Starting phenix.real_space_refine on Sat Jan 25 08:17:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asl_43818/01_2025/9asl_43818.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asl_43818/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9asl_43818/01_2025/9asl_43818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asl_43818/01_2025/9asl_43818.map" model { file = "/net/cci-nas-00/data/ceres_data/9asl_43818/01_2025/9asl_43818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asl_43818/01_2025/9asl_43818.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 14.73, per 1000 atoms: 0.64 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: 5.28 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.90 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: 8.51 Time building geometry restraints manager: 6.20 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: 0.06 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: 6.930 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: 0.000 Extract box with map and model: 0.640 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 51.730 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.200 ------------------------------------------------------------------------------- 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= 0.219 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 : 16.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), 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 TRP 0.016 0.001 TRP B 349 HIS 0.016 0.001 HIS A 85 PHE 0.018 0.001 PHE B 343 TYR 0.026 0.002 TYR B 228 ARG 0.009 0.001 ARG A 460 *********************** 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 : 2.643 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: 0.4686 (tpp) REVERT: D 94 GLU cc_start: 0.7572 (pm20) cc_final: 0.6955 (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: 0.3642 time to fit residues: 296.7479 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 : 2.741 ------------------------------------------------------------------------------- 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 249 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 0.0370 chunk 76 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 overall best weight: 1.3060 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.195467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.151432 restraints weight = 36849.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.153523 restraints weight = 19522.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.155022 restraints weight = 13233.508| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23528 Z= 0.317 Angle : 0.679 8.349 31824 Z= 0.347 Chirality : 0.043 0.173 3752 Planarity : 0.005 0.075 3980 Dihedral : 4.786 55.653 3169 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.09 % Rotamer: Outliers : 5.47 % Allowed : 33.51 % Favored : 61.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 2892 helix: -0.25 (0.13), residues: 1564 sheet: -0.05 (0.36), residues: 208 loop : -1.67 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 411 HIS 0.009 0.001 HIS A 85 PHE 0.015 0.002 PHE B 658 TYR 0.023 0.002 TYR B 239 ARG 0.007 0.001 ARG B 823 *********************** 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 518 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 381 time to evaluate : 2.526 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: 0.7778 (mmmt) cc_final: 0.7374 (tppt) REVERT: A 92 MET cc_start: 0.7730 (ttm) cc_final: 0.7045 (ttp) REVERT: A 93 PHE cc_start: 0.6388 (m-10) cc_final: 0.6170 (m-80) REVERT: A 152 GLU cc_start: 0.7795 (tp30) cc_final: 0.7316 (tm-30) REVERT: A 307 MET cc_start: 0.6325 (mmt) cc_final: 0.6032 (mpp) REVERT: A 713 MET cc_start: 0.8324 (tpt) cc_final: 0.7627 (tpt) REVERT: B 92 MET cc_start: 0.5914 (tpp) cc_final: 0.5570 (tpp) REVERT: B 94 GLU cc_start: 0.7997 (pm20) cc_final: 0.7144 (tm-30) REVERT: B 216 ASP cc_start: 0.8349 (m-30) cc_final: 0.7966 (m-30) REVERT: B 329 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8082 (mp) REVERT: B 634 ASP cc_start: 0.8057 (t0) cc_final: 0.7790 (t0) REVERT: B 639 MET cc_start: 0.6766 (mmt) cc_final: 0.5461 (mmt) REVERT: B 825 ASN cc_start: 0.7786 (t0) cc_final: 0.7576 (t0) REVERT: B 878 LEU cc_start: 0.8461 (mt) cc_final: 0.7882 (mt) REVERT: C 91 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7323 (tppt) REVERT: C 92 MET cc_start: 0.7253 (ttp) cc_final: 0.6781 (ttm) REVERT: C 93 PHE cc_start: 0.6476 (m-10) cc_final: 0.6222 (m-80) REVERT: C 152 GLU cc_start: 0.7824 (tp30) cc_final: 0.7386 (tm-30) REVERT: C 307 MET cc_start: 0.6350 (mmt) cc_final: 0.6027 (mpp) REVERT: D 92 MET cc_start: 0.5797 (tpp) cc_final: 0.4962 (tpp) REVERT: D 94 GLU cc_start: 0.8033 (pm20) cc_final: 0.7175 (tm-30) REVERT: D 144 LEU cc_start: 0.8603 (mm) cc_final: 0.8373 (mt) REVERT: D 152 GLU cc_start: 0.7900 (tp30) cc_final: 0.7328 (mt-10) REVERT: D 627 ASP cc_start: 0.8022 (m-30) cc_final: 0.7812 (m-30) REVERT: D 634 ASP cc_start: 0.8051 (t0) cc_final: 0.7722 (t0) REVERT: D 878 LEU cc_start: 0.8441 (mt) cc_final: 0.7859 (mt) outliers start: 137 outliers final: 59 residues processed: 478 average time/residue: 0.3217 time to fit residues: 251.2860 Evaluate side-chains 402 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 342 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 70 LEU 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 340 VAL 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 797 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 126 GLU 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 473 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 679 SER 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 679 SER Chi-restraints excluded: chain D residue 724 VAL 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 197 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 215 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 267 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** 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** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4491 r_free = 0.4491 target = 0.197119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.154063 restraints weight = 36827.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.156662 restraints weight = 18936.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.159066 restraints weight = 12911.756| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23528 Z= 0.201 Angle : 0.593 13.447 31824 Z= 0.298 Chirality : 0.041 0.261 3752 Planarity : 0.004 0.065 3980 Dihedral : 4.543 57.705 3165 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.15 % Allowed : 33.07 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 2892 helix: 0.13 (0.13), residues: 1560 sheet: 0.07 (0.35), residues: 208 loop : -1.47 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 411 HIS 0.007 0.001 HIS A 85 PHE 0.014 0.002 PHE C 787 TYR 0.018 0.001 TYR B 239 ARG 0.006 0.000 ARG A 668 *********************** 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 527 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 398 time to evaluate : 2.504 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 92 MET cc_start: 0.7616 (ttm) cc_final: 0.7396 (ttp) REVERT: A 93 PHE cc_start: 0.6547 (m-10) cc_final: 0.6245 (m-80) REVERT: A 121 LYS cc_start: 0.6602 (mtpt) cc_final: 0.5988 (ttpt) REVERT: A 191 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7869 (mm) REVERT: A 260 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: A 307 MET cc_start: 0.6160 (mmt) cc_final: 0.5863 (mpp) REVERT: A 680 MET cc_start: 0.7958 (mtm) cc_final: 0.7659 (mtm) REVERT: A 713 MET cc_start: 0.8288 (tpt) cc_final: 0.7763 (tpt) REVERT: B 142 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7686 (t80) REVERT: B 233 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8360 (tp) REVERT: B 351 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7068 (mt-10) REVERT: B 366 HIS cc_start: 0.3816 (OUTLIER) cc_final: 0.3232 (m-70) REVERT: B 550 MET cc_start: 0.7896 (tmm) cc_final: 0.7672 (tmm) REVERT: B 668 ARG cc_start: 0.6883 (mtp85) cc_final: 0.6617 (mmm-85) REVERT: B 680 MET cc_start: 0.7876 (mtm) cc_final: 0.7360 (mtm) REVERT: B 878 LEU cc_start: 0.8588 (mt) cc_final: 0.7982 (mt) REVERT: C 91 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7555 (tppt) REVERT: C 93 PHE cc_start: 0.6557 (m-10) cc_final: 0.6268 (m-80) REVERT: C 152 GLU cc_start: 0.7790 (tp30) cc_final: 0.7351 (mt-10) REVERT: C 307 MET cc_start: 0.6213 (mmt) cc_final: 0.5890 (mpp) REVERT: C 366 HIS cc_start: 0.3694 (OUTLIER) cc_final: 0.3113 (m-70) REVERT: C 713 MET cc_start: 0.8524 (tpt) cc_final: 0.7739 (tpt) REVERT: C 878 LEU cc_start: 0.8537 (mt) cc_final: 0.7960 (mt) REVERT: D 94 GLU cc_start: 0.7850 (pm20) cc_final: 0.7079 (tm-30) REVERT: D 144 LEU cc_start: 0.8547 (mm) cc_final: 0.8314 (mt) REVERT: D 152 GLU cc_start: 0.7939 (tp30) cc_final: 0.7411 (mt-10) REVERT: D 233 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8381 (tp) REVERT: D 550 MET cc_start: 0.7957 (tmm) cc_final: 0.7726 (tmm) REVERT: D 634 ASP cc_start: 0.8067 (t0) cc_final: 0.7679 (t0) REVERT: D 878 LEU cc_start: 0.8537 (mt) cc_final: 0.7950 (mt) outliers start: 129 outliers final: 63 residues processed: 494 average time/residue: 0.3113 time to fit residues: 247.8933 Evaluate side-chains 423 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 352 time to evaluate : 2.430 ------------------------------------------------------------------------------- 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 191 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 417 HIS 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 628 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 810 LEU 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 233 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 340 VAL 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 527 VAL Chi-restraints excluded: chain B residue 586 VAL 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 126 GLU 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 324 ASP 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 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 737 ILE Chi-restraints excluded: chain D residue 130 LEU 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 319 VAL Chi-restraints excluded: chain D residue 324 ASP 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 470 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 189 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 287 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** 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 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 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 HIS ** 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** ** D 712 GLN ** 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 = 0.4395 r_free = 0.4395 target = 0.182947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.138136 restraints weight = 36482.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140181 restraints weight = 20601.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.142295 restraints weight = 13657.280| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 23528 Z= 0.413 Angle : 0.714 15.777 31824 Z= 0.357 Chirality : 0.045 0.322 3752 Planarity : 0.005 0.063 3980 Dihedral : 4.673 57.000 3162 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.81 % Rotamer: Outliers : 6.27 % Allowed : 32.75 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 2892 helix: -0.09 (0.13), residues: 1600 sheet: -0.26 (0.31), residues: 256 loop : -1.43 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 411 HIS 0.007 0.001 HIS A 325 PHE 0.027 0.003 PHE C 670 TYR 0.017 0.002 TYR A 228 ARG 0.005 0.001 ARG C 696 *********************** 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 537 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 380 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.6857 (mtpt) cc_final: 0.6141 (ttpt) REVERT: A 152 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7528 (mt-10) REVERT: A 191 ILE cc_start: 0.8315 (mt) cc_final: 0.8023 (mm) REVERT: A 366 HIS cc_start: 0.4039 (OUTLIER) cc_final: 0.3500 (m-70) REVERT: A 458 ILE cc_start: 0.8224 (mt) cc_final: 0.7955 (mp) REVERT: A 657 MET cc_start: 0.6883 (mmm) cc_final: 0.6627 (mtm) REVERT: A 878 LEU cc_start: 0.8304 (mt) cc_final: 0.7714 (mt) REVERT: B 92 MET cc_start: 0.6234 (tpp) cc_final: 0.5867 (tpp) REVERT: B 121 LYS cc_start: 0.7556 (mtmm) cc_final: 0.7297 (ttpt) REVERT: B 142 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7937 (t80) REVERT: B 191 ILE cc_start: 0.8295 (mt) cc_final: 0.8054 (mm) REVERT: B 216 ASP cc_start: 0.8524 (m-30) cc_final: 0.8221 (m-30) REVERT: B 233 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8466 (tp) REVERT: B 351 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7057 (mt-10) REVERT: B 366 HIS cc_start: 0.4366 (OUTLIER) cc_final: 0.3826 (m-70) REVERT: B 423 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7686 (mp0) REVERT: B 550 MET cc_start: 0.7981 (tmm) cc_final: 0.7684 (tmm) REVERT: B 680 MET cc_start: 0.8221 (mtm) cc_final: 0.7977 (mpp) REVERT: B 792 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: B 878 LEU cc_start: 0.8722 (mt) cc_final: 0.7743 (mt) REVERT: C 152 GLU cc_start: 0.7817 (tp30) cc_final: 0.7448 (tm-30) REVERT: C 366 HIS cc_start: 0.4216 (OUTLIER) cc_final: 0.3708 (m-70) REVERT: C 680 MET cc_start: 0.8141 (mtm) cc_final: 0.7718 (mtm) REVERT: C 862 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.6040 (tp) REVERT: C 878 LEU cc_start: 0.8644 (mt) cc_final: 0.7686 (mt) REVERT: D 91 LYS cc_start: 0.7537 (tppt) cc_final: 0.7149 (tptp) REVERT: D 142 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7870 (t80) REVERT: D 152 GLU cc_start: 0.8014 (tp30) cc_final: 0.7654 (mt-10) REVERT: D 191 ILE cc_start: 0.8294 (mt) cc_final: 0.7979 (mm) REVERT: D 233 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8534 (tp) REVERT: D 366 HIS cc_start: 0.4336 (OUTLIER) cc_final: 0.3795 (m-70) REVERT: D 423 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7692 (mp0) REVERT: D 634 ASP cc_start: 0.7973 (t0) cc_final: 0.7605 (t0) REVERT: D 878 LEU cc_start: 0.8709 (mt) cc_final: 0.7694 (mt) REVERT: D 881 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7505 (tp30) outliers start: 157 outliers final: 99 residues processed: 504 average time/residue: 0.3176 time to fit residues: 257.2111 Evaluate side-chains 448 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 338 time to evaluate : 2.630 ------------------------------------------------------------------------------- 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 149 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL 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 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 552 THR 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 737 ILE Chi-restraints excluded: chain A residue 796 LEU 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 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 235 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 319 VAL Chi-restraints excluded: chain B residue 324 ASP 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 517 SER 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 608 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 126 GLU 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 207 MET 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 366 HIS Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 559 LEU 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 645 GLU Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 798 ARG Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain D residue 70 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 184 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 298 VAL 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 416 HIS 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 559 LEU Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 679 SER 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 64 optimal weight: 0.0870 chunk 214 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 289 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 260 GLN ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 195 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS ** C 646 ASN ** 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 195 ASN D 260 GLN ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.189694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.142420 restraints weight = 36713.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.147273 restraints weight = 18619.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.150269 restraints weight = 12574.420| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23528 Z= 0.206 Angle : 0.595 10.562 31824 Z= 0.300 Chirality : 0.041 0.264 3752 Planarity : 0.004 0.061 3980 Dihedral : 4.333 19.598 3160 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.39 % Allowed : 33.99 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 2892 helix: 0.08 (0.13), residues: 1604 sheet: -0.38 (0.30), residues: 276 loop : -1.37 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 411 HIS 0.006 0.001 HIS A 325 PHE 0.019 0.002 PHE B 343 TYR 0.016 0.001 TYR D 171 ARG 0.004 0.000 ARG C 668 *********************** 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 510 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 375 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7658 (tppt) REVERT: A 92 MET cc_start: 0.7784 (ttm) cc_final: 0.7289 (ttp) REVERT: A 121 LYS cc_start: 0.6758 (mtpt) cc_final: 0.6082 (ttpt) REVERT: A 152 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7514 (mt-10) REVERT: A 191 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7901 (mt) REVERT: A 307 MET cc_start: 0.6181 (mmt) cc_final: 0.5932 (mpp) REVERT: A 351 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: A 366 HIS cc_start: 0.3793 (OUTLIER) cc_final: 0.3211 (m-70) REVERT: A 458 ILE cc_start: 0.8131 (mt) cc_final: 0.7757 (mp) REVERT: A 634 ASP cc_start: 0.8050 (t0) cc_final: 0.7634 (t0) REVERT: A 718 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7541 (ttt-90) REVERT: A 878 LEU cc_start: 0.8380 (mt) cc_final: 0.7798 (mt) REVERT: B 81 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8441 (pp) REVERT: B 92 MET cc_start: 0.6703 (tpp) cc_final: 0.5988 (tpp) REVERT: B 142 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 166 ILE cc_start: 0.7807 (mp) cc_final: 0.7514 (pt) REVERT: B 233 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8508 (tp) REVERT: B 351 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: B 366 HIS cc_start: 0.4144 (OUTLIER) cc_final: 0.3629 (m-70) REVERT: B 423 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7415 (mp0) REVERT: B 680 MET cc_start: 0.8139 (mtm) cc_final: 0.7918 (mpp) REVERT: B 718 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7331 (ttt-90) REVERT: B 878 LEU cc_start: 0.8452 (mt) cc_final: 0.7871 (mt) REVERT: C 91 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7720 (tppt) REVERT: C 152 GLU cc_start: 0.7825 (tp30) cc_final: 0.7411 (mt-10) REVERT: C 307 MET cc_start: 0.6175 (mmt) cc_final: 0.5908 (mpp) REVERT: C 351 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: C 366 HIS cc_start: 0.4133 (OUTLIER) cc_final: 0.3644 (m-70) REVERT: C 718 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7391 (ttt-90) REVERT: C 878 LEU cc_start: 0.8389 (mt) cc_final: 0.7822 (mt) REVERT: D 142 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7883 (t80) REVERT: D 152 GLU cc_start: 0.7960 (tp30) cc_final: 0.7626 (mt-10) REVERT: D 191 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7879 (mm) REVERT: D 207 MET cc_start: 0.8459 (mmm) cc_final: 0.7978 (mmm) REVERT: D 233 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8161 (tp) REVERT: D 366 HIS cc_start: 0.4218 (OUTLIER) cc_final: 0.3668 (m-70) REVERT: D 423 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7466 (mp0) REVERT: D 630 ASP cc_start: 0.7912 (m-30) cc_final: 0.7515 (m-30) REVERT: D 634 ASP cc_start: 0.7918 (t0) cc_final: 0.7423 (t0) REVERT: D 680 MET cc_start: 0.8026 (mtm) cc_final: 0.7414 (mtm) REVERT: D 718 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7315 (ttt-90) REVERT: D 878 LEU cc_start: 0.8719 (mt) cc_final: 0.7762 (mt) outliers start: 135 outliers final: 69 residues processed: 481 average time/residue: 0.3281 time to fit residues: 253.1401 Evaluate side-chains 416 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 329 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 191 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 351 GLU 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 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU 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 168 VAL 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 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 527 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 366 HIS Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 527 VAL 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 D residue 102 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 233 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 329 LEU 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 527 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 718 ARG Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 201 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN D 85 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.191555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.144775 restraints weight = 36899.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.149308 restraints weight = 19264.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.152215 restraints weight = 13165.960| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23528 Z= 0.223 Angle : 0.596 10.999 31824 Z= 0.298 Chirality : 0.042 0.325 3752 Planarity : 0.004 0.066 3980 Dihedral : 4.291 19.377 3160 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.39 % Allowed : 33.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2892 helix: 0.15 (0.13), residues: 1608 sheet: -0.42 (0.29), residues: 296 loop : -1.36 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 673 HIS 0.006 0.001 HIS A 325 PHE 0.016 0.002 PHE B 343 TYR 0.016 0.001 TYR D 171 ARG 0.020 0.000 ARG A 696 *********************** 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 493 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 358 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7735 (tppt) REVERT: A 92 MET cc_start: 0.7903 (ttm) cc_final: 0.7419 (ttp) REVERT: A 121 LYS cc_start: 0.6791 (mtpt) cc_final: 0.6085 (ttpt) REVERT: A 152 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7515 (mt-10) REVERT: A 191 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7940 (mt) REVERT: A 351 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: A 366 HIS cc_start: 0.3820 (OUTLIER) cc_final: 0.3210 (m-70) REVERT: A 458 ILE cc_start: 0.8097 (mt) cc_final: 0.7874 (mp) REVERT: A 624 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7632 (p) REVERT: A 680 MET cc_start: 0.8210 (mtm) cc_final: 0.7798 (mpp) REVERT: A 718 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7578 (ttt-90) REVERT: A 878 LEU cc_start: 0.8417 (mt) cc_final: 0.7818 (mt) REVERT: B 92 MET cc_start: 0.6742 (tpp) cc_final: 0.5906 (tpp) REVERT: B 142 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7963 (t80) REVERT: B 166 ILE cc_start: 0.7875 (mp) cc_final: 0.7622 (pt) REVERT: B 351 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: B 366 HIS cc_start: 0.4243 (OUTLIER) cc_final: 0.3749 (m-70) REVERT: B 423 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7474 (mp0) REVERT: B 639 MET cc_start: 0.8364 (mmt) cc_final: 0.7419 (mmt) REVERT: B 718 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7323 (ttt-90) REVERT: B 878 LEU cc_start: 0.8471 (mt) cc_final: 0.7897 (mt) REVERT: C 92 MET cc_start: 0.7362 (ttp) cc_final: 0.7084 (ttp) REVERT: C 152 GLU cc_start: 0.7869 (tp30) cc_final: 0.7454 (mt-10) REVERT: C 351 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: C 366 HIS cc_start: 0.4181 (OUTLIER) cc_final: 0.3677 (m-70) REVERT: C 624 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7752 (p) REVERT: C 627 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: C 639 MET cc_start: 0.7024 (ppp) cc_final: 0.6628 (ptm) REVERT: C 680 MET cc_start: 0.8291 (mtm) cc_final: 0.7596 (mtm) REVERT: C 718 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7492 (ttt-90) REVERT: C 878 LEU cc_start: 0.8454 (mt) cc_final: 0.7859 (mt) REVERT: D 142 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7821 (t80) REVERT: D 152 GLU cc_start: 0.8001 (tp30) cc_final: 0.7621 (mt-10) REVERT: D 166 ILE cc_start: 0.7820 (mp) cc_final: 0.7517 (pt) REVERT: D 191 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7961 (mt) REVERT: D 207 MET cc_start: 0.8486 (mmm) cc_final: 0.8121 (mmm) REVERT: D 210 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7775 (mp) REVERT: D 366 HIS cc_start: 0.4343 (OUTLIER) cc_final: 0.3805 (m-70) REVERT: D 423 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7537 (mp0) REVERT: D 630 ASP cc_start: 0.7904 (m-30) cc_final: 0.7515 (m-30) REVERT: D 634 ASP cc_start: 0.7942 (t0) cc_final: 0.7409 (t0) REVERT: D 718 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7320 (ttt-90) REVERT: D 878 LEU cc_start: 0.8454 (mt) cc_final: 0.7835 (mt) outliers start: 135 outliers final: 83 residues processed: 465 average time/residue: 0.3234 time to fit residues: 242.3278 Evaluate side-chains 445 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 343 time to evaluate : 2.769 ------------------------------------------------------------------------------- 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 191 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 351 GLU 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 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU 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 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 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 597 SER Chi-restraints excluded: chain B residue 628 THR 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 168 VAL Chi-restraints excluded: chain C residue 218 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 351 GLU Chi-restraints excluded: chain C residue 361 PHE Chi-restraints excluded: chain C residue 366 HIS 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 508 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 559 LEU 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 718 ARG Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain D residue 102 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 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 559 LEU Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 628 THR 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 Chi-restraints excluded: chain D residue 859 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 89 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 265 optimal weight: 0.5980 chunk 269 optimal weight: 0.7980 chunk 251 optimal weight: 4.9990 chunk 275 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 242 optimal weight: 0.5980 chunk 255 optimal weight: 0.2980 chunk 169 optimal weight: 0.1980 chunk 208 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 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** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.194058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.147641 restraints weight = 37248.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152320 restraints weight = 19063.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.155211 restraints weight = 12962.490| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23528 Z= 0.181 Angle : 0.580 9.459 31824 Z= 0.289 Chirality : 0.041 0.322 3752 Planarity : 0.004 0.059 3980 Dihedral : 4.169 18.872 3160 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 4.87 % Allowed : 34.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 2892 helix: 0.24 (0.13), residues: 1612 sheet: -0.40 (0.28), residues: 336 loop : -1.47 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 673 HIS 0.007 0.001 HIS A 325 PHE 0.017 0.001 PHE B 343 TYR 0.021 0.001 TYR C 667 ARG 0.008 0.000 ARG A 696 *********************** 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 484 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 362 time to evaluate : 2.663 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: 0.7931 (ttm) cc_final: 0.7463 (ttp) REVERT: A 121 LYS cc_start: 0.6696 (mtpt) cc_final: 0.6035 (ttpt) REVERT: A 191 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7881 (mt) REVERT: A 351 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: A 366 HIS cc_start: 0.3756 (OUTLIER) cc_final: 0.3183 (m-70) REVERT: A 458 ILE cc_start: 0.8047 (mt) cc_final: 0.7843 (mp) REVERT: A 680 MET cc_start: 0.8158 (mtm) cc_final: 0.7840 (mpp) REVERT: A 718 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7536 (ttt-90) REVERT: A 878 LEU cc_start: 0.8475 (mt) cc_final: 0.7878 (mt) REVERT: B 81 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8475 (pp) REVERT: B 92 MET cc_start: 0.6563 (tpp) cc_final: 0.6295 (tpp) REVERT: B 142 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7861 (t80) REVERT: B 166 ILE cc_start: 0.7834 (mp) cc_final: 0.7572 (pt) REVERT: B 366 HIS cc_start: 0.4285 (OUTLIER) cc_final: 0.3753 (m-70) REVERT: B 423 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7548 (mp0) REVERT: B 718 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7246 (ttt-90) REVERT: B 878 LEU cc_start: 0.8499 (mt) cc_final: 0.7933 (mt) REVERT: C 152 GLU cc_start: 0.7911 (tp30) cc_final: 0.7470 (mt-10) REVERT: C 351 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: C 366 HIS cc_start: 0.4193 (OUTLIER) cc_final: 0.3705 (m-70) REVERT: C 587 MET cc_start: 0.8472 (tpp) cc_final: 0.8048 (tpt) REVERT: C 624 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7663 (p) REVERT: C 680 MET cc_start: 0.8266 (mtm) cc_final: 0.7509 (mtm) REVERT: C 718 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7512 (ttt-90) REVERT: C 878 LEU cc_start: 0.8457 (mt) cc_final: 0.7884 (mt) REVERT: D 142 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7757 (t80) REVERT: D 152 GLU cc_start: 0.8052 (tp30) cc_final: 0.7633 (mt-10) REVERT: D 166 ILE cc_start: 0.7834 (mp) cc_final: 0.7560 (pt) REVERT: D 191 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7840 (mm) REVERT: D 207 MET cc_start: 0.8493 (mmm) cc_final: 0.8133 (mmm) REVERT: D 210 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7750 (mp) REVERT: D 238 CYS cc_start: 0.8346 (m) cc_final: 0.7772 (p) REVERT: D 366 HIS cc_start: 0.4435 (OUTLIER) cc_final: 0.3924 (m-70) REVERT: D 423 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7590 (mp0) REVERT: D 634 ASP cc_start: 0.7961 (t0) cc_final: 0.7390 (t0) REVERT: D 718 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7220 (ttt-90) REVERT: D 878 LEU cc_start: 0.8460 (mt) cc_final: 0.7902 (mt) outliers start: 122 outliers final: 80 residues processed: 461 average time/residue: 0.3129 time to fit residues: 233.1675 Evaluate side-chains 440 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 343 time to evaluate : 2.626 ------------------------------------------------------------------------------- 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 123 LEU 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 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 351 GLU 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 679 SER Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 168 VAL 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 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 628 THR Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 859 MET 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 206 LYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 331 TYR 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 397 LEU 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 508 LEU 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 737 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain D residue 102 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 184 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 210 LEU 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 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 628 THR 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 130 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** 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** ** C 195 ASN ** 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 180 HIS ** D 417 HIS ** 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 = 0.4408 r_free = 0.4408 target = 0.189673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142213 restraints weight = 37214.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.146702 restraints weight = 19421.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.149565 restraints weight = 13268.888| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23528 Z= 0.270 Angle : 0.623 11.027 31824 Z= 0.309 Chirality : 0.043 0.434 3752 Planarity : 0.004 0.060 3980 Dihedral : 4.203 17.583 3160 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.07 % Allowed : 33.95 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2892 helix: 0.23 (0.13), residues: 1596 sheet: -0.33 (0.29), residues: 320 loop : -1.42 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 673 HIS 0.007 0.001 HIS A 325 PHE 0.013 0.002 PHE D 765 TYR 0.016 0.001 TYR B 171 ARG 0.006 0.000 ARG A 696 *********************** 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 477 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 350 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.6828 (mtpt) cc_final: 0.6148 (ttpt) REVERT: A 191 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7945 (mt) REVERT: A 351 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: A 366 HIS cc_start: 0.3940 (OUTLIER) cc_final: 0.3396 (m-70) REVERT: A 458 ILE cc_start: 0.8150 (mt) cc_final: 0.7856 (mp) REVERT: A 587 MET cc_start: 0.8497 (tpp) cc_final: 0.8036 (tpt) REVERT: A 718 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7644 (ttt-90) REVERT: A 878 LEU cc_start: 0.8473 (mt) cc_final: 0.7878 (mt) REVERT: B 92 MET cc_start: 0.6739 (tpp) cc_final: 0.6325 (tpp) REVERT: B 142 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7973 (t80) REVERT: B 166 ILE cc_start: 0.7791 (mp) cc_final: 0.7563 (pt) REVERT: B 423 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7544 (mp0) REVERT: B 718 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7374 (ttt-90) REVERT: B 878 LEU cc_start: 0.8554 (mt) cc_final: 0.8007 (mt) REVERT: C 152 GLU cc_start: 0.7921 (tp30) cc_final: 0.7471 (mt-10) REVERT: C 166 ILE cc_start: 0.8273 (mp) cc_final: 0.8017 (mp) REVERT: C 351 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: C 366 HIS cc_start: 0.4245 (OUTLIER) cc_final: 0.3770 (m-70) REVERT: C 587 MET cc_start: 0.8453 (tpp) cc_final: 0.8025 (tpt) REVERT: C 624 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7757 (p) REVERT: C 639 MET cc_start: 0.6964 (ppp) cc_final: 0.6596 (ptm) REVERT: C 680 MET cc_start: 0.8351 (mtm) cc_final: 0.8133 (mpp) REVERT: C 718 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7391 (ttt-90) REVERT: C 878 LEU cc_start: 0.8498 (mt) cc_final: 0.7913 (mt) REVERT: D 142 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7850 (t80) REVERT: D 152 GLU cc_start: 0.8033 (tp30) cc_final: 0.7599 (mt-10) REVERT: D 166 ILE cc_start: 0.7884 (mp) cc_final: 0.7630 (pt) REVERT: D 191 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (mt) REVERT: D 210 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7801 (mp) REVERT: D 238 CYS cc_start: 0.8344 (m) cc_final: 0.7794 (p) REVERT: D 366 HIS cc_start: 0.4567 (OUTLIER) cc_final: 0.4107 (m-70) REVERT: D 423 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7584 (mp0) REVERT: D 477 MET cc_start: 0.6791 (tpt) cc_final: 0.6514 (tpt) REVERT: D 634 ASP cc_start: 0.7892 (t0) cc_final: 0.7322 (t0) REVERT: D 718 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7341 (ttt-90) REVERT: D 878 LEU cc_start: 0.8564 (mt) cc_final: 0.7955 (mt) outliers start: 127 outliers final: 96 residues processed: 451 average time/residue: 0.3204 time to fit residues: 234.5723 Evaluate side-chains 447 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 336 time to evaluate : 2.594 ------------------------------------------------------------------------------- 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 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 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 796 LEU 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 149 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 CYS 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 319 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 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 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 628 THR 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 168 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 218 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 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 397 LEU 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 508 LEU 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 810 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 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 180 HIS 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 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 552 THR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 628 THR 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 254 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 272 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 196 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 138 optimal weight: 0.1980 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 325 HIS 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** ** C 195 ASN ** 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.192694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.145868 restraints weight = 36961.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.150442 restraints weight = 19080.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153416 restraints weight = 12982.571| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23528 Z= 0.191 Angle : 0.596 8.827 31824 Z= 0.296 Chirality : 0.042 0.408 3752 Planarity : 0.004 0.056 3980 Dihedral : 4.155 18.290 3160 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.51 % Allowed : 34.31 % Favored : 61.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2892 helix: 0.35 (0.13), residues: 1568 sheet: -0.34 (0.29), residues: 324 loop : -1.22 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 673 HIS 0.008 0.001 HIS A 325 PHE 0.015 0.001 PHE B 343 TYR 0.036 0.001 TYR D 667 ARG 0.005 0.000 ARG C 193 *********************** 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 463 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 350 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.6788 (mtpt) cc_final: 0.6248 (ttpt) REVERT: A 191 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7885 (mt) REVERT: A 351 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: A 366 HIS cc_start: 0.3883 (OUTLIER) cc_final: 0.3325 (m-70) REVERT: A 458 ILE cc_start: 0.8066 (mt) cc_final: 0.7858 (mp) REVERT: A 587 MET cc_start: 0.8495 (tpp) cc_final: 0.8034 (tpt) REVERT: A 718 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7563 (ttt-90) REVERT: A 878 LEU cc_start: 0.8493 (mt) cc_final: 0.7897 (mt) REVERT: B 92 MET cc_start: 0.6630 (tpp) cc_final: 0.6302 (tpp) REVERT: B 142 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7899 (t80) REVERT: B 366 HIS cc_start: 0.4464 (OUTLIER) cc_final: 0.4034 (m-70) REVERT: B 422 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7795 (t80) REVERT: B 423 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7573 (mp0) REVERT: B 718 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7248 (ttt-90) REVERT: B 878 LEU cc_start: 0.8565 (mt) cc_final: 0.8016 (mt) REVERT: C 152 GLU cc_start: 0.7938 (tp30) cc_final: 0.7482 (mt-10) REVERT: C 166 ILE cc_start: 0.8225 (mp) cc_final: 0.7970 (mp) REVERT: C 366 HIS cc_start: 0.4326 (OUTLIER) cc_final: 0.3861 (m-70) REVERT: C 587 MET cc_start: 0.8456 (tpp) cc_final: 0.8030 (tpt) REVERT: C 639 MET cc_start: 0.6939 (ppp) cc_final: 0.6658 (ptm) REVERT: C 718 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7512 (ttt-90) REVERT: C 878 LEU cc_start: 0.8507 (mt) cc_final: 0.7926 (mt) REVERT: D 142 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7797 (t80) REVERT: D 152 GLU cc_start: 0.8006 (tp30) cc_final: 0.7654 (mt-10) REVERT: D 191 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7872 (mt) REVERT: D 210 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7745 (mp) REVERT: D 238 CYS cc_start: 0.8369 (m) cc_final: 0.7798 (p) REVERT: D 366 HIS cc_start: 0.4578 (OUTLIER) cc_final: 0.4148 (m-70) REVERT: D 423 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7515 (mp0) REVERT: D 634 ASP cc_start: 0.7908 (t0) cc_final: 0.7371 (t0) REVERT: D 718 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7552 (ttt-90) REVERT: D 878 LEU cc_start: 0.8553 (mt) cc_final: 0.7986 (mt) outliers start: 113 outliers final: 78 residues processed: 441 average time/residue: 0.3257 time to fit residues: 232.8960 Evaluate side-chains 430 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 337 time to evaluate : 2.466 ------------------------------------------------------------------------------- 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 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 559 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU 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 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 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 528 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 859 MET 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 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 361 PHE 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 473 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 628 THR 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 102 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 149 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 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 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 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 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 60 optimal weight: 0.1980 chunk 95 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 104 optimal weight: 0.0770 chunk 135 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 279 ASN A 825 ASN 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 ** 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 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.193124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.146285 restraints weight = 37154.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.150932 restraints weight = 19120.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.153822 restraints weight = 13007.123| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4621 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= 0.192 Angle : 0.614 12.438 31824 Z= 0.300 Chirality : 0.042 0.409 3752 Planarity : 0.004 0.057 3980 Dihedral : 4.096 18.067 3160 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 4.27 % Allowed : 34.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2892 helix: 0.48 (0.13), residues: 1568 sheet: -0.22 (0.29), residues: 324 loop : -1.21 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 673 HIS 0.007 0.001 HIS B 716 PHE 0.015 0.001 PHE B 343 TYR 0.029 0.001 TYR D 667 ARG 0.005 0.000 ARG C 193 ********************** 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 456 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 349 time to evaluate : 2.445 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 121 LYS cc_start: 0.6778 (mtpt) cc_final: 0.6260 (ttpt) REVERT: A 191 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7851 (mt) REVERT: A 351 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: A 366 HIS cc_start: 0.3907 (OUTLIER) cc_final: 0.3356 (m-70) REVERT: A 458 ILE cc_start: 0.8089 (mt) cc_final: 0.7883 (mp) REVERT: A 680 MET cc_start: 0.8193 (mpp) cc_final: 0.7961 (mpp) REVERT: A 713 MET cc_start: 0.8566 (tpt) cc_final: 0.8071 (tpt) REVERT: A 718 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7564 (ttt-90) REVERT: A 878 LEU cc_start: 0.8525 (mt) cc_final: 0.7931 (mt) REVERT: B 92 MET cc_start: 0.6593 (tpp) cc_final: 0.6229 (tpp) REVERT: B 142 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7891 (t80) REVERT: B 329 LEU cc_start: 0.8230 (mp) cc_final: 0.8016 (mp) REVERT: B 366 HIS cc_start: 0.4516 (OUTLIER) cc_final: 0.4073 (m-70) REVERT: B 422 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 423 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7494 (mp0) REVERT: B 718 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7226 (ttt-90) REVERT: B 878 LEU cc_start: 0.8590 (mt) cc_final: 0.8047 (mt) REVERT: C 152 GLU cc_start: 0.7930 (tp30) cc_final: 0.7452 (mt-10) REVERT: C 366 HIS cc_start: 0.4358 (OUTLIER) cc_final: 0.3860 (m-70) REVERT: C 438 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7875 (mmm160) REVERT: C 587 MET cc_start: 0.8469 (tpp) cc_final: 0.8017 (tpt) REVERT: C 639 MET cc_start: 0.6876 (ppp) cc_final: 0.6601 (ptm) REVERT: C 718 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7495 (ttt-90) REVERT: C 878 LEU cc_start: 0.8494 (mt) cc_final: 0.7925 (mt) REVERT: D 91 LYS cc_start: 0.7390 (tppt) cc_final: 0.6843 (tptp) REVERT: D 142 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7751 (t80) REVERT: D 152 GLU cc_start: 0.8024 (tp30) cc_final: 0.7569 (mt-10) REVERT: D 191 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7833 (mt) REVERT: D 210 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7721 (mp) REVERT: D 238 CYS cc_start: 0.8383 (m) cc_final: 0.7800 (p) REVERT: D 366 HIS cc_start: 0.4556 (OUTLIER) cc_final: 0.4133 (m-70) REVERT: D 423 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7510 (mp0) REVERT: D 634 ASP cc_start: 0.7920 (t0) cc_final: 0.7285 (t0) REVERT: D 718 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7587 (ttt-90) REVERT: D 878 LEU cc_start: 0.8562 (mt) cc_final: 0.8003 (mt) outliers start: 107 outliers final: 82 residues processed: 436 average time/residue: 0.3174 time to fit residues: 224.4182 Evaluate side-chains 437 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 340 time to evaluate : 2.461 ------------------------------------------------------------------------------- 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 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 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 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 590 LEU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 796 LEU 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 184 LEU Chi-restraints excluded: chain B residue 189 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 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 463 ILE Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 628 THR 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 149 VAL Chi-restraints excluded: chain C residue 168 VAL 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 361 PHE 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 473 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 628 THR 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 149 VAL Chi-restraints excluded: chain D residue 175 THR 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 463 ILE Chi-restraints excluded: chain D residue 473 THR 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 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 155 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 295 optimal weight: 0.9990 chunk 294 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 207 optimal weight: 0.6980 chunk 247 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 0.0570 chunk 149 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 279 ASN A 825 ASN ** B 85 HIS ** 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 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** D 417 HIS ** 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 = 0.4446 r_free = 0.4446 target = 0.193195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.146589 restraints weight = 36947.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.151136 restraints weight = 18816.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.153999 restraints weight = 12847.254| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 23528 Z= 0.258 Angle : 0.759 59.190 31824 Z= 0.414 Chirality : 0.043 0.567 3752 Planarity : 0.004 0.071 3980 Dihedral : 4.192 49.963 3160 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 4.15 % Allowed : 34.46 % Favored : 61.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 2892 helix: 0.48 (0.13), residues: 1568 sheet: -0.24 (0.30), residues: 300 loop : -1.15 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 673 HIS 0.006 0.001 HIS B 85 PHE 0.027 0.001 PHE A 670 TYR 0.024 0.001 TYR D 667 ARG 0.007 0.000 ARG A 696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8141.31 seconds wall clock time: 147 minutes 6.12 seconds (8826.12 seconds total)