded: chain 2 residue 322 LEU Chi-restraints excluded: chain 2 residue 363 VAL Chi-restraints excluded: chain 2 residue 389 ARG Chi-restraints excluded: chain 2 residue 410 ASP Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 2 residue 775 GLU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 47 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 86 SER Chi-restraints excluded: chain 3 residue 125 VAL Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 204 MET Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 252 THR Chi-restraints excluded: chain 3 residue 258 THR Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 406 VAL Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 3 residue 482 LEU Chi-restraints excluded: chain 3 residue 508 ARG Chi-restraints excluded: chain 3 residue 524 VAL Chi-restraints excluded: chain 3 residue 637 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 3 residue 654 PHE Chi-restraints excluded: chain 4 residue 139 ILE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 283 ILE Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 418 VAL Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 607 LEU Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 4 residue 733 GLN Chi-restraints excluded: chain 4 residue 833 ILE Chi-restraints excluded: chain 4 residue 839 MET Chi-restraints excluded: chain 5 residue 89 TYR Chi-restraints excluded: chain 5 residue 289 ILE Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 343 ILE Chi-restraints excluded: chain 5 residue 475 THR Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 708 ILE Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 302 CYS Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 469 ASP Chi-restraints excluded: chain 6 residue 609 VAL Chi-restraints excluded: chain 6 residue 610 THR Chi-restraints excluded: chain 6 residue 617 THR Chi-restraints excluded: chain 6 residue 622 GLU Chi-restraints excluded: chain 6 residue 715 LEU Chi-restraints excluded: chain 6 residue 730 HIS Chi-restraints excluded: chain 6 residue 791 THR Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 235 MET Chi-restraints excluded: chain 7 residue 289 VAL Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 428 THR Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 482 CYS Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 521 ILE Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 537 ILE Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 272 optimal weight: 0.5980 chunk 78 optimal weight: 0.0050 chunk 84 optimal weight: 1.9990 chunk 160 optimal weight: 0.0020 chunk 52 optimal weight: 0.2980 chunk 386 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 242 HIS ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 722 GLN 6 730 HIS B 761 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.150691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118903 restraints weight = 53856.318| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.93 r_work: 0.3305 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33465 Z= 0.102 Angle : 0.590 13.670 45162 Z= 0.293 Chirality : 0.042 0.211 5112 Planarity : 0.004 0.070 5853 Dihedral : 6.103 101.091 4649 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.15 % Favored : 91.70 % Rotamer: Outliers : 2.46 % Allowed : 22.30 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 4096 helix: 1.48 (0.14), residues: 1566 sheet: -0.71 (0.20), residues: 705 loop : -1.91 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 169 TYR 0.035 0.001 TYR 4 671 PHE 0.025 0.001 PHE 5 447 TRP 0.027 0.002 TRP 6 751 HIS 0.009 0.001 HIS 5 596 Details of bonding type rmsd covalent geometry : bond 0.00223 (33465) covalent geometry : angle 0.58959 (45162) hydrogen bonds : bond 0.02803 ( 1296) hydrogen bonds : angle 4.29671 ( 3780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7132.55 seconds wall clock time: 123 minutes 19.51 seconds (7399.51 seconds total)