Starting phenix.real_space_refine on Sun Aug 24 21:25:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asl_43818/08_2025/9asl_43818.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asl_43818/08_2025/9asl_43818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9asl_43818/08_2025/9asl_43818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asl_43818/08_2025/9asl_43818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9asl_43818/08_2025/9asl_43818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asl_43818/08_2025/9asl_43818.map" } resolution = 3.5 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= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 14828 2.51 5 N 3956 2.21 5 O 4196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23128 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 4.42, per 1000 atoms: 0.19 Number of scatterers: 23128 At special positions: 0 Unit cell: (129.72, 138.92, 140.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 4196 8.00 N 3956 7.00 C 14828 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: 1.54 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5568 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 23 sheets defined 56.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 93 through 102 removed outlier: 3.527A pdb=" N ALA A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.707A pdb=" N GLY A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 4.179A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.903A pdb=" N GLY A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 4.105A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.685A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.031A pdb=" N LEU A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 365 removed outlier: 3.659A pdb=" N CYS A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.528A pdb=" N GLU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.867A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 Processing helix chain 'A' and resid 421 through 435 removed outlier: 4.008A pdb=" N ASP A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.968A pdb=" N GLN A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 removed outlier: 4.248A pdb=" N LYS A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.500A pdb=" N ILE A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.850A pdb=" N MET A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.563A pdb=" N VAL A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 592 " --> pdb=" O TRP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.632A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 647 through 653 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 677 through 687 removed outlier: 3.914A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 729 removed outlier: 3.511A pdb=" N ASP A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 744 through 769 removed outlier: 4.122A pdb=" N SER A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 Processing helix chain 'A' and resid 780 through 788 removed outlier: 3.562A pdb=" N PHE A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 799 removed outlier: 4.329A pdb=" N ASP A 795 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 797 " --> pdb=" O CYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 827 through 835 removed outlier: 4.220A pdb=" N VAL A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 removed outlier: 3.510A pdb=" N VAL A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.534A pdb=" N ALA B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.816A pdb=" N GLY B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 136 removed outlier: 4.274A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.860A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 3.634A pdb=" N LEU B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.904A pdb=" N LEU B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 364 removed outlier: 4.073A pdb=" N ASN B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.532A pdb=" N LEU B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.894A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 Processing helix chain 'B' and resid 421 through 435 removed outlier: 4.046A pdb=" N ASP B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 470 through 476 removed outlier: 3.961A pdb=" N GLN B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 removed outlier: 4.221A pdb=" N LYS B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 removed outlier: 4.021A pdb=" N ARG B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.797A pdb=" N MET B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.823A pdb=" N VAL B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 592 " --> pdb=" O TRP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 624 through 641 removed outlier: 3.610A pdb=" N LEU B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 677 through 687 removed outlier: 3.903A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 684 " --> pdb=" O MET B 680 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 729 removed outlier: 3.750A pdb=" N ASP B 727 " --> pdb=" O LEU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.505A pdb=" N GLN B 749 " --> pdb=" O ARG B 745 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 780 through 788 removed outlier: 3.515A pdb=" N PHE B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 799 removed outlier: 4.288A pdb=" N ASP B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 797 " --> pdb=" O CYS B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 827 through 835 removed outlier: 4.218A pdb=" N VAL B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 890 removed outlier: 3.559A pdb=" N VAL B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.542A pdb=" N ALA C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.695A pdb=" N GLY C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 136 removed outlier: 4.296A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 162 Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.882A pdb=" N GLY C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 245 removed outlier: 3.694A pdb=" N LEU C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.923A pdb=" N LEU C 329 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 365 removed outlier: 3.553A pdb=" N CYS C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.516A pdb=" N GLU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 3.815A pdb=" N LYS C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 411 Processing helix chain 'C' and resid 421 through 435 removed outlier: 4.008A pdb=" N ASP C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 470 through 479 removed outlier: 3.990A pdb=" N GLN C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 510 removed outlier: 4.245A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 540 removed outlier: 4.024A pdb=" N ARG C 533 " --> pdb=" O GLY C 529 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 538 " --> pdb=" O ALA C 534 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 554 Processing helix chain 'C' and resid 557 through 563 removed outlier: 3.854A pdb=" N MET C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 removed outlier: 3.587A pdb=" N VAL C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TRP C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 592 " --> pdb=" O TRP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 624 through 636 removed outlier: 3.643A pdb=" N LEU C 629 " --> pdb=" O PRO C 625 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 639 No H-bonds generated for 'chain 'C' and resid 637 through 639' Processing helix chain 'C' and resid 647 through 653 Processing helix chain 'C' and resid 665 through 676 Processing helix chain 'C' and resid 677 through 687 removed outlier: 3.865A pdb=" N VAL C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 684 " --> pdb=" O MET C 680 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 685 " --> pdb=" O LYS C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 729 removed outlier: 3.501A pdb=" N ASP C 727 " --> pdb=" O LEU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 744 through 769 removed outlier: 4.112A pdb=" N SER C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 757 " --> pdb=" O GLN C 753 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 779 Processing helix chain 'C' and resid 780 through 788 removed outlier: 3.626A pdb=" N PHE C 787 " --> pdb=" O LYS C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 799 removed outlier: 4.306A pdb=" N ASP C 795 " --> pdb=" O GLU C 792 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 797 " --> pdb=" O CYS C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 812 Processing helix chain 'C' and resid 817 through 822 Processing helix chain 'C' and resid 827 through 835 removed outlier: 4.202A pdb=" N VAL C 831 " --> pdb=" O VAL C 827 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 832 " --> pdb=" O GLU C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 890 removed outlier: 3.523A pdb=" N VAL C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 887 " --> pdb=" O ALA C 883 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN C 888 " --> pdb=" O ARG C 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 93 through 102 removed outlier: 3.502A pdb=" N ALA D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.757A pdb=" N GLY D 120 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 136 removed outlier: 4.296A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.790A pdb=" N GLY D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 245 removed outlier: 3.635A pdb=" N LEU D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.936A pdb=" N LEU D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS D 335 " --> pdb=" O TYR D 331 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 365 removed outlier: 4.056A pdb=" N ASN D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 removed outlier: 3.540A pdb=" N GLU D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.903A pdb=" N LYS D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 421 through 435 removed outlier: 4.052A pdb=" N ASP D 426 " --> pdb=" O PHE D 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 Processing helix chain 'D' and resid 470 through 478 removed outlier: 3.882A pdb=" N GLN D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 478 " --> pdb=" O TYR D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 510 removed outlier: 4.243A pdb=" N LYS D 503 " --> pdb=" O SER D 499 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 507 " --> pdb=" O LYS D 503 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 540 removed outlier: 4.027A pdb=" N ARG D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 557 through 563 removed outlier: 3.827A pdb=" N MET D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 592 removed outlier: 3.830A pdb=" N VAL D 586 " --> pdb=" O ILE D 582 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 592 " --> pdb=" O TRP D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 622 Processing helix chain 'D' and resid 624 through 636 removed outlier: 3.606A pdb=" N LEU D 629 " --> pdb=" O PRO D 625 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 653 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 677 through 687 removed outlier: 3.892A pdb=" N VAL D 683 " --> pdb=" O SER D 679 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 684 " --> pdb=" O MET D 680 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 729 removed outlier: 3.632A pdb=" N ASP D 727 " --> pdb=" O LEU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 744 through 769 removed outlier: 4.032A pdb=" N SER D 754 " --> pdb=" O SER D 750 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 757 " --> pdb=" O GLN D 753 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL D 764 " --> pdb=" O GLY D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 778 Processing helix chain 'D' and resid 780 through 788 removed outlier: 3.512A pdb=" N PHE D 787 " --> pdb=" O LYS D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 799 removed outlier: 4.301A pdb=" N ASP D 795 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 797 " --> pdb=" O CYS D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 812 Processing helix chain 'D' and resid 817 through 822 Processing helix chain 'D' and resid 827 through 835 removed outlier: 4.223A pdb=" N VAL D 831 " --> pdb=" O VAL D 827 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 832 " --> pdb=" O GLU D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 890 removed outlier: 3.568A pdb=" N VAL D 880 " --> pdb=" O ALA D 876 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN D 888 " --> pdb=" O ARG D 884 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 4.111A pdb=" N VAL A 112 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 283 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.384A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS A 139 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 212 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 264 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 311 removed outlier: 4.028A pdb=" N ARG A 311 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 293 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU A 494 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 295 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 440 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 598 removed outlier: 3.507A pdb=" N HIS A 610 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 608 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 265 removed outlier: 7.224A pdb=" N TYR B 113 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 283 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 168 through 171 removed outlier: 5.689A pdb=" N LYS B 139 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET B 212 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 309 through 311 removed outlier: 4.039A pdb=" N ARG B 311 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 440 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 442 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AB2, first strand: chain 'B' and resid 595 through 597 removed outlier: 3.607A pdb=" N HIS B 610 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 862 through 863 Processing sheet with id=AB4, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.950A pdb=" N TYR C 283 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 168 through 171 removed outlier: 6.500A pdb=" N ASP C 169 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR C 190 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR C 171 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA C 140 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N CYS C 189 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 142 " --> pdb=" O CYS C 189 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LYS C 139 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET C 212 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 309 through 311 removed outlier: 4.026A pdb=" N ARG C 311 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 297 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 457 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 440 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 463 through 464 Processing sheet with id=AB8, first strand: chain 'C' and resid 595 through 598 removed outlier: 3.507A pdb=" N HIS C 610 " --> pdb=" O GLN C 596 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 608 " --> pdb=" O THR C 598 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 862 through 863 Processing sheet with id=AC1, first strand: chain 'D' and resid 168 through 171 removed outlier: 5.684A pdb=" N LYS D 139 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET D 212 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET D 264 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR D 283 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 309 through 311 removed outlier: 4.037A pdb=" N ARG D 311 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL D 457 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU D 341 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 440 " --> pdb=" O VAL D 340 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 463 through 464 Processing sheet with id=AC4, first strand: chain 'D' and resid 595 through 597 removed outlier: 3.607A pdb=" N HIS D 610 " --> pdb=" O GLN D 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 862 through 863 1034 hydrogen bonds defined for protein. 2937 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7509 1.34 - 1.46: 5043 1.46 - 1.58: 10740 1.58 - 1.70: 0 1.70 - 1.81: 236 Bond restraints: 23528 Sorted by residual: bond pdb=" CA VAL D 409 " pdb=" CB VAL D 409 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 4.46e+00 bond pdb=" C LEU A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.332 1.350 -0.019 1.26e-02 6.30e+03 2.19e+00 bond pdb=" C LEU B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.34e-02 5.57e+03 2.07e+00 bond pdb=" C LEU D 76 " pdb=" N PRO D 77 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.34e-02 5.57e+03 2.01e+00 bond pdb=" C LEU C 76 " pdb=" N PRO C 77 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.33e-02 5.65e+03 2.01e+00 ... (remaining 23523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 31072 1.85 - 3.70: 607 3.70 - 5.56: 113 5.56 - 7.41: 23 7.41 - 9.26: 9 Bond angle restraints: 31824 Sorted by residual: angle pdb=" N VAL A 687 " pdb=" CA VAL A 687 " pdb=" C VAL A 687 " ideal model delta sigma weight residual 113.10 110.03 3.07 9.70e-01 1.06e+00 1.00e+01 angle pdb=" N GLN D 805 " pdb=" CA GLN D 805 " pdb=" C GLN D 805 " ideal model delta sigma weight residual 114.04 110.14 3.90 1.24e+00 6.50e-01 9.88e+00 angle pdb=" N GLU D 126 " pdb=" CA GLU D 126 " pdb=" CB GLU D 126 " ideal model delta sigma weight residual 110.16 114.77 -4.61 1.48e+00 4.57e-01 9.71e+00 angle pdb=" N GLU B 126 " pdb=" CA GLU B 126 " pdb=" CB GLU B 126 " ideal model delta sigma weight residual 110.16 114.72 -4.56 1.48e+00 4.57e-01 9.51e+00 angle pdb=" CA GLU B 736 " pdb=" CB GLU B 736 " pdb=" CG GLU B 736 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.48e+00 ... (remaining 31819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 11605 17.55 - 35.10: 1929 35.10 - 52.64: 478 52.64 - 70.19: 98 70.19 - 87.74: 42 Dihedral angle restraints: 14152 sinusoidal: 5580 harmonic: 8572 Sorted by residual: dihedral pdb=" CA ASP D 304 " pdb=" CB ASP D 304 " pdb=" CG ASP D 304 " pdb=" OD1 ASP D 304 " ideal model delta sinusoidal sigma weight residual -30.00 -88.05 58.05 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA HIS B 180 " pdb=" C HIS B 180 " pdb=" N PHE B 181 " pdb=" CA PHE B 181 " ideal model delta harmonic sigma weight residual -180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CG ARG D 533 " pdb=" CD ARG D 533 " pdb=" NE ARG D 533 " pdb=" CZ ARG D 533 " ideal model delta sinusoidal sigma weight residual -90.00 -134.95 44.95 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 14149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2552 0.038 - 0.076: 947 0.076 - 0.113: 193 0.113 - 0.151: 58 0.151 - 0.189: 2 Chirality restraints: 3752 Sorted by residual: chirality pdb=" CA GLU B 126 " pdb=" N GLU B 126 " pdb=" C GLU B 126 " pdb=" CB GLU B 126 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA GLU D 126 " pdb=" N GLU D 126 " pdb=" C GLU D 126 " pdb=" CB GLU D 126 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CG LEU B 619 " pdb=" CB LEU B 619 " pdb=" CD1 LEU B 619 " pdb=" CD2 LEU B 619 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3749 not shown) Planarity restraints: 3980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 344 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 345 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 344 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO B 345 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 345 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 345 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 344 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO D 345 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO D 345 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 345 " -0.057 5.00e-02 4.00e+02 ... (remaining 3977 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 671 2.70 - 3.25: 23644 3.25 - 3.80: 36484 3.80 - 4.35: 46676 4.35 - 4.90: 76177 Nonbonded interactions: 183652 Sorted by model distance: nonbonded pdb=" NZ LYS C 109 " pdb=" OE1 GLU C 281 " model vdw 2.155 3.120 nonbonded pdb=" O HIS B 180 " pdb=" OG SER B 183 " model vdw 2.160 3.040 nonbonded pdb=" O LYS A 83 " pdb=" OG SER A 86 " model vdw 2.167 3.040 nonbonded pdb=" O HIS D 180 " pdb=" OG SER D 183 " model vdw 2.190 3.040 nonbonded pdb=" OG SER A 114 " pdb=" O ALA A 266 " model vdw 2.207 3.040 ... (remaining 183647 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.140 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 0.054 23528 Z= 0.150 Angle : 0.660 9.260 31824 Z= 0.350 Chirality : 0.041 0.189 3752 Planarity : 0.005 0.115 3980 Dihedral : 18.706 87.741 8584 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.48 % Allowed : 35.90 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -1.52 (0.15), residues: 2892 helix: -0.75 (0.13), residues: 1468 sheet: -0.13 (0.38), residues: 204 loop : -1.35 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 460 TYR 0.026 0.002 TYR B 228 PHE 0.018 0.001 PHE B 343 TRP 0.016 0.001 TRP B 349 HIS 0.016 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00336 (23528) covalent geometry : angle 0.66025 (31824) hydrogen bonds : bond 0.29167 ( 1034) hydrogen bonds : angle 8.82251 ( 2937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 525 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8614 (mp) cc_final: 0.8397 (mp) REVERT: A 713 MET cc_start: 0.8336 (tpt) cc_final: 0.7679 (tpt) REVERT: B 94 GLU cc_start: 0.7609 (pm20) cc_final: 0.6863 (tm-30) REVERT: B 634 ASP cc_start: 0.7879 (t0) cc_final: 0.7471 (t0) REVERT: B 639 MET cc_start: 0.6455 (mmt) cc_final: 0.5721 (mmt) REVERT: B 774 MET cc_start: 0.6779 (ptp) cc_final: 0.6548 (ptp) REVERT: D 92 MET cc_start: 0.5388 (tpp) cc_final: 0.4696 (tpp) REVERT: D 94 GLU cc_start: 0.7572 (pm20) cc_final: 0.6954 (tm-30) REVERT: D 634 ASP cc_start: 0.7867 (t0) cc_final: 0.7494 (t0) outliers start: 12 outliers final: 6 residues processed: 530 average time/residue: 0.1321 time to fit residues: 107.9756 Evaluate side-chains 363 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 357 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 443 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 HIS A 498 ASN A 646 ASN A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN C 416 HIS C 498 ASN C 646 ASN C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 ASN ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.198642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.154999 restraints weight = 37070.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157389 restraints weight = 19423.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.159010 restraints weight = 13020.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.159536 restraints weight = 13166.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.159726 restraints weight = 11447.673| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23528 Z= 0.170 Angle : 0.650 8.596 31824 Z= 0.333 Chirality : 0.043 0.180 3752 Planarity : 0.005 0.073 3980 Dihedral : 4.736 56.350 3169 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.70 % Favored : 95.16 % Rotamer: Outliers : 5.47 % Allowed : 33.03 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -1.19 (0.15), residues: 2892 helix: -0.21 (0.13), residues: 1576 sheet: -0.04 (0.36), residues: 208 loop : -1.69 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 823 TYR 0.024 0.002 TYR B 239 PHE 0.015 0.002 PHE C 787 TRP 0.011 0.001 TRP B 411 HIS 0.009 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00398 (23528) covalent geometry : angle 0.64961 (31824) hydrogen bonds : bond 0.04943 ( 1034) hydrogen bonds : angle 5.66507 ( 2937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 390 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7446 (tppt) REVERT: A 92 MET cc_start: 0.7732 (ttm) cc_final: 0.7060 (ttp) REVERT: A 93 PHE cc_start: 0.6346 (m-10) cc_final: 0.6129 (m-80) REVERT: A 152 GLU cc_start: 0.7837 (tp30) cc_final: 0.7307 (tm-30) REVERT: A 307 MET cc_start: 0.6275 (mmt) cc_final: 0.5978 (mpp) REVERT: A 329 LEU cc_start: 0.8604 (mp) cc_final: 0.8397 (mp) REVERT: A 713 MET cc_start: 0.8241 (tpt) cc_final: 0.7542 (tpt) REVERT: B 92 MET cc_start: 0.5899 (tpp) cc_final: 0.5667 (tpp) REVERT: B 94 GLU cc_start: 0.7926 (pm20) cc_final: 0.7117 (tm-30) REVERT: B 329 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8052 (mp) REVERT: B 627 ASP cc_start: 0.7997 (m-30) cc_final: 0.7762 (m-30) REVERT: B 634 ASP cc_start: 0.7911 (t0) cc_final: 0.7643 (t0) REVERT: B 639 MET cc_start: 0.6657 (mmt) cc_final: 0.5351 (mmt) REVERT: B 680 MET cc_start: 0.7789 (mtm) cc_final: 0.7451 (mtm) REVERT: B 825 ASN cc_start: 0.7751 (t0) cc_final: 0.7543 (t0) REVERT: B 878 LEU cc_start: 0.8475 (mt) cc_final: 0.7888 (mt) REVERT: C 91 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7306 (tppt) REVERT: C 93 PHE cc_start: 0.6327 (m-10) cc_final: 0.6121 (m-80) REVERT: C 152 GLU cc_start: 0.7850 (tp30) cc_final: 0.7388 (tm-30) REVERT: C 307 MET cc_start: 0.6235 (mmt) cc_final: 0.5938 (mpp) REVERT: D 94 GLU cc_start: 0.7976 (pm20) cc_final: 0.7160 (tm-30) REVERT: D 144 LEU cc_start: 0.8541 (mm) cc_final: 0.8308 (mt) REVERT: D 152 GLU cc_start: 0.7966 (tp30) cc_final: 0.7339 (mt-10) REVERT: D 622 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8595 (t) REVERT: D 627 ASP cc_start: 0.7986 (m-30) cc_final: 0.7754 (m-30) REVERT: D 634 ASP cc_start: 0.8010 (t0) cc_final: 0.7673 (t0) REVERT: D 878 LEU cc_start: 0.8459 (mt) cc_final: 0.7864 (mt) outliers start: 137 outliers final: 59 residues processed: 487 average time/residue: 0.1220 time to fit residues: 98.4374 Evaluate side-chains 410 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 349 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 142 PHE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 622 SER Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 859 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 138 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 285 optimal weight: 0.5980 chunk 150 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 282 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS C 646 ASN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 260 GLN D 325 HIS ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.191646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.147768 restraints weight = 37211.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.150152 restraints weight = 20561.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.151721 restraints weight = 13836.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.152395 restraints weight = 13909.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.152253 restraints weight = 12161.802| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23528 Z= 0.200 Angle : 0.655 15.163 31824 Z= 0.329 Chirality : 0.044 0.332 3752 Planarity : 0.005 0.068 3980 Dihedral : 4.653 59.965 3165 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.91 % Favored : 94.99 % Rotamer: Outliers : 6.43 % Allowed : 32.23 % Favored : 61.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.83 (0.15), residues: 2892 helix: 0.05 (0.13), residues: 1564 sheet: -0.29 (0.31), residues: 256 loop : -1.40 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 668 TYR 0.019 0.002 TYR B 239 PHE 0.016 0.002 PHE B 765 TRP 0.016 0.001 TRP C 411 HIS 0.007 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00475 (23528) covalent geometry : angle 0.65502 (31824) hydrogen bonds : bond 0.04170 ( 1034) hydrogen bonds : angle 5.02665 ( 2937) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 403 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.6627 (m-10) cc_final: 0.6286 (m-80) REVERT: A 152 GLU cc_start: 0.7865 (tp30) cc_final: 0.7429 (tm-30) REVERT: A 191 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7969 (mm) REVERT: A 193 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7728 (ttm110) REVERT: A 260 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: A 307 MET cc_start: 0.6113 (mmt) cc_final: 0.5764 (mpp) REVERT: A 366 HIS cc_start: 0.3690 (OUTLIER) cc_final: 0.3149 (m-70) REVERT: A 680 MET cc_start: 0.8114 (mtm) cc_final: 0.7597 (mtm) REVERT: A 878 LEU cc_start: 0.8606 (mt) cc_final: 0.7699 (mt) REVERT: A 881 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7525 (tp30) REVERT: B 142 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7869 (t80) REVERT: B 169 ASP cc_start: 0.7495 (t0) cc_final: 0.7216 (t0) REVERT: B 191 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7824 (mm) REVERT: B 233 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8407 (tp) REVERT: B 351 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: B 366 HIS cc_start: 0.4002 (OUTLIER) cc_final: 0.3445 (m-70) REVERT: B 422 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8538 (t80) REVERT: B 550 MET cc_start: 0.8053 (tmm) cc_final: 0.7749 (tmm) REVERT: B 668 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6793 (mtt-85) REVERT: B 878 LEU cc_start: 0.8678 (mt) cc_final: 0.7759 (mt) REVERT: B 881 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7451 (tp30) REVERT: C 93 PHE cc_start: 0.6632 (m-10) cc_final: 0.6319 (m-80) REVERT: C 152 GLU cc_start: 0.7807 (tp30) cc_final: 0.7435 (tm-30) REVERT: C 191 ILE cc_start: 0.8215 (mt) cc_final: 0.7936 (mm) REVERT: C 307 MET cc_start: 0.6151 (mmt) cc_final: 0.5782 (mpp) REVERT: C 342 LEU cc_start: 0.7867 (tp) cc_final: 0.7655 (mt) REVERT: C 366 HIS cc_start: 0.3923 (OUTLIER) cc_final: 0.3357 (m-70) REVERT: C 713 MET cc_start: 0.8500 (tpt) cc_final: 0.7772 (tpt) REVERT: C 878 LEU cc_start: 0.8669 (mt) cc_final: 0.7719 (mt) REVERT: D 92 MET cc_start: 0.6822 (tpp) cc_final: 0.6486 (tpp) REVERT: D 144 LEU cc_start: 0.8695 (mm) cc_final: 0.8462 (mp) REVERT: D 152 GLU cc_start: 0.8037 (tp30) cc_final: 0.7456 (mt-10) REVERT: D 233 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8314 (tp) REVERT: D 366 HIS cc_start: 0.4025 (OUTLIER) cc_final: 0.3384 (m-70) REVERT: D 550 MET cc_start: 0.8065 (tmm) cc_final: 0.7781 (tmm) REVERT: D 634 ASP cc_start: 0.8068 (t0) cc_final: 0.7680 (t0) REVERT: D 680 MET cc_start: 0.7931 (mtp) cc_final: 0.7688 (mtp) REVERT: D 878 LEU cc_start: 0.8632 (mt) cc_final: 0.7700 (mt) REVERT: D 881 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7543 (tp30) outliers start: 161 outliers final: 76 residues processed: 522 average time/residue: 0.1268 time to fit residues: 108.2278 Evaluate side-chains 435 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 346 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 646 ASN Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 724 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 273 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 184 optimal weight: 0.2980 chunk 172 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN D 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.193221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.149778 restraints weight = 37045.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.152431 restraints weight = 19161.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.153290 restraints weight = 13180.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.154097 restraints weight = 14409.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.154148 restraints weight = 11983.521| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23528 Z= 0.137 Angle : 0.596 12.073 31824 Z= 0.298 Chirality : 0.041 0.281 3752 Planarity : 0.004 0.063 3980 Dihedral : 4.418 59.067 3162 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.39 % Allowed : 33.39 % Favored : 61.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.68 (0.15), residues: 2892 helix: 0.19 (0.13), residues: 1564 sheet: -0.46 (0.30), residues: 276 loop : -1.30 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 668 TYR 0.016 0.001 TYR C 171 PHE 0.014 0.002 PHE B 658 TRP 0.011 0.001 TRP A 411 HIS 0.006 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00326 (23528) covalent geometry : angle 0.59584 (31824) hydrogen bonds : bond 0.03416 ( 1034) hydrogen bonds : angle 4.73688 ( 2937) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 379 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7811 (mmmt) cc_final: 0.7457 (tppt) REVERT: A 121 LYS cc_start: 0.6674 (mtpt) cc_final: 0.6014 (ttpt) REVERT: A 152 GLU cc_start: 0.7876 (tp30) cc_final: 0.7436 (tm-30) REVERT: A 191 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7943 (mm) REVERT: A 329 LEU cc_start: 0.8623 (mp) cc_final: 0.8347 (mp) REVERT: A 366 HIS cc_start: 0.3727 (OUTLIER) cc_final: 0.3221 (m-70) REVERT: A 680 MET cc_start: 0.8180 (mtm) cc_final: 0.7582 (mtm) REVERT: A 862 ILE cc_start: 0.4564 (OUTLIER) cc_final: 0.4259 (tt) REVERT: A 878 LEU cc_start: 0.8654 (mt) cc_final: 0.7676 (mt) REVERT: B 81 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8394 (pp) REVERT: B 142 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7725 (t80) REVERT: B 169 ASP cc_start: 0.7549 (t0) cc_final: 0.7274 (t0) REVERT: B 351 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: B 366 HIS cc_start: 0.3970 (OUTLIER) cc_final: 0.3386 (m-70) REVERT: B 422 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 423 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7338 (mp0) REVERT: B 550 MET cc_start: 0.7940 (tmm) cc_final: 0.7664 (tmm) REVERT: B 630 ASP cc_start: 0.7796 (m-30) cc_final: 0.7593 (m-30) REVERT: B 680 MET cc_start: 0.8028 (mtm) cc_final: 0.7803 (mpp) REVERT: B 718 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7222 (ttt-90) REVERT: B 878 LEU cc_start: 0.8703 (mt) cc_final: 0.7765 (mt) REVERT: C 93 PHE cc_start: 0.6658 (m-10) cc_final: 0.6304 (m-80) REVERT: C 152 GLU cc_start: 0.7852 (tp30) cc_final: 0.7422 (mt-10) REVERT: C 191 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7888 (mm) REVERT: C 264 MET cc_start: 0.8115 (mpp) cc_final: 0.7820 (mpp) REVERT: C 342 LEU cc_start: 0.7981 (tp) cc_final: 0.7712 (mt) REVERT: C 366 HIS cc_start: 0.3901 (OUTLIER) cc_final: 0.3348 (m-70) REVERT: C 718 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7439 (ttt-90) REVERT: C 878 LEU cc_start: 0.8304 (mt) cc_final: 0.7740 (mt) REVERT: D 92 MET cc_start: 0.7020 (tpp) cc_final: 0.6263 (tpp) REVERT: D 142 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7867 (t80) REVERT: D 152 GLU cc_start: 0.8020 (tp30) cc_final: 0.7558 (mt-10) REVERT: D 191 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7812 (mm) REVERT: D 210 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7749 (mp) REVERT: D 233 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8245 (tp) REVERT: D 366 HIS cc_start: 0.4050 (OUTLIER) cc_final: 0.3448 (m-70) REVERT: D 423 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7397 (mp0) REVERT: D 634 ASP cc_start: 0.8005 (t0) cc_final: 0.7466 (t0) REVERT: D 680 MET cc_start: 0.7871 (mtp) cc_final: 0.7572 (mtp) REVERT: D 718 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7235 (ttt-90) REVERT: D 878 LEU cc_start: 0.8663 (mt) cc_final: 0.7704 (mt) outliers start: 135 outliers final: 74 residues processed: 487 average time/residue: 0.1318 time to fit residues: 103.7834 Evaluate side-chains 445 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 353 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 55 optimal weight: 0.6980 chunk 287 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN D 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.192196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.148792 restraints weight = 37033.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151367 restraints weight = 19204.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.151967 restraints weight = 13485.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152849 restraints weight = 14757.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.152847 restraints weight = 12285.453| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23528 Z= 0.149 Angle : 0.596 11.670 31824 Z= 0.297 Chirality : 0.042 0.303 3752 Planarity : 0.004 0.061 3980 Dihedral : 4.358 58.739 3162 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.55 % Allowed : 33.67 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.15), residues: 2892 helix: 0.22 (0.13), residues: 1588 sheet: -0.38 (0.30), residues: 280 loop : -1.39 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG D 696 TYR 0.020 0.001 TYR A 667 PHE 0.011 0.002 PHE B 658 TRP 0.011 0.001 TRP C 411 HIS 0.006 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00363 (23528) covalent geometry : angle 0.59553 (31824) hydrogen bonds : bond 0.03314 ( 1034) hydrogen bonds : angle 4.58233 ( 2937) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 368 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.7687 (ttm) cc_final: 0.7441 (ttp) REVERT: A 121 LYS cc_start: 0.6744 (mtpt) cc_final: 0.6073 (ttpt) REVERT: A 152 GLU cc_start: 0.7875 (tp30) cc_final: 0.7446 (tm-30) REVERT: A 191 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7943 (mm) REVERT: A 193 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7638 (ttm110) REVERT: A 307 MET cc_start: 0.6021 (mmt) cc_final: 0.5732 (mpp) REVERT: A 329 LEU cc_start: 0.8623 (mp) cc_final: 0.8408 (mp) REVERT: A 351 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: A 366 HIS cc_start: 0.3788 (OUTLIER) cc_final: 0.3284 (m-70) REVERT: A 458 ILE cc_start: 0.8146 (mt) cc_final: 0.7861 (mp) REVERT: A 627 ASP cc_start: 0.7922 (m-30) cc_final: 0.7702 (m-30) REVERT: A 718 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7541 (ttt-90) REVERT: A 862 ILE cc_start: 0.4330 (OUTLIER) cc_final: 0.3999 (tt) REVERT: A 878 LEU cc_start: 0.8338 (mt) cc_final: 0.7769 (mt) REVERT: B 81 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8407 (pp) REVERT: B 142 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7785 (t80) REVERT: B 166 ILE cc_start: 0.7876 (mp) cc_final: 0.7550 (pt) REVERT: B 169 ASP cc_start: 0.7633 (t0) cc_final: 0.7334 (t0) REVERT: B 233 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8565 (tp) REVERT: B 351 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: B 366 HIS cc_start: 0.4137 (OUTLIER) cc_final: 0.3563 (m-70) REVERT: B 423 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7391 (mp0) REVERT: B 550 MET cc_start: 0.7973 (tmm) cc_final: 0.7674 (tmm) REVERT: B 680 MET cc_start: 0.8045 (mtm) cc_final: 0.7844 (mpp) REVERT: B 718 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7249 (ttt-90) REVERT: B 878 LEU cc_start: 0.8409 (mt) cc_final: 0.7824 (mt) REVERT: C 81 LEU cc_start: 0.8959 (pp) cc_final: 0.8386 (pp) REVERT: C 121 LYS cc_start: 0.6677 (mtpt) cc_final: 0.5851 (ttpt) REVERT: C 152 GLU cc_start: 0.7837 (tp30) cc_final: 0.7443 (mt-10) REVERT: C 191 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 307 MET cc_start: 0.6027 (mmt) cc_final: 0.5714 (mpp) REVERT: C 366 HIS cc_start: 0.3978 (OUTLIER) cc_final: 0.3447 (m-70) REVERT: C 627 ASP cc_start: 0.7951 (m-30) cc_final: 0.7736 (m-30) REVERT: C 634 ASP cc_start: 0.8134 (t0) cc_final: 0.7725 (t0) REVERT: C 718 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7465 (ttt-90) REVERT: C 878 LEU cc_start: 0.8363 (mt) cc_final: 0.7781 (mt) REVERT: D 92 MET cc_start: 0.7030 (tpp) cc_final: 0.6399 (tpp) REVERT: D 142 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7886 (t80) REVERT: D 152 GLU cc_start: 0.7959 (tp30) cc_final: 0.7619 (mt-10) REVERT: D 210 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7784 (mp) REVERT: D 233 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8251 (tp) REVERT: D 366 HIS cc_start: 0.4176 (OUTLIER) cc_final: 0.3609 (m-70) REVERT: D 423 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7545 (mp0) REVERT: D 634 ASP cc_start: 0.8026 (t0) cc_final: 0.7455 (t0) REVERT: D 680 MET cc_start: 0.7914 (mtp) cc_final: 0.7593 (mtp) REVERT: D 718 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7228 (ttt-90) REVERT: D 878 LEU cc_start: 0.8348 (mt) cc_final: 0.7765 (mt) outliers start: 139 outliers final: 87 residues processed: 475 average time/residue: 0.1332 time to fit residues: 102.6892 Evaluate side-chains 453 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 346 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 859 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 258 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 646 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN D 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.188143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142882 restraints weight = 37437.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145862 restraints weight = 19307.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.147160 restraints weight = 12740.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.148131 restraints weight = 12046.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.148371 restraints weight = 10783.441| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23528 Z= 0.220 Angle : 0.663 12.573 31824 Z= 0.329 Chirality : 0.044 0.317 3752 Planarity : 0.004 0.073 3980 Dihedral : 4.559 58.098 3162 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.63 % Allowed : 32.55 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.74 (0.15), residues: 2892 helix: 0.13 (0.13), residues: 1592 sheet: -0.47 (0.30), residues: 280 loop : -1.36 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 696 TYR 0.015 0.002 TYR D 171 PHE 0.020 0.002 PHE C 93 TRP 0.015 0.001 TRP C 411 HIS 0.006 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00536 (23528) covalent geometry : angle 0.66337 (31824) hydrogen bonds : bond 0.03565 ( 1034) hydrogen bonds : angle 4.64062 ( 2937) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 363 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8016 (ttm) cc_final: 0.7775 (ttp) REVERT: A 121 LYS cc_start: 0.6895 (mtpt) cc_final: 0.6188 (ttpt) REVERT: A 152 GLU cc_start: 0.7861 (tp30) cc_final: 0.7515 (tm-30) REVERT: A 191 ILE cc_start: 0.8239 (mt) cc_final: 0.8012 (mt) REVERT: A 193 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7786 (ttm110) REVERT: A 351 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: A 366 HIS cc_start: 0.4023 (OUTLIER) cc_final: 0.3486 (m-70) REVERT: A 458 ILE cc_start: 0.8145 (mt) cc_final: 0.7929 (mp) REVERT: A 627 ASP cc_start: 0.7945 (m-30) cc_final: 0.7581 (m-30) REVERT: A 718 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7358 (ttt-90) REVERT: A 792 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: A 878 LEU cc_start: 0.8431 (mt) cc_final: 0.7839 (mt) REVERT: B 121 LYS cc_start: 0.7480 (mtmm) cc_final: 0.7213 (ttpt) REVERT: B 122 THR cc_start: 0.8097 (p) cc_final: 0.7817 (t) REVERT: B 142 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7876 (t80) REVERT: B 166 ILE cc_start: 0.7924 (mp) cc_final: 0.7641 (pt) REVERT: B 169 ASP cc_start: 0.7689 (t0) cc_final: 0.7378 (t0) REVERT: B 191 ILE cc_start: 0.8201 (mt) cc_final: 0.7984 (mt) REVERT: B 233 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8531 (tp) REVERT: B 351 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: B 366 HIS cc_start: 0.4305 (OUTLIER) cc_final: 0.3868 (m-70) REVERT: B 667 TYR cc_start: 0.7048 (t80) cc_final: 0.6830 (t80) REVERT: B 680 MET cc_start: 0.8239 (mtm) cc_final: 0.8024 (mpp) REVERT: B 718 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7339 (ttt-90) REVERT: B 878 LEU cc_start: 0.8468 (mt) cc_final: 0.7899 (mt) REVERT: C 152 GLU cc_start: 0.7937 (tp30) cc_final: 0.7483 (mt-10) REVERT: C 264 MET cc_start: 0.8242 (mpp) cc_final: 0.7939 (mpp) REVERT: C 343 PHE cc_start: 0.8252 (m-80) cc_final: 0.8009 (m-80) REVERT: C 351 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: C 366 HIS cc_start: 0.4270 (OUTLIER) cc_final: 0.3809 (m-70) REVERT: C 627 ASP cc_start: 0.7942 (m-30) cc_final: 0.7576 (m-30) REVERT: C 639 MET cc_start: 0.7156 (ppp) cc_final: 0.6478 (ptm) REVERT: C 713 MET cc_start: 0.8691 (tpt) cc_final: 0.7955 (tpt) REVERT: C 718 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7397 (ttt-90) REVERT: C 792 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: C 862 ILE cc_start: 0.6436 (OUTLIER) cc_final: 0.6218 (tp) REVERT: C 878 LEU cc_start: 0.8453 (mt) cc_final: 0.7885 (mt) REVERT: D 92 MET cc_start: 0.7275 (tpp) cc_final: 0.6654 (tpp) REVERT: D 142 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7863 (t80) REVERT: D 152 GLU cc_start: 0.8053 (tp30) cc_final: 0.7632 (mt-10) REVERT: D 166 ILE cc_start: 0.7898 (mp) cc_final: 0.7573 (pt) REVERT: D 191 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7969 (mt) REVERT: D 210 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7819 (mp) REVERT: D 233 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8381 (tp) REVERT: D 366 HIS cc_start: 0.4440 (OUTLIER) cc_final: 0.3965 (m-70) REVERT: D 423 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7696 (mp0) REVERT: D 634 ASP cc_start: 0.7910 (t0) cc_final: 0.7388 (t0) REVERT: D 680 MET cc_start: 0.8028 (mtp) cc_final: 0.7659 (mtp) REVERT: D 718 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7328 (ttt-90) REVERT: D 878 LEU cc_start: 0.8440 (mt) cc_final: 0.7812 (mt) outliers start: 166 outliers final: 108 residues processed: 497 average time/residue: 0.1258 time to fit residues: 101.0850 Evaluate side-chains 468 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 339 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 189 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 200 optimal weight: 0.1980 chunk 159 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN D 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.191312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.144574 restraints weight = 37073.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.149066 restraints weight = 19129.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151966 restraints weight = 13040.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.153406 restraints weight = 10517.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.154542 restraints weight = 9403.402| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23528 Z= 0.134 Angle : 0.601 13.508 31824 Z= 0.298 Chirality : 0.041 0.292 3752 Planarity : 0.004 0.059 3980 Dihedral : 4.290 19.136 3160 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.87 % Allowed : 33.39 % Favored : 60.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.15), residues: 2892 helix: 0.20 (0.13), residues: 1604 sheet: -0.43 (0.29), residues: 316 loop : -1.43 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 696 TYR 0.028 0.001 TYR D 667 PHE 0.011 0.001 PHE B 658 TRP 0.010 0.001 TRP C 411 HIS 0.006 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00325 (23528) covalent geometry : angle 0.60059 (31824) hydrogen bonds : bond 0.03164 ( 1034) hydrogen bonds : angle 4.46423 ( 2937) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 365 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7640 (tppt) REVERT: A 92 MET cc_start: 0.7878 (ttm) cc_final: 0.7622 (ttm) REVERT: A 121 LYS cc_start: 0.6723 (mtpt) cc_final: 0.6078 (ttpt) REVERT: A 152 GLU cc_start: 0.7858 (tp30) cc_final: 0.7425 (mt-10) REVERT: A 191 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7904 (mt) REVERT: A 351 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: A 366 HIS cc_start: 0.3873 (OUTLIER) cc_final: 0.3337 (m-70) REVERT: A 458 ILE cc_start: 0.8091 (mt) cc_final: 0.7794 (mp) REVERT: A 634 ASP cc_start: 0.8069 (t0) cc_final: 0.7844 (t0) REVERT: A 718 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7299 (ttt-90) REVERT: A 774 MET cc_start: 0.7743 (mmm) cc_final: 0.6776 (mtt) REVERT: A 878 LEU cc_start: 0.8527 (mt) cc_final: 0.7924 (mt) REVERT: B 81 LEU cc_start: 0.8823 (tt) cc_final: 0.8524 (pp) REVERT: B 121 LYS cc_start: 0.7384 (mtmm) cc_final: 0.7099 (ttpt) REVERT: B 142 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7805 (t80) REVERT: B 166 ILE cc_start: 0.7891 (mp) cc_final: 0.7619 (pt) REVERT: B 351 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: B 366 HIS cc_start: 0.4372 (OUTLIER) cc_final: 0.3874 (m-70) REVERT: B 423 GLU cc_start: 0.7932 (mp0) cc_final: 0.7677 (mp0) REVERT: B 718 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7241 (ttt-90) REVERT: B 878 LEU cc_start: 0.8506 (mt) cc_final: 0.7954 (mt) REVERT: C 121 LYS cc_start: 0.6644 (mtpt) cc_final: 0.5822 (ttpt) REVERT: C 152 GLU cc_start: 0.7936 (tp30) cc_final: 0.7486 (mt-10) REVERT: C 343 PHE cc_start: 0.8188 (m-80) cc_final: 0.7879 (m-80) REVERT: C 351 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: C 366 HIS cc_start: 0.4239 (OUTLIER) cc_final: 0.3739 (m-70) REVERT: C 634 ASP cc_start: 0.8042 (t0) cc_final: 0.7749 (t0) REVERT: C 718 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7321 (ttt-90) REVERT: C 878 LEU cc_start: 0.8440 (mt) cc_final: 0.7870 (mt) REVERT: D 92 MET cc_start: 0.7213 (tpp) cc_final: 0.6581 (tpp) REVERT: D 142 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7808 (t80) REVERT: D 152 GLU cc_start: 0.8045 (tp30) cc_final: 0.7643 (mt-10) REVERT: D 166 ILE cc_start: 0.7850 (mp) cc_final: 0.7617 (pt) REVERT: D 191 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7865 (mt) REVERT: D 207 MET cc_start: 0.8513 (mmm) cc_final: 0.8179 (mmm) REVERT: D 210 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7758 (mp) REVERT: D 366 HIS cc_start: 0.4470 (OUTLIER) cc_final: 0.3972 (m-70) REVERT: D 423 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7641 (mp0) REVERT: D 634 ASP cc_start: 0.7942 (t0) cc_final: 0.7384 (t0) REVERT: D 680 MET cc_start: 0.7962 (mtp) cc_final: 0.7581 (mtp) REVERT: D 718 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7219 (ttt-90) REVERT: D 878 LEU cc_start: 0.8500 (mt) cc_final: 0.7930 (mt) outliers start: 147 outliers final: 96 residues processed: 485 average time/residue: 0.1249 time to fit residues: 98.5580 Evaluate side-chains 451 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 339 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 82 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 129 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 258 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 888 GLN ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN D 73 ASN D 85 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.191105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.144146 restraints weight = 36999.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148747 restraints weight = 19260.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.151581 restraints weight = 13172.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.153141 restraints weight = 10655.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.154120 restraints weight = 9504.814| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23528 Z= 0.142 Angle : 0.617 12.540 31824 Z= 0.303 Chirality : 0.042 0.341 3752 Planarity : 0.004 0.080 3980 Dihedral : 4.241 17.432 3160 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.67 % Allowed : 33.83 % Favored : 60.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.61 (0.15), residues: 2892 helix: 0.27 (0.13), residues: 1596 sheet: -0.36 (0.29), residues: 316 loop : -1.41 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 696 TYR 0.036 0.002 TYR B 667 PHE 0.010 0.001 PHE C 658 TRP 0.015 0.001 TRP A 673 HIS 0.005 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00346 (23528) covalent geometry : angle 0.61717 (31824) hydrogen bonds : bond 0.03119 ( 1034) hydrogen bonds : angle 4.45865 ( 2937) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 350 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7720 (tppt) REVERT: A 92 MET cc_start: 0.7939 (ttm) cc_final: 0.7688 (ttm) REVERT: A 121 LYS cc_start: 0.6676 (mtpt) cc_final: 0.6099 (ttpt) REVERT: A 152 GLU cc_start: 0.7862 (tp30) cc_final: 0.7421 (mt-10) REVERT: A 191 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7947 (mt) REVERT: A 351 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 366 HIS cc_start: 0.3975 (OUTLIER) cc_final: 0.3403 (m-70) REVERT: A 458 ILE cc_start: 0.8057 (mt) cc_final: 0.7837 (mp) REVERT: A 587 MET cc_start: 0.8460 (tpp) cc_final: 0.8023 (tpt) REVERT: A 634 ASP cc_start: 0.8024 (t0) cc_final: 0.7718 (t0) REVERT: A 718 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7296 (ttt-90) REVERT: A 878 LEU cc_start: 0.8467 (mt) cc_final: 0.7871 (mt) REVERT: B 121 LYS cc_start: 0.7411 (mtmm) cc_final: 0.7055 (mtpt) REVERT: B 142 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7836 (t80) REVERT: B 166 ILE cc_start: 0.7799 (mp) cc_final: 0.7548 (pt) REVERT: B 351 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: B 366 HIS cc_start: 0.4402 (OUTLIER) cc_final: 0.3892 (m-70) REVERT: B 718 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7237 (ttt-90) REVERT: B 878 LEU cc_start: 0.8565 (mt) cc_final: 0.8010 (mt) REVERT: C 121 LYS cc_start: 0.6595 (mtpt) cc_final: 0.5785 (ttpt) REVERT: C 152 GLU cc_start: 0.7948 (tp30) cc_final: 0.7487 (mt-10) REVERT: C 343 PHE cc_start: 0.8171 (m-80) cc_final: 0.7871 (m-80) REVERT: C 351 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: C 366 HIS cc_start: 0.4168 (OUTLIER) cc_final: 0.3724 (m-70) REVERT: C 634 ASP cc_start: 0.8031 (t0) cc_final: 0.7760 (t0) REVERT: C 718 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7346 (ttt-90) REVERT: C 878 LEU cc_start: 0.8484 (mt) cc_final: 0.7933 (mt) REVERT: D 92 MET cc_start: 0.7202 (tpp) cc_final: 0.6971 (tpp) REVERT: D 142 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7842 (t80) REVERT: D 152 GLU cc_start: 0.7991 (tp30) cc_final: 0.7670 (mt-10) REVERT: D 166 ILE cc_start: 0.7887 (mp) cc_final: 0.7661 (pt) REVERT: D 207 MET cc_start: 0.8510 (mmm) cc_final: 0.8228 (mmm) REVERT: D 210 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7747 (mp) REVERT: D 238 CYS cc_start: 0.8341 (m) cc_final: 0.7799 (p) REVERT: D 366 HIS cc_start: 0.4552 (OUTLIER) cc_final: 0.4087 (m-70) REVERT: D 422 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: D 423 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7603 (mp0) REVERT: D 634 ASP cc_start: 0.7908 (t0) cc_final: 0.7370 (t0) REVERT: D 680 MET cc_start: 0.7962 (mtp) cc_final: 0.7563 (mtp) REVERT: D 718 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7241 (ttt-90) REVERT: D 878 LEU cc_start: 0.8541 (mt) cc_final: 0.7978 (mt) outliers start: 142 outliers final: 100 residues processed: 461 average time/residue: 0.1278 time to fit residues: 96.6066 Evaluate side-chains 454 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 338 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 416 HIS Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 105 optimal weight: 0.0980 chunk 285 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 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 = 0.4438 r_free = 0.4438 target = 0.192992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.146402 restraints weight = 37142.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.151042 restraints weight = 19179.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153945 restraints weight = 13044.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.155550 restraints weight = 10543.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.156516 restraints weight = 9383.068| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23528 Z= 0.124 Angle : 0.612 12.125 31824 Z= 0.300 Chirality : 0.041 0.352 3752 Planarity : 0.004 0.057 3980 Dihedral : 4.184 22.303 3160 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.91 % Allowed : 34.31 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.15), residues: 2892 helix: 0.35 (0.13), residues: 1572 sheet: -0.28 (0.29), residues: 316 loop : -1.40 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 696 TYR 0.026 0.001 TYR B 667 PHE 0.013 0.001 PHE C 693 TRP 0.017 0.001 TRP D 673 HIS 0.007 0.001 HIS B 716 Details of bonding type rmsd covalent geometry : bond 0.00299 (23528) covalent geometry : angle 0.61173 (31824) hydrogen bonds : bond 0.03012 ( 1034) hydrogen bonds : angle 4.41868 ( 2937) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 348 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7492 (tppt) REVERT: A 92 MET cc_start: 0.7767 (ttm) cc_final: 0.7320 (ttm) REVERT: A 121 LYS cc_start: 0.6667 (mtpt) cc_final: 0.6123 (ttpt) REVERT: A 152 GLU cc_start: 0.7806 (tp30) cc_final: 0.7402 (mt-10) REVERT: A 166 ILE cc_start: 0.7974 (mp) cc_final: 0.7729 (mp) REVERT: A 191 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7914 (mt) REVERT: A 351 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: A 458 ILE cc_start: 0.8111 (mt) cc_final: 0.7901 (mp) REVERT: A 587 MET cc_start: 0.8436 (tpp) cc_final: 0.7998 (tpt) REVERT: A 718 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7526 (ttt-90) REVERT: A 878 LEU cc_start: 0.8519 (mt) cc_final: 0.7925 (mt) REVERT: B 91 LYS cc_start: 0.7244 (tmtt) cc_final: 0.6971 (mmmt) REVERT: B 142 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 166 ILE cc_start: 0.7799 (mp) cc_final: 0.7579 (pt) REVERT: B 329 LEU cc_start: 0.8211 (mp) cc_final: 0.8009 (mp) REVERT: B 351 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6874 (mt-10) REVERT: B 366 HIS cc_start: 0.4354 (OUTLIER) cc_final: 0.3885 (m-70) REVERT: B 718 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7293 (ttt-90) REVERT: B 878 LEU cc_start: 0.8600 (mt) cc_final: 0.8041 (mt) REVERT: C 121 LYS cc_start: 0.6696 (mtpt) cc_final: 0.5908 (ttpt) REVERT: C 152 GLU cc_start: 0.7918 (tp30) cc_final: 0.7489 (mt-10) REVERT: C 233 LEU cc_start: 0.8620 (tt) cc_final: 0.8406 (tp) REVERT: C 343 PHE cc_start: 0.8159 (m-80) cc_final: 0.7908 (m-80) REVERT: C 351 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: C 366 HIS cc_start: 0.4178 (OUTLIER) cc_final: 0.3732 (m-70) REVERT: C 718 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7379 (ttt-90) REVERT: C 878 LEU cc_start: 0.8525 (mt) cc_final: 0.7982 (mt) REVERT: D 92 MET cc_start: 0.7170 (tpp) cc_final: 0.6821 (tpt) REVERT: D 142 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7822 (t80) REVERT: D 152 GLU cc_start: 0.7953 (tp30) cc_final: 0.7667 (mt-10) REVERT: D 166 ILE cc_start: 0.7957 (mp) cc_final: 0.7726 (pt) REVERT: D 207 MET cc_start: 0.8516 (mmm) cc_final: 0.8257 (mmm) REVERT: D 210 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7741 (mp) REVERT: D 238 CYS cc_start: 0.8272 (m) cc_final: 0.7796 (p) REVERT: D 366 HIS cc_start: 0.4501 (OUTLIER) cc_final: 0.4068 (m-70) REVERT: D 422 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: D 423 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7503 (mp0) REVERT: D 477 MET cc_start: 0.6700 (tpt) cc_final: 0.6264 (tpt) REVERT: D 634 ASP cc_start: 0.7869 (t0) cc_final: 0.7313 (t0) REVERT: D 680 MET cc_start: 0.7939 (mtp) cc_final: 0.7533 (mtp) REVERT: D 718 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7230 (ttt-90) REVERT: D 878 LEU cc_start: 0.8560 (mt) cc_final: 0.7992 (mt) outliers start: 123 outliers final: 94 residues processed: 450 average time/residue: 0.1174 time to fit residues: 86.3824 Evaluate side-chains 440 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 331 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 416 HIS Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 195 optimal weight: 0.8980 chunk 281 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 42 optimal weight: 8.9990 chunk 277 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.192247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145257 restraints weight = 37170.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.149848 restraints weight = 19318.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.152760 restraints weight = 13189.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.154167 restraints weight = 10667.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.155232 restraints weight = 9561.242| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23528 Z= 0.139 Angle : 0.626 11.900 31824 Z= 0.305 Chirality : 0.042 0.391 3752 Planarity : 0.004 0.056 3980 Dihedral : 4.158 18.663 3160 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.71 % Allowed : 34.35 % Favored : 60.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 2892 helix: 0.35 (0.13), residues: 1596 sheet: -0.24 (0.29), residues: 316 loop : -1.37 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 668 TYR 0.024 0.001 TYR B 667 PHE 0.010 0.001 PHE A 719 TRP 0.026 0.001 TRP A 673 HIS 0.006 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00341 (23528) covalent geometry : angle 0.62613 (31824) hydrogen bonds : bond 0.03035 ( 1034) hydrogen bonds : angle 4.40056 ( 2937) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 345 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.6704 (mtpt) cc_final: 0.6202 (ttpt) REVERT: A 152 GLU cc_start: 0.7845 (tp30) cc_final: 0.7395 (mt-10) REVERT: A 166 ILE cc_start: 0.7957 (mp) cc_final: 0.7732 (mp) REVERT: A 191 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7883 (mt) REVERT: A 351 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: A 587 MET cc_start: 0.8465 (tpp) cc_final: 0.8009 (tpt) REVERT: A 718 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7522 (ttt-90) REVERT: A 752 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: A 878 LEU cc_start: 0.8514 (mt) cc_final: 0.7918 (mt) REVERT: B 91 LYS cc_start: 0.7360 (tmtt) cc_final: 0.7062 (mmmt) REVERT: B 122 THR cc_start: 0.8142 (p) cc_final: 0.7895 (t) REVERT: B 142 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 329 LEU cc_start: 0.8254 (mp) cc_final: 0.8053 (mp) REVERT: B 351 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: B 366 HIS cc_start: 0.4492 (OUTLIER) cc_final: 0.4048 (m-70) REVERT: B 422 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: B 718 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7234 (ttt-90) REVERT: B 878 LEU cc_start: 0.8613 (mt) cc_final: 0.8059 (mt) REVERT: C 121 LYS cc_start: 0.6673 (mtpt) cc_final: 0.5873 (ttpt) REVERT: C 152 GLU cc_start: 0.7959 (tp30) cc_final: 0.7494 (mt-10) REVERT: C 220 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7332 (ptt) REVERT: C 233 LEU cc_start: 0.8611 (tt) cc_final: 0.8394 (tp) REVERT: C 343 PHE cc_start: 0.8142 (m-80) cc_final: 0.7898 (m-80) REVERT: C 351 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: C 366 HIS cc_start: 0.4350 (OUTLIER) cc_final: 0.3911 (m-70) REVERT: C 438 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7744 (mmm160) REVERT: C 680 MET cc_start: 0.8190 (mtm) cc_final: 0.7976 (mpp) REVERT: C 718 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7345 (ttt-90) REVERT: C 878 LEU cc_start: 0.8529 (mt) cc_final: 0.7999 (mt) REVERT: D 92 MET cc_start: 0.7141 (tpp) cc_final: 0.6719 (tpt) REVERT: D 142 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7819 (t80) REVERT: D 152 GLU cc_start: 0.7979 (tp30) cc_final: 0.7657 (mt-10) REVERT: D 210 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7776 (mp) REVERT: D 238 CYS cc_start: 0.8363 (m) cc_final: 0.7788 (p) REVERT: D 366 HIS cc_start: 0.4628 (OUTLIER) cc_final: 0.4189 (m-70) REVERT: D 422 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: D 423 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7387 (mp0) REVERT: D 477 MET cc_start: 0.6687 (tpt) cc_final: 0.6226 (tpt) REVERT: D 634 ASP cc_start: 0.7901 (t0) cc_final: 0.7337 (t0) REVERT: D 680 MET cc_start: 0.8068 (mtp) cc_final: 0.7612 (mtp) REVERT: D 718 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7197 (ttt-90) REVERT: D 878 LEU cc_start: 0.8590 (mt) cc_final: 0.8022 (mt) outliers start: 118 outliers final: 94 residues processed: 439 average time/residue: 0.1226 time to fit residues: 86.9525 Evaluate side-chains 446 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 334 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 416 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 416 HIS Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 187 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 250 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 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 = 0.4441 r_free = 0.4441 target = 0.193241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.146517 restraints weight = 37132.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.151135 restraints weight = 19269.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.154031 restraints weight = 13161.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.155526 restraints weight = 10614.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.156093 restraints weight = 9492.132| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23528 Z= 0.127 Angle : 0.633 16.635 31824 Z= 0.305 Chirality : 0.042 0.386 3752 Planarity : 0.004 0.055 3980 Dihedral : 4.143 19.610 3160 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.55 % Allowed : 34.54 % Favored : 60.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -0.43 (0.15), residues: 2892 helix: 0.41 (0.13), residues: 1564 sheet: -0.22 (0.30), residues: 292 loop : -1.27 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 873 TYR 0.023 0.001 TYR B 667 PHE 0.016 0.001 PHE D 669 TRP 0.022 0.001 TRP D 673 HIS 0.005 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00308 (23528) covalent geometry : angle 0.63302 (31824) hydrogen bonds : bond 0.02991 ( 1034) hydrogen bonds : angle 4.40075 ( 2937) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.12 seconds wall clock time: 69 minutes 55.78 seconds (4195.78 seconds total)