Starting phenix.real_space_refine on Thu Mar 5 16:16:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kgh_22870/03_2026/7kgh_22870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kgh_22870/03_2026/7kgh_22870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kgh_22870/03_2026/7kgh_22870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kgh_22870/03_2026/7kgh_22870.map" model { file = "/net/cci-nas-00/data/ceres_data/7kgh_22870/03_2026/7kgh_22870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kgh_22870/03_2026/7kgh_22870.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 135 5.16 5 C 15234 2.51 5 N 3801 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "B" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "C" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' ET': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Time building chain proxies: 5.38, per 1000 atoms: 0.23 Number of scatterers: 23505 At special positions: 0 Unit cell: (122.04, 113.4, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 3 15.00 O 4332 8.00 N 3801 7.00 C 15234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 761.8 milliseconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 24 sheets defined 61.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.205A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.504A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.750A pdb=" N ASP A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.697A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.512A pdb=" N VAL A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.920A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.768A pdb=" N LEU A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.964A pdb=" N VAL A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.670A pdb=" N THR A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 387 removed outlier: 4.435A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.624A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 3.783A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.391A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.905A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.658A pdb=" N ALA A 459 " --> pdb=" O MET A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 497 removed outlier: 3.698A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.857A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 Processing helix chain 'A' and resid 535 through 556 Processing helix chain 'A' and resid 580 through 598 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 683 through 701 removed outlier: 4.160A pdb=" N LEU A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 745 Processing helix chain 'A' and resid 773 through 780 removed outlier: 4.212A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 4.385A pdb=" N VAL A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 842 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 860 through 884 removed outlier: 4.267A pdb=" N MET A 864 " --> pdb=" O SER A 860 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 893 Processing helix chain 'A' and resid 895 through 911 Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.630A pdb=" N LYS A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 981 removed outlier: 5.053A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix removed outlier: 3.788A pdb=" N ILE A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1027 removed outlier: 4.340A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.629A pdb=" N PHE B 5 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.610A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.860A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.559A pdb=" N ALA B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.575A pdb=" N VAL B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 317 removed outlier: 4.070A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 360 removed outlier: 4.072A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.616A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 4.188A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 423 Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 438 through 458 removed outlier: 3.719A pdb=" N ILE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.897A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 496 removed outlier: 3.619A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 533 Processing helix chain 'B' and resid 534 through 556 removed outlier: 3.528A pdb=" N ALA B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.562A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 650 removed outlier: 3.622A pdb=" N SER B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.565A pdb=" N LEU B 688 " --> pdb=" O MET B 684 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.585A pdb=" N ILE B 740 " --> pdb=" O ASP B 736 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 772 removed outlier: 4.244A pdb=" N MET B 772 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 779 removed outlier: 4.173A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 827 through 841 removed outlier: 3.740A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 884 removed outlier: 3.658A pdb=" N GLN B 856 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA B 865 " --> pdb=" O GLU B 861 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE B 866 " --> pdb=" O SER B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 removed outlier: 3.746A pdb=" N SER B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 892 " --> pdb=" O ILE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 911 removed outlier: 3.614A pdb=" N GLY B 899 " --> pdb=" O VAL B 895 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 946 removed outlier: 4.222A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 946 " --> pdb=" O MET B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 961 Processing helix chain 'B' and resid 961 through 982 removed outlier: 3.502A pdb=" N ILE B 965 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1007 removed outlier: 3.780A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1027 Proline residue: B1013 - end of helix removed outlier: 3.598A pdb=" N VAL B1023 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.957A pdb=" N ILE C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.563A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.583A pdb=" N VAL C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.971A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 117 removed outlier: 4.368A pdb=" N ALA C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.518A pdb=" N LYS C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 261 through 264 Processing helix chain 'C' and resid 298 through 316 removed outlier: 3.802A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.526A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 4.306A pdb=" N THR C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix removed outlier: 3.550A pdb=" N PHE C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.409A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 453 removed outlier: 5.453A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 461 through 497 removed outlier: 3.799A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix removed outlier: 3.538A pdb=" N LEU C 497 " --> pdb=" O CYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 534 removed outlier: 3.663A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 removed outlier: 3.934A pdb=" N MET C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET C 539 " --> pdb=" O THR C 535 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 541 " --> pdb=" O PRO C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 596 removed outlier: 3.582A pdb=" N LEU C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 647 removed outlier: 3.531A pdb=" N MET C 647 " --> pdb=" O VAL C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 701 removed outlier: 3.663A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 746 removed outlier: 3.937A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 780 Processing helix chain 'C' and resid 792 through 795 No H-bonds generated for 'chain 'C' and resid 792 through 795' Processing helix chain 'C' and resid 827 through 840 Processing helix chain 'C' and resid 852 through 860 Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 894 removed outlier: 4.204A pdb=" N SER C 891 " --> pdb=" O ALA C 887 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 892 " --> pdb=" O ILE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 911 removed outlier: 4.288A pdb=" N GLY C 899 " --> pdb=" O VAL C 895 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 900 " --> pdb=" O VAL C 896 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 946 Processing helix chain 'C' and resid 949 through 981 removed outlier: 4.765A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1027 removed outlier: 3.746A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C1002 " --> pdb=" O PHE C 998 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix removed outlier: 3.770A pdb=" N GLU C1024 " --> pdb=" O LEU C1020 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.346A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 83 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A 817 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.346A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 83 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.788A pdb=" N GLN A 292 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 175 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA A 290 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 177 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA A 288 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.788A pdb=" N GLN A 292 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 175 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA A 290 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 177 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA A 288 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.569A pdb=" N GLU A 269 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS A 182 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 761 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 removed outlier: 6.881A pdb=" N SER A 235 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE C 722 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 799 through 803 removed outlier: 3.704A pdb=" N ILE B 232 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 removed outlier: 7.638A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 7.638A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.983A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 293 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 137 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP B 328 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.885A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 603 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 621 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.644A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB6, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 782 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.861A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.712A pdb=" N PHE C 136 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C 293 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.457A pdb=" N LYS C 182 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN C 761 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 251 through 252 Processing sheet with id=AC4, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.270A pdb=" N SER C 603 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 605 " --> pdb=" O PHE C 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 704 through 710 removed outlier: 4.116A pdb=" N SER C 817 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 782 1553 hydrogen bonds defined for protein. 4521 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: 5.53 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 3843 1.26 - 1.40: 5291 1.40 - 1.54: 14153 1.54 - 1.68: 383 1.68 - 1.82: 264 Bond restraints: 23934 Sorted by residual: bond pdb=" C ASN B 205 " pdb=" O ASN B 205 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.17e-02 7.31e+03 8.21e+01 bond pdb=" C HIS C 342 " pdb=" O HIS C 342 " ideal model delta sigma weight residual 1.237 1.132 0.105 1.17e-02 7.31e+03 8.02e+01 bond pdb=" C GLN C 863 " pdb=" O GLN C 863 " ideal model delta sigma weight residual 1.236 1.126 0.110 1.26e-02 6.30e+03 7.68e+01 bond pdb=" C8 PTY B1101 " pdb=" O7 PTY B1101 " ideal model delta sigma weight residual 1.331 1.458 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C ASN C 298 " pdb=" O ASN C 298 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.21e-02 6.83e+03 3.55e+01 ... (remaining 23929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 32105 3.40 - 6.80: 312 6.80 - 10.21: 19 10.21 - 13.61: 4 13.61 - 17.01: 2 Bond angle restraints: 32442 Sorted by residual: angle pdb=" C ASN C 298 " pdb=" N ALA C 299 " pdb=" CA ALA C 299 " ideal model delta sigma weight residual 120.44 130.93 -10.49 1.30e+00 5.92e-01 6.51e+01 angle pdb=" CA ASN C 298 " pdb=" C ASN C 298 " pdb=" O ASN C 298 " ideal model delta sigma weight residual 120.49 112.27 8.22 1.16e+00 7.43e-01 5.02e+01 angle pdb=" CA HIS C 342 " pdb=" C HIS C 342 " pdb=" O HIS C 342 " ideal model delta sigma weight residual 120.55 113.11 7.44 1.06e+00 8.90e-01 4.92e+01 angle pdb=" CA ASN B 205 " pdb=" C ASN B 205 " pdb=" O ASN B 205 " ideal model delta sigma weight residual 120.55 113.41 7.14 1.06e+00 8.90e-01 4.54e+01 angle pdb=" CA PHE C 550 " pdb=" C PHE C 550 " pdb=" O PHE C 550 " ideal model delta sigma weight residual 119.97 112.47 7.50 1.15e+00 7.56e-01 4.25e+01 ... (remaining 32437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 14112 32.59 - 65.19: 351 65.19 - 97.78: 34 97.78 - 130.38: 1 130.38 - 162.97: 1 Dihedral angle restraints: 14499 sinusoidal: 5682 harmonic: 8817 Sorted by residual: dihedral pdb=" C TYR A 77 " pdb=" N TYR A 77 " pdb=" CA TYR A 77 " pdb=" CB TYR A 77 " ideal model delta harmonic sigma weight residual -122.60 -137.51 14.91 0 2.50e+00 1.60e-01 3.56e+01 dihedral pdb=" N TYR A 77 " pdb=" C TYR A 77 " pdb=" CA TYR A 77 " pdb=" CB TYR A 77 " ideal model delta harmonic sigma weight residual 122.80 136.64 -13.84 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" C ASN A 74 " pdb=" N ASN A 74 " pdb=" CA ASN A 74 " pdb=" CB ASN A 74 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 ... (remaining 14496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3733 0.111 - 0.221: 125 0.221 - 0.332: 13 0.332 - 0.443: 0 0.443 - 0.553: 2 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA TYR A 77 " pdb=" N TYR A 77 " pdb=" C TYR A 77 " pdb=" CB TYR A 77 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CA ASN A 74 " pdb=" N ASN A 74 " pdb=" C ASN A 74 " pdb=" CB ASN A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA ILE A 291 " pdb=" N ILE A 291 " pdb=" C ILE A 291 " pdb=" CB ILE A 291 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 3870 not shown) Planarity restraints: 4066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 330 " 0.077 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO B 331 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 765 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLN B 765 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN B 765 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL B 766 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 44 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASN A 44 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN A 44 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 45 " -0.025 2.00e-02 2.50e+03 ... (remaining 4063 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 100 2.51 - 3.11: 18582 3.11 - 3.70: 35769 3.70 - 4.30: 50957 4.30 - 4.90: 85576 Nonbonded interactions: 190984 Sorted by model distance: nonbonded pdb=" O ASN B 248 " pdb=" ND2 ASN B 248 " model vdw 1.910 3.120 nonbonded pdb=" OH TYR A 749 " pdb=" OD1 ASP A 752 " model vdw 2.062 3.040 nonbonded pdb=" O LEU B 898 " pdb=" OG SER B1003 " model vdw 2.074 3.040 nonbonded pdb=" OE1 GLN B 120 " pdb=" NH2 ARG B 123 " model vdw 2.093 3.120 nonbonded pdb=" NZ LYS C 602 " pdb=" O LYS C 627 " model vdw 2.095 3.120 ... (remaining 190979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1027 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1027 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'C' and (resid 1 through 1027 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C \ 34 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O \ 12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )))) } 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.610 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 : 0.005 0.127 23934 Z= 0.298 Angle : 0.803 17.008 32442 Z= 0.504 Chirality : 0.047 0.553 3873 Planarity : 0.006 0.114 4066 Dihedral : 14.424 162.970 8793 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.97 % Allowed : 1.33 % Favored : 97.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.15), residues: 3048 helix: 1.80 (0.13), residues: 1644 sheet: -0.01 (0.24), residues: 402 loop : -0.08 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 961 TYR 0.028 0.002 TYR C 78 PHE 0.038 0.001 PHE B 136 TRP 0.010 0.001 TRP A 800 HIS 0.003 0.001 HIS C 991 Details of bonding type rmsd covalent geometry : bond 0.00462 (23934) covalent geometry : angle 0.80312 (32442) hydrogen bonds : bond 0.14830 ( 1505) hydrogen bonds : angle 6.08394 ( 4521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 569 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6741 (mm-30) REVERT: A 156 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6621 (t70) REVERT: A 280 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6270 (mm) REVERT: A 304 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6586 (tt0) REVERT: A 376 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6291 (mp) REVERT: A 693 GLU cc_start: 0.7370 (tp30) cc_final: 0.6907 (tm-30) REVERT: A 807 TYR cc_start: 0.7869 (m-80) cc_final: 0.7449 (m-80) REVERT: A 1001 MET cc_start: 0.5261 (ttm) cc_final: 0.4998 (ttm) REVERT: B 165 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: B 184 MET cc_start: 0.6705 (mmm) cc_final: 0.6097 (mmm) REVERT: B 309 LYS cc_start: 0.7709 (tptp) cc_final: 0.7283 (tptp) REVERT: B 527 MET cc_start: 0.6965 (ttt) cc_final: 0.6667 (ttm) REVERT: B 654 GLU cc_start: 0.6316 (mt-10) cc_final: 0.5681 (pt0) REVERT: B 695 MET cc_start: 0.7395 (mmm) cc_final: 0.6715 (mmt) REVERT: B 813 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6966 (mtt-85) REVERT: B 844 LYS cc_start: 0.7329 (tppt) cc_final: 0.7085 (tppt) REVERT: B 931 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7341 (tttm) REVERT: C 8 ARG cc_start: 0.7374 (mtt180) cc_final: 0.7032 (mmm-85) REVERT: C 68 GLU cc_start: 0.6175 (mp0) cc_final: 0.5501 (mp0) REVERT: C 363 ARG cc_start: 0.7138 (mmt180) cc_final: 0.6759 (mmt-90) REVERT: C 423 GLU cc_start: 0.7086 (mp0) cc_final: 0.6673 (mp0) REVERT: C 467 TYR cc_start: 0.7398 (m-10) cc_final: 0.7116 (m-80) REVERT: C 471 THR cc_start: 0.7946 (m) cc_final: 0.7712 (p) REVERT: C 533 LYS cc_start: 0.7601 (tmtt) cc_final: 0.7371 (tptp) REVERT: C 589 ASN cc_start: 0.6050 (m110) cc_final: 0.5624 (m-40) REVERT: C 826 THR cc_start: 0.8084 (m) cc_final: 0.7878 (m) outliers start: 25 outliers final: 5 residues processed: 589 average time/residue: 0.1496 time to fit residues: 142.1472 Evaluate side-chains 520 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 508 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 813 ARG Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 204 ASN A 342 HIS A 590 GLN A 701 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN B 360 HIS B 566 GLN B 617 GLN B 801 ASN B 859 GLN B 863 GLN C 273 GLN C 282 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 991 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.179583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.149385 restraints weight = 27394.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.148950 restraints weight = 29426.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.151363 restraints weight = 26803.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.150713 restraints weight = 19844.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.151023 restraints weight = 16956.433| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23934 Z= 0.181 Angle : 0.670 13.142 32442 Z= 0.346 Chirality : 0.045 0.280 3873 Planarity : 0.005 0.058 4066 Dihedral : 7.855 167.883 3318 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.72 % Allowed : 9.59 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 3048 helix: 1.65 (0.12), residues: 1676 sheet: -0.07 (0.22), residues: 442 loop : -0.15 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 418 TYR 0.021 0.002 TYR C 848 PHE 0.034 0.002 PHE A 517 TRP 0.012 0.001 TRP A 800 HIS 0.006 0.002 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00417 (23934) covalent geometry : angle 0.66961 (32442) hydrogen bonds : bond 0.05254 ( 1505) hydrogen bonds : angle 4.92060 ( 4521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 539 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.7769 (ptm) cc_final: 0.7563 (ptm) REVERT: A 280 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6709 (mt) REVERT: A 304 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6376 (tt0) REVERT: A 311 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 374 ILE cc_start: 0.6853 (mt) cc_final: 0.6250 (mt) REVERT: A 376 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7088 (mt) REVERT: A 693 GLU cc_start: 0.7362 (tp30) cc_final: 0.7033 (tp30) REVERT: A 769 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6345 (ttpt) REVERT: B 165 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: B 182 LYS cc_start: 0.7004 (mtmm) cc_final: 0.6533 (ptpp) REVERT: B 518 ASP cc_start: 0.6450 (t0) cc_final: 0.6206 (t0) REVERT: B 522 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7341 (mtmm) REVERT: B 527 MET cc_start: 0.6935 (ttt) cc_final: 0.6672 (ttm) REVERT: B 554 LYS cc_start: 0.7437 (mptt) cc_final: 0.7152 (tppt) REVERT: B 654 GLU cc_start: 0.6317 (mt-10) cc_final: 0.5919 (pt0) REVERT: B 656 MET cc_start: 0.7502 (tpp) cc_final: 0.7071 (tpt) REVERT: B 783 MET cc_start: 0.4090 (mmm) cc_final: 0.3596 (mmm) REVERT: C 68 GLU cc_start: 0.6450 (mp0) cc_final: 0.5571 (mp0) REVERT: C 213 GLU cc_start: 0.7257 (tt0) cc_final: 0.6823 (tt0) REVERT: C 321 MET cc_start: 0.6577 (mtm) cc_final: 0.6251 (mtm) REVERT: C 356 TYR cc_start: 0.6433 (t80) cc_final: 0.6050 (t80) REVERT: C 423 GLU cc_start: 0.7021 (mp0) cc_final: 0.6673 (mp0) REVERT: C 467 TYR cc_start: 0.7442 (m-10) cc_final: 0.6984 (m-80) REVERT: C 528 LEU cc_start: 0.5826 (tp) cc_final: 0.5606 (tp) REVERT: C 589 ASN cc_start: 0.6186 (m110) cc_final: 0.5796 (m-40) REVERT: C 826 THR cc_start: 0.8182 (m) cc_final: 0.7685 (p) REVERT: C 849 GLU cc_start: 0.7003 (mp0) cc_final: 0.5954 (tt0) outliers start: 44 outliers final: 22 residues processed: 563 average time/residue: 0.1530 time to fit residues: 137.6822 Evaluate side-chains 533 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 506 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 821 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 147 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 590 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 360 HIS C 566 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.179233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.149287 restraints weight = 27332.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.148762 restraints weight = 31180.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.150771 restraints weight = 27428.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.150275 restraints weight = 22293.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.150597 restraints weight = 19598.243| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23934 Z= 0.149 Angle : 0.603 10.939 32442 Z= 0.310 Chirality : 0.043 0.210 3873 Planarity : 0.005 0.055 4066 Dihedral : 7.148 166.881 3304 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.99 % Allowed : 12.01 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3048 helix: 1.67 (0.12), residues: 1684 sheet: -0.24 (0.22), residues: 468 loop : -0.08 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 418 TYR 0.024 0.001 TYR C 848 PHE 0.031 0.001 PHE A 517 TRP 0.015 0.001 TRP A 800 HIS 0.003 0.001 HIS A 991 Details of bonding type rmsd covalent geometry : bond 0.00340 (23934) covalent geometry : angle 0.60278 (32442) hydrogen bonds : bond 0.04741 ( 1505) hydrogen bonds : angle 4.64670 ( 4521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 526 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4918 (tpp) cc_final: 0.4651 (mmt) REVERT: A 99 ASP cc_start: 0.5368 (m-30) cc_final: 0.5139 (p0) REVERT: A 304 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: A 376 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7205 (mt) REVERT: A 390 ILE cc_start: 0.7468 (pt) cc_final: 0.7240 (pt) REVERT: A 474 MET cc_start: 0.6547 (ttt) cc_final: 0.6253 (ttt) REVERT: A 570 MET cc_start: 0.7866 (ttp) cc_final: 0.7533 (ttm) REVERT: A 572 SER cc_start: 0.8343 (t) cc_final: 0.7906 (m) REVERT: A 693 GLU cc_start: 0.7137 (tp30) cc_final: 0.6823 (tm-30) REVERT: A 769 LYS cc_start: 0.6947 (pttm) cc_final: 0.6232 (ttpt) REVERT: A 939 PHE cc_start: 0.6609 (m-80) cc_final: 0.6209 (t80) REVERT: B 182 LYS cc_start: 0.6928 (mtmm) cc_final: 0.6716 (mtmm) REVERT: B 518 ASP cc_start: 0.6398 (t0) cc_final: 0.6104 (t0) REVERT: B 522 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7299 (mtmm) REVERT: B 527 MET cc_start: 0.7007 (ttt) cc_final: 0.6743 (ttm) REVERT: B 554 LYS cc_start: 0.7427 (mptt) cc_final: 0.7211 (tppt) REVERT: B 654 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5931 (pt0) REVERT: B 771 ARG cc_start: 0.8002 (ptt90) cc_final: 0.7719 (ptt90) REVERT: B 783 MET cc_start: 0.3705 (mmm) cc_final: 0.3223 (mmm) REVERT: B 844 LYS cc_start: 0.7635 (tppt) cc_final: 0.7130 (mmtm) REVERT: C 59 ASP cc_start: 0.7401 (m-30) cc_final: 0.7200 (m-30) REVERT: C 68 GLU cc_start: 0.6399 (mp0) cc_final: 0.5553 (mp0) REVERT: C 102 MET cc_start: 0.5985 (mmt) cc_final: 0.5722 (mmt) REVERT: C 213 GLU cc_start: 0.7269 (tt0) cc_final: 0.6843 (tt0) REVERT: C 356 TYR cc_start: 0.6383 (t80) cc_final: 0.6033 (t80) REVERT: C 423 GLU cc_start: 0.7013 (mp0) cc_final: 0.6666 (mp0) REVERT: C 589 ASN cc_start: 0.6093 (m110) cc_final: 0.5699 (m-40) REVERT: C 769 LYS cc_start: 0.7894 (tmmt) cc_final: 0.7514 (tmtt) REVERT: C 826 THR cc_start: 0.8153 (m) cc_final: 0.7671 (p) outliers start: 51 outliers final: 32 residues processed: 553 average time/residue: 0.1454 time to fit residues: 129.3184 Evaluate side-chains 536 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 502 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 277 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 88 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 269 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 108 GLN A 360 HIS A 574 GLN A 590 GLN ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 760 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN C 677 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.177620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.147734 restraints weight = 27219.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.147050 restraints weight = 32621.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.149076 restraints weight = 29702.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.148593 restraints weight = 23645.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.148965 restraints weight = 21435.341| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23934 Z= 0.163 Angle : 0.619 12.433 32442 Z= 0.316 Chirality : 0.043 0.312 3873 Planarity : 0.005 0.058 4066 Dihedral : 6.755 158.213 3299 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.61 % Allowed : 13.68 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 3048 helix: 1.63 (0.12), residues: 1676 sheet: -0.25 (0.22), residues: 474 loop : -0.11 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 418 TYR 0.015 0.001 TYR A 77 PHE 0.028 0.002 PHE A 517 TRP 0.015 0.001 TRP A 800 HIS 0.008 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00380 (23934) covalent geometry : angle 0.61856 (32442) hydrogen bonds : bond 0.04759 ( 1505) hydrogen bonds : angle 4.59592 ( 4521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 518 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.5321 (m-30) cc_final: 0.5048 (p0) REVERT: A 357 LEU cc_start: 0.7917 (mm) cc_final: 0.7677 (mm) REVERT: A 376 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7249 (mt) REVERT: A 570 MET cc_start: 0.7908 (ttp) cc_final: 0.7643 (ttm) REVERT: A 572 SER cc_start: 0.8379 (t) cc_final: 0.7917 (m) REVERT: A 693 GLU cc_start: 0.7121 (tp30) cc_final: 0.6900 (tp30) REVERT: A 748 MET cc_start: 0.6327 (pmm) cc_final: 0.6101 (pmm) REVERT: A 769 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6258 (ttpt) REVERT: A 939 PHE cc_start: 0.6441 (m-80) cc_final: 0.5966 (t80) REVERT: B 182 LYS cc_start: 0.6909 (mtmm) cc_final: 0.6678 (mtmm) REVERT: B 522 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7494 (mmmt) REVERT: B 527 MET cc_start: 0.7004 (ttt) cc_final: 0.6709 (ttm) REVERT: B 553 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5940 (ttp) REVERT: B 638 LYS cc_start: 0.7222 (tmtt) cc_final: 0.6768 (tmtt) REVERT: B 654 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5758 (pt0) REVERT: B 771 ARG cc_start: 0.7983 (ptt90) cc_final: 0.7680 (ptt90) REVERT: B 783 MET cc_start: 0.3679 (mmm) cc_final: 0.3235 (mmm) REVERT: B 807 TYR cc_start: 0.7717 (m-80) cc_final: 0.7375 (m-80) REVERT: C 8 ARG cc_start: 0.7507 (mtt180) cc_final: 0.7273 (mtt180) REVERT: C 59 ASP cc_start: 0.7390 (m-30) cc_final: 0.7178 (m-30) REVERT: C 68 GLU cc_start: 0.6431 (mp0) cc_final: 0.5559 (mp0) REVERT: C 213 GLU cc_start: 0.7314 (tt0) cc_final: 0.6862 (tt0) REVERT: C 356 TYR cc_start: 0.6436 (t80) cc_final: 0.6103 (t80) REVERT: C 363 ARG cc_start: 0.7326 (mmt180) cc_final: 0.6904 (mmt-90) REVERT: C 423 GLU cc_start: 0.7027 (mp0) cc_final: 0.6665 (mp0) REVERT: C 589 ASN cc_start: 0.6241 (m-40) cc_final: 0.5832 (m-40) REVERT: C 769 LYS cc_start: 0.7863 (tmmt) cc_final: 0.7504 (tmtt) REVERT: C 826 THR cc_start: 0.8282 (m) cc_final: 0.7769 (p) REVERT: C 849 GLU cc_start: 0.7111 (mp0) cc_final: 0.6654 (mp0) outliers start: 67 outliers final: 40 residues processed: 550 average time/residue: 0.1460 time to fit residues: 128.2166 Evaluate side-chains 535 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 492 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 281 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 590 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 773 GLN ** C 574 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 = 0.3784 r_free = 0.3784 target = 0.174670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.144095 restraints weight = 27271.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.143527 restraints weight = 32371.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.145207 restraints weight = 28830.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.145256 restraints weight = 22699.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.145443 restraints weight = 21023.239| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23934 Z= 0.206 Angle : 0.654 11.057 32442 Z= 0.336 Chirality : 0.044 0.376 3873 Planarity : 0.005 0.067 4066 Dihedral : 6.717 149.425 3296 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.73 % Allowed : 15.79 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3048 helix: 1.52 (0.12), residues: 1676 sheet: -0.18 (0.23), residues: 460 loop : -0.25 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 771 TYR 0.026 0.002 TYR C 848 PHE 0.028 0.002 PHE A 517 TRP 0.016 0.001 TRP A 800 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00490 (23934) covalent geometry : angle 0.65386 (32442) hydrogen bonds : bond 0.05068 ( 1505) hydrogen bonds : angle 4.69391 ( 4521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 519 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6331 (mt-10) REVERT: A 304 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6559 (tt0) REVERT: A 357 LEU cc_start: 0.7902 (mm) cc_final: 0.7675 (mm) REVERT: A 435 MET cc_start: 0.4682 (mmm) cc_final: 0.4477 (mmm) REVERT: A 570 MET cc_start: 0.7996 (ttp) cc_final: 0.7758 (ttm) REVERT: A 572 SER cc_start: 0.8466 (t) cc_final: 0.7953 (m) REVERT: A 684 MET cc_start: 0.7343 (mpp) cc_final: 0.5563 (mmm) REVERT: A 693 GLU cc_start: 0.7106 (tp30) cc_final: 0.6866 (tp30) REVERT: A 748 MET cc_start: 0.6237 (pmm) cc_final: 0.5989 (pmm) REVERT: A 769 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6281 (ttpt) REVERT: A 939 PHE cc_start: 0.6426 (m-80) cc_final: 0.5942 (t80) REVERT: B 5 PHE cc_start: 0.8500 (m-80) cc_final: 0.8288 (m-80) REVERT: B 164 GLU cc_start: 0.6638 (tp30) cc_final: 0.6414 (tp30) REVERT: B 182 LYS cc_start: 0.6867 (mtmm) cc_final: 0.6662 (mtmm) REVERT: B 518 ASP cc_start: 0.6603 (t0) cc_final: 0.6275 (t0) REVERT: B 522 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7472 (mtmm) REVERT: B 527 MET cc_start: 0.7005 (ttt) cc_final: 0.6748 (ttm) REVERT: B 553 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.5940 (ttp) REVERT: B 638 LYS cc_start: 0.7399 (tmtt) cc_final: 0.6935 (tptp) REVERT: B 654 GLU cc_start: 0.6199 (mt-10) cc_final: 0.5984 (pt0) REVERT: B 656 MET cc_start: 0.7993 (tpt) cc_final: 0.7001 (tpt) REVERT: B 771 ARG cc_start: 0.8014 (ptt90) cc_final: 0.7694 (ptt90) REVERT: B 783 MET cc_start: 0.3567 (mmm) cc_final: 0.3146 (mmm) REVERT: B 807 TYR cc_start: 0.7729 (m-80) cc_final: 0.7441 (m-80) REVERT: B 844 LYS cc_start: 0.7639 (tppt) cc_final: 0.7218 (mmtm) REVERT: B 890 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8002 (tt) REVERT: C 8 ARG cc_start: 0.7611 (mtt180) cc_final: 0.7381 (mtt180) REVERT: C 59 ASP cc_start: 0.7528 (m-30) cc_final: 0.7288 (m-30) REVERT: C 356 TYR cc_start: 0.6496 (t80) cc_final: 0.6225 (t80) REVERT: C 363 ARG cc_start: 0.7409 (mmt180) cc_final: 0.6972 (mmt-90) REVERT: C 423 GLU cc_start: 0.7035 (mp0) cc_final: 0.6638 (mp0) REVERT: C 589 ASN cc_start: 0.6248 (m-40) cc_final: 0.5860 (m-40) REVERT: C 704 PHE cc_start: 0.8007 (m-10) cc_final: 0.7701 (m-10) REVERT: C 769 LYS cc_start: 0.7898 (tmmt) cc_final: 0.7548 (tmtt) REVERT: C 826 THR cc_start: 0.8302 (m) cc_final: 0.7790 (p) REVERT: C 849 GLU cc_start: 0.7220 (mp0) cc_final: 0.5802 (mm-30) outliers start: 70 outliers final: 52 residues processed: 551 average time/residue: 0.1473 time to fit residues: 130.3826 Evaluate side-chains 559 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 501 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 928 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 82 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 70 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 228 GLN A 415 ASN A 574 GLN A 590 GLN B 176 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.178312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.147698 restraints weight = 27144.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.147180 restraints weight = 31492.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.149378 restraints weight = 28548.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.149191 restraints weight = 20240.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.149394 restraints weight = 17724.937| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23934 Z= 0.135 Angle : 0.600 12.262 32442 Z= 0.306 Chirality : 0.042 0.328 3873 Planarity : 0.005 0.066 4066 Dihedral : 6.278 145.488 3294 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.61 % Allowed : 17.43 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 3048 helix: 1.66 (0.12), residues: 1666 sheet: -0.16 (0.23), residues: 460 loop : -0.18 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 418 TYR 0.039 0.001 TYR C 467 PHE 0.026 0.001 PHE A 517 TRP 0.016 0.001 TRP A 800 HIS 0.007 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00300 (23934) covalent geometry : angle 0.59980 (32442) hydrogen bonds : bond 0.04350 ( 1505) hydrogen bonds : angle 4.48268 ( 4521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 521 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6330 (mt-10) REVERT: A 228 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.7052 (mm110) REVERT: A 304 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6505 (tt0) REVERT: A 357 LEU cc_start: 0.7864 (mm) cc_final: 0.7653 (mm) REVERT: A 435 MET cc_start: 0.4832 (mmm) cc_final: 0.4593 (mmm) REVERT: A 570 MET cc_start: 0.7882 (ttp) cc_final: 0.7609 (ttm) REVERT: A 572 SER cc_start: 0.8291 (t) cc_final: 0.7827 (m) REVERT: A 590 GLN cc_start: 0.6103 (mt0) cc_final: 0.5861 (mt0) REVERT: A 684 MET cc_start: 0.7324 (mpp) cc_final: 0.5468 (mmm) REVERT: A 693 GLU cc_start: 0.7262 (tp30) cc_final: 0.6893 (tp30) REVERT: A 769 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6309 (ttpt) REVERT: A 939 PHE cc_start: 0.6320 (m-80) cc_final: 0.5911 (t80) REVERT: B 518 ASP cc_start: 0.6538 (t0) cc_final: 0.6128 (t0) REVERT: B 522 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7445 (mtmm) REVERT: B 527 MET cc_start: 0.6873 (ttt) cc_final: 0.6615 (ttm) REVERT: B 564 GLU cc_start: 0.7679 (tp30) cc_final: 0.6988 (tp30) REVERT: B 638 LYS cc_start: 0.7255 (tmtt) cc_final: 0.6782 (tptp) REVERT: B 656 MET cc_start: 0.7886 (tpt) cc_final: 0.6990 (tpt) REVERT: B 771 ARG cc_start: 0.8034 (ptt90) cc_final: 0.7663 (ptt90) REVERT: B 783 MET cc_start: 0.3398 (mmm) cc_final: 0.3012 (mmm) REVERT: B 807 TYR cc_start: 0.7672 (m-80) cc_final: 0.7294 (m-80) REVERT: B 844 LYS cc_start: 0.7594 (tppt) cc_final: 0.7130 (mmtm) REVERT: B 890 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7840 (tt) REVERT: C 356 TYR cc_start: 0.6449 (t80) cc_final: 0.6185 (t80) REVERT: C 363 ARG cc_start: 0.7414 (mmt180) cc_final: 0.6967 (mmt-90) REVERT: C 423 GLU cc_start: 0.7087 (mp0) cc_final: 0.6607 (mp0) REVERT: C 589 ASN cc_start: 0.6188 (m-40) cc_final: 0.5772 (m-40) REVERT: C 769 LYS cc_start: 0.7831 (tmmt) cc_final: 0.7442 (tmtt) REVERT: C 826 THR cc_start: 0.8210 (m) cc_final: 0.7738 (p) REVERT: C 849 GLU cc_start: 0.7179 (mp0) cc_final: 0.6695 (mp0) outliers start: 67 outliers final: 37 residues processed: 557 average time/residue: 0.1458 time to fit residues: 129.5358 Evaluate side-chains 540 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 497 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 821 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 250 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 279 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 293 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 415 ASN A 574 GLN B 108 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.178959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.148799 restraints weight = 27013.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.148514 restraints weight = 30142.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.149348 restraints weight = 25906.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.149327 restraints weight = 22926.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.149719 restraints weight = 19233.800| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23934 Z= 0.133 Angle : 0.612 11.834 32442 Z= 0.310 Chirality : 0.043 0.362 3873 Planarity : 0.005 0.066 4066 Dihedral : 6.149 142.703 3294 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.50 % Allowed : 17.78 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 3048 helix: 1.66 (0.12), residues: 1674 sheet: -0.21 (0.23), residues: 470 loop : -0.17 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 418 TYR 0.052 0.001 TYR C 467 PHE 0.028 0.001 PHE A 901 TRP 0.017 0.001 TRP A 800 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00300 (23934) covalent geometry : angle 0.61239 (32442) hydrogen bonds : bond 0.04266 ( 1505) hydrogen bonds : angle 4.42910 ( 4521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 519 time to evaluate : 0.836 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 68 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6940 (tp30) REVERT: A 164 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: A 570 MET cc_start: 0.7890 (ttp) cc_final: 0.7588 (ttm) REVERT: A 572 SER cc_start: 0.8277 (t) cc_final: 0.7887 (m) REVERT: A 684 MET cc_start: 0.7259 (mpp) cc_final: 0.5383 (mmm) REVERT: A 693 GLU cc_start: 0.7186 (tp30) cc_final: 0.6922 (tm-30) REVERT: A 697 MET cc_start: 0.7531 (mpp) cc_final: 0.6948 (mmp) REVERT: A 745 MET cc_start: 0.6285 (tpp) cc_final: 0.5755 (tmm) REVERT: A 769 LYS cc_start: 0.6866 (pttm) cc_final: 0.6201 (ttpt) REVERT: A 939 PHE cc_start: 0.6295 (m-80) cc_final: 0.5866 (t80) REVERT: A 951 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7137 (mm) REVERT: B 182 LYS cc_start: 0.6704 (mtmm) cc_final: 0.5921 (ptpp) REVERT: B 518 ASP cc_start: 0.6493 (t0) cc_final: 0.6084 (t0) REVERT: B 522 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7448 (mtmm) REVERT: B 527 MET cc_start: 0.6888 (ttt) cc_final: 0.6586 (ttm) REVERT: B 553 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5792 (tpp) REVERT: B 564 GLU cc_start: 0.7666 (tp30) cc_final: 0.7019 (tp30) REVERT: B 638 LYS cc_start: 0.7284 (tmtt) cc_final: 0.6841 (tptp) REVERT: B 684 MET cc_start: 0.6372 (tpt) cc_final: 0.5902 (tpt) REVERT: B 719 SER cc_start: 0.8809 (t) cc_final: 0.8242 (m) REVERT: B 771 ARG cc_start: 0.7975 (ptt90) cc_final: 0.7622 (ptt90) REVERT: B 783 MET cc_start: 0.3467 (mmm) cc_final: 0.3078 (mmm) REVERT: B 807 TYR cc_start: 0.7687 (m-80) cc_final: 0.7338 (m-80) REVERT: B 890 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7835 (tt) REVERT: B 1001 MET cc_start: 0.7242 (tpt) cc_final: 0.7037 (tpt) REVERT: C 59 ASP cc_start: 0.7453 (m-30) cc_final: 0.7219 (m-30) REVERT: C 356 TYR cc_start: 0.6419 (t80) cc_final: 0.6134 (t80) REVERT: C 363 ARG cc_start: 0.7423 (mmt180) cc_final: 0.6975 (mmt-90) REVERT: C 423 GLU cc_start: 0.7104 (mp0) cc_final: 0.6640 (mp0) REVERT: C 589 ASN cc_start: 0.6266 (m-40) cc_final: 0.6009 (m-40) REVERT: C 769 LYS cc_start: 0.7786 (tmmt) cc_final: 0.7416 (tmtt) REVERT: C 826 THR cc_start: 0.8235 (m) cc_final: 0.7737 (p) outliers start: 64 outliers final: 43 residues processed: 549 average time/residue: 0.1428 time to fit residues: 125.4959 Evaluate side-chains 555 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 507 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 948 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 50 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 228 GLN A 574 GLN A 590 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.179235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.148561 restraints weight = 27203.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.147992 restraints weight = 32194.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.149496 restraints weight = 28792.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.149301 restraints weight = 23303.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.149545 restraints weight = 20509.367| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23934 Z= 0.141 Angle : 0.630 14.876 32442 Z= 0.319 Chirality : 0.043 0.348 3873 Planarity : 0.005 0.066 4066 Dihedral : 6.083 138.682 3294 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.61 % Allowed : 18.01 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 3048 helix: 1.64 (0.12), residues: 1677 sheet: -0.18 (0.23), residues: 470 loop : -0.24 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 418 TYR 0.024 0.001 TYR C 848 PHE 0.029 0.001 PHE A 901 TRP 0.018 0.001 TRP A 800 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00319 (23934) covalent geometry : angle 0.63041 (32442) hydrogen bonds : bond 0.04299 ( 1505) hydrogen bonds : angle 4.42455 ( 4521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 512 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6401 (mt-10) REVERT: A 359 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6565 (mm) REVERT: A 456 MET cc_start: 0.7638 (ptm) cc_final: 0.7329 (ptm) REVERT: A 473 THR cc_start: 0.7893 (t) cc_final: 0.6597 (p) REVERT: A 570 MET cc_start: 0.7877 (ttp) cc_final: 0.7595 (ttm) REVERT: A 572 SER cc_start: 0.8331 (t) cc_final: 0.7917 (m) REVERT: A 684 MET cc_start: 0.7297 (mpp) cc_final: 0.5427 (mmm) REVERT: A 693 GLU cc_start: 0.7186 (tp30) cc_final: 0.6930 (tm-30) REVERT: A 697 MET cc_start: 0.7514 (mpp) cc_final: 0.6969 (mmp) REVERT: A 745 MET cc_start: 0.6323 (tpp) cc_final: 0.5882 (tmm) REVERT: A 769 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6252 (ttpt) REVERT: A 939 PHE cc_start: 0.6236 (m-80) cc_final: 0.5839 (t80) REVERT: A 951 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7212 (mm) REVERT: B 1 MET cc_start: 0.5150 (ppp) cc_final: 0.4744 (ppp) REVERT: B 115 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5112 (pp20) REVERT: B 182 LYS cc_start: 0.6747 (mtmm) cc_final: 0.5974 (ptpp) REVERT: B 184 MET cc_start: 0.6035 (mmm) cc_final: 0.5704 (mmm) REVERT: B 284 LYS cc_start: 0.7072 (mmtm) cc_final: 0.6840 (mmmt) REVERT: B 309 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7699 (tptp) REVERT: B 313 LEU cc_start: 0.7182 (mt) cc_final: 0.6978 (mt) REVERT: B 518 ASP cc_start: 0.6474 (t0) cc_final: 0.6085 (t0) REVERT: B 522 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7328 (mtmm) REVERT: B 527 MET cc_start: 0.6899 (ttt) cc_final: 0.6618 (ttm) REVERT: B 553 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.5796 (tpp) REVERT: B 564 GLU cc_start: 0.7684 (tp30) cc_final: 0.7033 (tp30) REVERT: B 638 LYS cc_start: 0.7300 (tmtt) cc_final: 0.6853 (tptp) REVERT: B 656 MET cc_start: 0.7877 (tpt) cc_final: 0.7068 (tpt) REVERT: B 684 MET cc_start: 0.6376 (tpt) cc_final: 0.5886 (tpt) REVERT: B 719 SER cc_start: 0.8799 (t) cc_final: 0.8274 (m) REVERT: B 771 ARG cc_start: 0.7941 (ptt90) cc_final: 0.7573 (ptt90) REVERT: B 783 MET cc_start: 0.3356 (mmm) cc_final: 0.3012 (mmm) REVERT: B 807 TYR cc_start: 0.7703 (m-80) cc_final: 0.7320 (m-80) REVERT: B 844 LYS cc_start: 0.7583 (tppt) cc_final: 0.6807 (mmmm) REVERT: B 890 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7835 (tt) REVERT: C 59 ASP cc_start: 0.7511 (m-30) cc_final: 0.7264 (m-30) REVERT: C 68 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5759 (mp0) REVERT: C 356 TYR cc_start: 0.6400 (t80) cc_final: 0.6120 (t80) REVERT: C 363 ARG cc_start: 0.7465 (mmt180) cc_final: 0.6985 (mmt-90) REVERT: C 423 GLU cc_start: 0.7139 (mp0) cc_final: 0.6644 (mp0) REVERT: C 467 TYR cc_start: 0.7358 (m-80) cc_final: 0.6774 (m-80) REVERT: C 589 ASN cc_start: 0.6257 (m-40) cc_final: 0.6037 (m-40) REVERT: C 602 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7336 (mmtt) REVERT: C 704 PHE cc_start: 0.8023 (m-10) cc_final: 0.7758 (m-10) REVERT: C 769 LYS cc_start: 0.7839 (tmmt) cc_final: 0.7466 (tmtt) REVERT: C 826 THR cc_start: 0.8225 (m) cc_final: 0.7730 (p) outliers start: 67 outliers final: 50 residues processed: 541 average time/residue: 0.1482 time to fit residues: 128.0380 Evaluate side-chains 562 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 503 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 948 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 5.9990 chunk 247 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 292 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN A 574 GLN A 590 GLN B 360 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.181030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.147365 restraints weight = 27320.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.147837 restraints weight = 26279.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.149951 restraints weight = 20635.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.150236 restraints weight = 16435.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.150334 restraints weight = 14278.785| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23934 Z= 0.129 Angle : 0.626 14.315 32442 Z= 0.316 Chirality : 0.042 0.343 3873 Planarity : 0.005 0.064 4066 Dihedral : 5.944 135.318 3294 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.42 % Allowed : 18.25 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3048 helix: 1.66 (0.12), residues: 1674 sheet: 0.01 (0.23), residues: 470 loop : -0.26 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 418 TYR 0.025 0.001 TYR C 848 PHE 0.029 0.001 PHE A 901 TRP 0.018 0.001 TRP A 800 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00283 (23934) covalent geometry : angle 0.62620 (32442) hydrogen bonds : bond 0.04068 ( 1505) hydrogen bonds : angle 4.36566 ( 4521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 513 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.6778 (mmmt) cc_final: 0.6236 (mmtt) REVERT: A 164 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6330 (mt-10) REVERT: A 359 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6548 (mm) REVERT: A 398 MET cc_start: 0.7633 (mtp) cc_final: 0.7310 (mtt) REVERT: A 456 MET cc_start: 0.7680 (ptm) cc_final: 0.7375 (ptm) REVERT: A 473 THR cc_start: 0.7954 (t) cc_final: 0.6457 (p) REVERT: A 570 MET cc_start: 0.7776 (ttp) cc_final: 0.7495 (ttm) REVERT: A 572 SER cc_start: 0.8251 (t) cc_final: 0.7886 (m) REVERT: A 684 MET cc_start: 0.7260 (mpp) cc_final: 0.5302 (mmm) REVERT: A 693 GLU cc_start: 0.7344 (tp30) cc_final: 0.7100 (tp30) REVERT: A 697 MET cc_start: 0.7564 (mpp) cc_final: 0.7194 (mmt) REVERT: A 745 MET cc_start: 0.6488 (tpp) cc_final: 0.5879 (tmm) REVERT: A 769 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6396 (ttpt) REVERT: A 939 PHE cc_start: 0.6221 (m-80) cc_final: 0.5847 (t80) REVERT: A 951 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7153 (mm) REVERT: B 1 MET cc_start: 0.5328 (ppp) cc_final: 0.4780 (ppp) REVERT: B 115 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5426 (pp20) REVERT: B 182 LYS cc_start: 0.6702 (mtmm) cc_final: 0.6028 (ptpp) REVERT: B 284 LYS cc_start: 0.7001 (mmtm) cc_final: 0.6747 (mmmt) REVERT: B 309 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7713 (tptp) REVERT: B 522 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7425 (mmmt) REVERT: B 527 MET cc_start: 0.6875 (ttt) cc_final: 0.6602 (ttm) REVERT: B 564 GLU cc_start: 0.7644 (tp30) cc_final: 0.7032 (tp30) REVERT: B 631 GLU cc_start: 0.6502 (tp30) cc_final: 0.6295 (tp30) REVERT: B 638 LYS cc_start: 0.7347 (tmtt) cc_final: 0.6863 (tptp) REVERT: B 656 MET cc_start: 0.7787 (tpt) cc_final: 0.7004 (tpt) REVERT: B 684 MET cc_start: 0.6322 (tpt) cc_final: 0.6118 (tpt) REVERT: B 719 SER cc_start: 0.8771 (t) cc_final: 0.8210 (m) REVERT: B 771 ARG cc_start: 0.7846 (ptt90) cc_final: 0.7483 (ptt90) REVERT: B 783 MET cc_start: 0.3277 (mmm) cc_final: 0.2613 (mmm) REVERT: B 807 TYR cc_start: 0.7675 (m-80) cc_final: 0.7265 (m-80) REVERT: B 844 LYS cc_start: 0.7599 (tppt) cc_final: 0.6612 (ttmm) REVERT: B 890 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7736 (tt) REVERT: C 8 ARG cc_start: 0.7232 (mtt180) cc_final: 0.6917 (mtt180) REVERT: C 68 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5741 (mp0) REVERT: C 356 TYR cc_start: 0.6369 (t80) cc_final: 0.6074 (t80) REVERT: C 363 ARG cc_start: 0.7489 (mmt180) cc_final: 0.7037 (mmt-90) REVERT: C 423 GLU cc_start: 0.7155 (mp0) cc_final: 0.6567 (mp0) REVERT: C 467 TYR cc_start: 0.7449 (m-80) cc_final: 0.6815 (m-80) REVERT: C 602 LYS cc_start: 0.7633 (mmtt) cc_final: 0.7172 (mptt) REVERT: C 704 PHE cc_start: 0.7933 (m-10) cc_final: 0.7720 (m-10) REVERT: C 745 MET cc_start: 0.8022 (mmm) cc_final: 0.7619 (tpp) REVERT: C 769 LYS cc_start: 0.7844 (tmmt) cc_final: 0.7448 (tmtt) REVERT: C 771 ARG cc_start: 0.7705 (ptt90) cc_final: 0.7424 (ptt-90) REVERT: C 826 THR cc_start: 0.8191 (m) cc_final: 0.7706 (p) REVERT: C 948 MET cc_start: 0.3593 (ptp) cc_final: 0.2798 (ptt) outliers start: 62 outliers final: 42 residues processed: 537 average time/residue: 0.1550 time to fit residues: 133.0357 Evaluate side-chains 552 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 502 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 948 MET Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 241 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 122 optimal weight: 30.0000 chunk 262 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 293 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN A 590 GLN B 360 HIS B 415 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.180925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.151255 restraints weight = 27205.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.150079 restraints weight = 33013.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.152075 restraints weight = 29937.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.151956 restraints weight = 21811.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.152015 restraints weight = 19700.636| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23934 Z= 0.128 Angle : 0.639 13.916 32442 Z= 0.320 Chirality : 0.043 0.353 3873 Planarity : 0.005 0.063 4066 Dihedral : 5.850 131.048 3294 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.91 % Allowed : 18.79 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 3048 helix: 1.65 (0.12), residues: 1676 sheet: -0.05 (0.23), residues: 485 loop : -0.19 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 418 TYR 0.014 0.001 TYR C 848 PHE 0.029 0.001 PHE A 901 TRP 0.019 0.001 TRP A 800 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00289 (23934) covalent geometry : angle 0.63914 (32442) hydrogen bonds : bond 0.04049 ( 1505) hydrogen bonds : angle 4.35372 ( 4521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 508 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7393 (pt) cc_final: 0.6288 (mm) REVERT: A 110 LYS cc_start: 0.6976 (mmmt) cc_final: 0.6288 (mmtt) REVERT: A 164 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6320 (mt-10) REVERT: A 398 MET cc_start: 0.7544 (mtp) cc_final: 0.7219 (mtt) REVERT: A 456 MET cc_start: 0.7593 (ptm) cc_final: 0.7270 (ptm) REVERT: A 473 THR cc_start: 0.7879 (t) cc_final: 0.6442 (p) REVERT: A 570 MET cc_start: 0.7818 (ttp) cc_final: 0.7507 (ttm) REVERT: A 572 SER cc_start: 0.8245 (t) cc_final: 0.7883 (m) REVERT: A 684 MET cc_start: 0.7359 (mpp) cc_final: 0.5477 (mmm) REVERT: A 697 MET cc_start: 0.7537 (mpp) cc_final: 0.7209 (mmt) REVERT: A 745 MET cc_start: 0.6470 (tpp) cc_final: 0.6123 (tmm) REVERT: A 769 LYS cc_start: 0.6965 (pttm) cc_final: 0.6334 (ttpt) REVERT: A 939 PHE cc_start: 0.6152 (m-80) cc_final: 0.5779 (t80) REVERT: A 951 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7222 (mm) REVERT: B 1 MET cc_start: 0.5129 (ppp) cc_final: 0.4560 (ppp) REVERT: B 115 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5571 (pp20) REVERT: B 182 LYS cc_start: 0.6714 (mtmm) cc_final: 0.6068 (ptpp) REVERT: B 527 MET cc_start: 0.6892 (ttt) cc_final: 0.6623 (ttm) REVERT: B 631 GLU cc_start: 0.6463 (tp30) cc_final: 0.6251 (tp30) REVERT: B 638 LYS cc_start: 0.7354 (tmtt) cc_final: 0.6911 (tptp) REVERT: B 656 MET cc_start: 0.7802 (tpt) cc_final: 0.7022 (tpt) REVERT: B 684 MET cc_start: 0.6324 (tpt) cc_final: 0.5830 (tpt) REVERT: B 719 SER cc_start: 0.8766 (t) cc_final: 0.8223 (m) REVERT: B 771 ARG cc_start: 0.7851 (ptt90) cc_final: 0.7489 (ptt90) REVERT: B 783 MET cc_start: 0.3351 (mmm) cc_final: 0.2673 (mmm) REVERT: B 807 TYR cc_start: 0.7663 (m-80) cc_final: 0.7251 (m-80) REVERT: B 844 LYS cc_start: 0.7593 (tppt) cc_final: 0.6605 (ttmm) REVERT: B 890 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7763 (tt) REVERT: C 68 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5531 (mp0) REVERT: C 102 MET cc_start: 0.5677 (mmt) cc_final: 0.5457 (mmt) REVERT: C 182 LYS cc_start: 0.7497 (mtmt) cc_final: 0.6784 (mtmt) REVERT: C 248 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6175 (t0) REVERT: C 356 TYR cc_start: 0.6312 (t80) cc_final: 0.6022 (t80) REVERT: C 363 ARG cc_start: 0.7472 (mmt180) cc_final: 0.7009 (mmt-90) REVERT: C 423 GLU cc_start: 0.7134 (mp0) cc_final: 0.6561 (mp0) REVERT: C 467 TYR cc_start: 0.7519 (m-80) cc_final: 0.6885 (m-80) REVERT: C 553 MET cc_start: 0.7172 (mtp) cc_final: 0.6866 (mtp) REVERT: C 602 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7381 (mptt) REVERT: C 704 PHE cc_start: 0.7958 (m-10) cc_final: 0.7749 (m-10) REVERT: C 745 MET cc_start: 0.8037 (mmm) cc_final: 0.7725 (tpp) REVERT: C 769 LYS cc_start: 0.7833 (tmmt) cc_final: 0.7472 (tmtt) REVERT: C 771 ARG cc_start: 0.7834 (ptt90) cc_final: 0.7591 (ptt-90) REVERT: C 826 THR cc_start: 0.8206 (m) cc_final: 0.7756 (p) outliers start: 49 outliers final: 40 residues processed: 532 average time/residue: 0.1529 time to fit residues: 129.7744 Evaluate side-chains 549 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 503 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 791 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 948 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 157 optimal weight: 0.0050 chunk 20 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 124 optimal weight: 40.0000 chunk 90 optimal weight: 0.9980 chunk 256 optimal weight: 0.0030 chunk 273 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 1.5806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN A 590 GLN A 859 GLN B 108 GLN B 360 HIS C 147 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.181594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.151314 restraints weight = 27315.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.150431 restraints weight = 32711.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.152446 restraints weight = 29973.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.152214 restraints weight = 23002.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.152640 restraints weight = 20524.578| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23934 Z= 0.129 Angle : 0.637 13.964 32442 Z= 0.320 Chirality : 0.043 0.329 3873 Planarity : 0.005 0.057 4066 Dihedral : 5.787 126.930 3294 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.03 % Allowed : 18.79 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 3048 helix: 1.65 (0.13), residues: 1678 sheet: -0.02 (0.23), residues: 485 loop : -0.17 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 418 TYR 0.025 0.001 TYR C 848 PHE 0.029 0.001 PHE A 901 TRP 0.019 0.001 TRP A 800 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00292 (23934) covalent geometry : angle 0.63660 (32442) hydrogen bonds : bond 0.04048 ( 1505) hydrogen bonds : angle 4.34489 ( 4521) =============================================================================== Job complete usr+sys time: 3714.93 seconds wall clock time: 65 minutes 11.83 seconds (3911.83 seconds total)