Starting phenix.real_space_refine on Tue Sep 15 21:14:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6f44_4183/09_2026/6f44_4183.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f44_4183/09_2026/6f44_4183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6f44_4183/09_2026/6f44_4183.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6f44_4183/09_2026/6f44_4183.cif" model { file = "/net/cci-nas-00/data/ceres_data/6f44_4183/09_2026/6f44_4183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f44_4183/09_2026/6f44_4183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6f44_4183/09_2026/6f44_4183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f44_4183/09_2026/6f44_4183.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 88 5.49 5 S 232 5.16 5 C 28430 2.51 5 N 7830 2.21 5 O 8664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 45251 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 10974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1399, 10974 Classifications: {'peptide': 1399} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1333} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8784 Classifications: {'peptide': 1114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 43, 'TRANS': 1070} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1448 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 255 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1387 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "O" Number of atoms: 4290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4290 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 515} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 827 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain breaks: 2 Chain: "Q" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 273 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 5, 'TRANS': 29} Chain: "U" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Chain: "V" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2674 Classifications: {'peptide': 337} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 326} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "W" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1442 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "X" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "Y" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 908 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 509 SG CYS A 70 90.805 76.996 77.888 1.00154.02 S ATOM 794 SG CYS A 107 73.280 122.472 91.940 1.00165.43 S ATOM 19331 SG CYS B1095 93.599 92.524 70.509 1.00136.71 S ATOM 28419 SG CYS I 5 80.846 127.497 157.591 1.00147.21 S ATOM 28438 SG CYS I 8 80.252 124.054 156.967 1.00133.20 S ATOM 28566 SG CYS I 26 79.692 127.982 154.260 1.00151.32 S ATOM 28712 SG CYS J 10 143.682 50.937 124.325 1.00105.59 S ATOM 28998 SG CYS J 46 143.083 50.369 127.894 1.00122.44 S ATOM 30046 SG CYS L 34 97.848 34.594 126.966 1.00118.72 S ATOM 30150 SG CYS L 48 95.128 37.730 124.312 1.00129.82 S ATOM 39528 SG CYS V 28 107.941 55.829 74.408 1.00277.77 S Time building chain proxies: 8.47, per 1000 atoms: 0.19 Number of scatterers: 45251 At special positions: 0 Unit cell: (201.15, 172.8, 205.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 232 16.00 P 88 15.00 O 8664 8.00 N 7830 7.00 C 28430 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: 3.69 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 34 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 28 " 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10340 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 55 sheets defined 38.6% alpha, 13.1% beta 26 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 5.43 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.973A pdb=" N GLN A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 30' Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.941A pdb=" N GLY A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.759A pdb=" N LYS A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.789A pdb=" N ARG A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 149 removed outlier: 3.515A pdb=" N MET A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.533A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.981A pdb=" N ASP A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 239 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU A 240 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 243 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 4.380A pdb=" N ARG A 252 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.677A pdb=" N TYR A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 306 removed outlier: 5.014A pdb=" N GLU A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 removed outlier: 4.658A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.975A pdb=" N SER A 331 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.868A pdb=" N LYS A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.668A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.647A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.927A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 removed outlier: 4.124A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.698A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.538A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.761A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 685 Processing helix chain 'A' and resid 685 through 709 removed outlier: 4.169A pdb=" N GLU A 689 " --> pdb=" O TYR A 685 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 743 removed outlier: 4.185A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 765 removed outlier: 3.737A pdb=" N LYS A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 784 removed outlier: 4.031A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 777 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 781 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 3.631A pdb=" N ALA A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 797 " --> pdb=" O ILE A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 removed outlier: 3.559A pdb=" N MET A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 874 removed outlier: 4.140A pdb=" N LEU A 862 " --> pdb=" O PRO A 858 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 892 removed outlier: 3.735A pdb=" N LYS A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 889 " --> pdb=" O MET A 885 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 removed outlier: 3.634A pdb=" N ALA A 930 " --> pdb=" O GLU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.642A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 965 removed outlier: 4.145A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 973 removed outlier: 3.863A pdb=" N LEU A 970 " --> pdb=" O ILE A 966 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 972 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 966 through 973' Processing helix chain 'A' and resid 999 through 1026 removed outlier: 3.780A pdb=" N TYR A1011 " --> pdb=" O SER A1007 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A1013 " --> pdb=" O ARG A1009 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A1015 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 removed outlier: 3.804A pdb=" N LYS A1053 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A1057 " --> pdb=" O LYS A1053 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN A1058 " --> pdb=" O THR A1054 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1069 removed outlier: 3.836A pdb=" N ARG A1068 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1081 removed outlier: 3.683A pdb=" N ILE A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1098 Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 5.127A pdb=" N GLU A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A1129 " --> pdb=" O ARG A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1162 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.874A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1211 removed outlier: 3.844A pdb=" N ALA A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 3.749A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A1260 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A1265 " --> pdb=" O GLN A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1306 removed outlier: 3.520A pdb=" N MET A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.898A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.573A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A1339 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A1341 " --> pdb=" O ARG A1337 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A1344 " --> pdb=" O ASN A1340 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1363 removed outlier: 3.794A pdb=" N GLN A1356 " --> pdb=" O PRO A1352 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A1357 " --> pdb=" O ARG A1353 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A1358 " --> pdb=" O HIS A1354 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A1360 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1380 removed outlier: 4.188A pdb=" N LYS A1378 " --> pdb=" O PHE A1374 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1379 " --> pdb=" O GLY A1375 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A1380 " --> pdb=" O LEU A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1388 removed outlier: 3.653A pdb=" N SER A1388 " --> pdb=" O LEU A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1402 removed outlier: 4.119A pdb=" N ASP A1398 " --> pdb=" O ASP A1394 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A1399 " --> pdb=" O HIS A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1418 removed outlier: 3.871A pdb=" N ILE A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.931A pdb=" N SER A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1441 removed outlier: 4.004A pdb=" N ASP A1440 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 47 through 55 removed outlier: 4.020A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.741A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 252 through 257 removed outlier: 4.162A pdb=" N VAL B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 278 through 284 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.807A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.555A pdb=" N GLY B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.638A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 366 removed outlier: 3.615A pdb=" N ILE B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 366' Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 380 through 401 removed outlier: 3.554A pdb=" N SER B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 429 through 439 removed outlier: 3.580A pdb=" N LEU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.650A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 536 removed outlier: 3.781A pdb=" N LYS B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.922A pdb=" N LEU B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 581 removed outlier: 3.936A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 581 " --> pdb=" O HIS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 633 removed outlier: 3.775A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 removed outlier: 3.940A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 removed outlier: 4.365A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.943A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 694 removed outlier: 3.736A pdb=" N HIS B 693 " --> pdb=" O TYR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.827A pdb=" N THR B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 701 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 945 through 947 No H-bonds generated for 'chain 'B' and resid 945 through 947' Processing helix chain 'B' and resid 948 through 953 Processing helix chain 'B' and resid 954 through 970 removed outlier: 4.112A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 995 removed outlier: 3.733A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 993 " --> pdb=" O LYS B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1034 removed outlier: 3.934A pdb=" N ASP B1033 " --> pdb=" O MET B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1073 removed outlier: 3.633A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B1073 " --> pdb=" O CYS B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1082 Processing helix chain 'B' and resid 1123 through 1127 Processing helix chain 'B' and resid 1127 through 1135 removed outlier: 4.382A pdb=" N LEU B1133 " --> pdb=" O PHE B1129 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 60 through 72 removed outlier: 3.711A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.586A pdb=" N LEU C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 309 through 328 removed outlier: 3.674A pdb=" N ILE C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'D' and resid 12 through 26 removed outlier: 3.663A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 4.224A pdb=" N ARG D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 99 through 104 removed outlier: 3.970A pdb=" N PHE D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.814A pdb=" N LEU D 121 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 138 removed outlier: 3.583A pdb=" N ILE D 137 " --> pdb=" O HIS D 133 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 133 through 138' Processing helix chain 'D' and resid 148 through 158 removed outlier: 3.913A pdb=" N LEU D 154 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.555A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.982A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.629A pdb=" N PHE E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.803A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.969A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE E 100 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 4.069A pdb=" N MET E 121 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 165 removed outlier: 3.738A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.575A pdb=" N GLY E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 removed outlier: 3.620A pdb=" N ARG F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.602A pdb=" N ILE F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.658A pdb=" N LYS G 33 " --> pdb=" O GLN G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 211 removed outlier: 3.724A pdb=" N TRP G 210 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP G 211 " --> pdb=" O VAL G 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 207 through 211' Processing helix chain 'I' and resid 18 through 20 No H-bonds generated for 'chain 'I' and resid 18 through 20' Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.782A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.803A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.071A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 50 through 54 removed outlier: 3.511A pdb=" N ALA K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 50 through 54' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.579A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.616A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 131 removed outlier: 3.519A pdb=" N TYR M 131 " --> pdb=" O GLN M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 removed outlier: 3.839A pdb=" N SER M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 198 removed outlier: 3.577A pdb=" N ALA M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 236 removed outlier: 3.715A pdb=" N LYS M 235 " --> pdb=" O LEU M 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 231 through 236' Processing helix chain 'M' and resid 251 through 261 removed outlier: 3.828A pdb=" N ILE M 259 " --> pdb=" O PHE M 255 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS M 261 " --> pdb=" O ASP M 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 278 Processing helix chain 'N' and resid 279 through 297 removed outlier: 3.924A pdb=" N HIS N 287 " --> pdb=" O LEU N 283 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN N 288 " --> pdb=" O ASN N 284 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS N 289 " --> pdb=" O ALA N 285 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG N 292 " --> pdb=" O GLN N 288 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS N 293 " --> pdb=" O HIS N 289 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET N 297 " --> pdb=" O LYS N 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 3.703A pdb=" N THR O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 41' Processing helix chain 'O' and resid 45 through 56 removed outlier: 3.654A pdb=" N GLU O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 61 through 70 removed outlier: 3.557A pdb=" N GLY O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 83 removed outlier: 3.680A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.753A pdb=" N VAL O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 133 removed outlier: 3.610A pdb=" N ILE O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 144 removed outlier: 3.797A pdb=" N ILE O 141 " --> pdb=" O ILE O 137 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 164 removed outlier: 3.611A pdb=" N ALA O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL O 160 " --> pdb=" O VAL O 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN O 161 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE O 164 " --> pdb=" O VAL O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 176 removed outlier: 3.504A pdb=" N LEU O 175 " --> pdb=" O VAL O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 197 removed outlier: 3.856A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 220 removed outlier: 3.878A pdb=" N PHE O 217 " --> pdb=" O ASP O 213 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU O 220 " --> pdb=" O GLN O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 237 Processing helix chain 'O' and resid 238 through 253 removed outlier: 3.989A pdb=" N ASN O 244 " --> pdb=" O GLN O 240 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 258 removed outlier: 4.172A pdb=" N ASN O 257 " --> pdb=" O ILE O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 297 Processing helix chain 'O' and resid 297 through 304 removed outlier: 3.858A pdb=" N LYS O 301 " --> pdb=" O ILE O 297 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 removed outlier: 3.778A pdb=" N LYS O 313 " --> pdb=" O ALA O 309 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA O 315 " --> pdb=" O VAL O 311 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU O 316 " --> pdb=" O TYR O 312 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG O 317 " --> pdb=" O LYS O 313 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 332 Processing helix chain 'O' and resid 338 through 348 removed outlier: 4.345A pdb=" N GLN O 346 " --> pdb=" O ALA O 342 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 355 Processing helix chain 'O' and resid 366 through 370 removed outlier: 3.602A pdb=" N LEU O 370 " --> pdb=" O ALA O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 457 removed outlier: 3.698A pdb=" N ASN O 454 " --> pdb=" O ALA O 450 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 463 removed outlier: 3.622A pdb=" N ALA O 461 " --> pdb=" O LEU O 457 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 500 removed outlier: 3.620A pdb=" N TYR O 492 " --> pdb=" O LYS O 488 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU O 493 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR O 499 " --> pdb=" O VAL O 495 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU O 500 " --> pdb=" O ILE O 496 " (cutoff:3.500A) Processing helix chain 'O' and resid 502 through 514 removed outlier: 3.831A pdb=" N ILE O 511 " --> pdb=" O LEU O 507 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG O 512 " --> pdb=" O SER O 508 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP O 513 " --> pdb=" O ARG O 509 " (cutoff:3.500A) Processing helix chain 'O' and resid 521 through 526 Processing helix chain 'O' and resid 532 through 542 removed outlier: 3.578A pdb=" N SER O 539 " --> pdb=" O SER O 535 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 554 through 558 removed outlier: 4.230A pdb=" N ARG O 557 " --> pdb=" O THR O 554 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER O 558 " --> pdb=" O ALA O 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 554 through 558' Processing helix chain 'O' and resid 571 through 598 removed outlier: 3.726A pdb=" N MET O 577 " --> pdb=" O SER O 573 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU O 581 " --> pdb=" O MET O 577 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN O 584 " --> pdb=" O ASN O 580 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA O 586 " --> pdb=" O GLU O 582 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU O 588 " --> pdb=" O ASN O 584 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU O 595 " --> pdb=" O LYS O 591 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 606 removed outlier: 3.606A pdb=" N LEU O 603 " --> pdb=" O ASN O 599 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS O 604 " --> pdb=" O SER O 600 " (cutoff:3.500A) Processing helix chain 'O' and resid 624 through 649 removed outlier: 3.796A pdb=" N LYS O 628 " --> pdb=" O LEU O 624 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET O 629 " --> pdb=" O ASN O 625 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL O 630 " --> pdb=" O GLN O 626 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN O 631 " --> pdb=" O LEU O 627 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU O 634 " --> pdb=" O VAL O 630 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL O 637 " --> pdb=" O ARG O 633 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG O 643 " --> pdb=" O ALA O 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 650 through 653 removed outlier: 3.763A pdb=" N MET O 653 " --> pdb=" O VAL O 650 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 650 through 653' Processing helix chain 'P' and resid 175 through 188 removed outlier: 3.595A pdb=" N THR P 180 " --> pdb=" O ASN P 176 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP P 183 " --> pdb=" O LEU P 179 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG P 184 " --> pdb=" O THR P 180 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE P 185 " --> pdb=" O ILE P 181 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE P 186 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER P 187 " --> pdb=" O TRP P 183 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU P 188 " --> pdb=" O ARG P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 226 removed outlier: 3.850A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR P 226 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 250 removed outlier: 3.511A pdb=" N ILE P 240 " --> pdb=" O THR P 236 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER P 242 " --> pdb=" O SER P 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU P 245 " --> pdb=" O ARG P 241 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL P 246 " --> pdb=" O SER P 242 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU P 247 " --> pdb=" O LEU P 243 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL P 248 " --> pdb=" O CYS P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 271 Processing helix chain 'Q' and resid 48 through 67 removed outlier: 4.019A pdb=" N SER Q 53 " --> pdb=" O ASN Q 49 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR Q 58 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN Q 60 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE Q 61 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 87 removed outlier: 3.552A pdb=" N ALA U 86 " --> pdb=" O LEU U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 129 through 144 removed outlier: 3.680A pdb=" N LYS U 133 " --> pdb=" O GLU U 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE U 142 " --> pdb=" O LYS U 138 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE U 143 " --> pdb=" O TYR U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 179 Processing helix chain 'U' and resid 221 through 235 removed outlier: 4.106A pdb=" N GLN U 225 " --> pdb=" O GLU U 221 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA U 226 " --> pdb=" O GLU U 222 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU U 228 " --> pdb=" O TYR U 224 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA U 229 " --> pdb=" O GLN U 225 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE U 230 " --> pdb=" O ALA U 226 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR U 231 " --> pdb=" O PHE U 227 " (cutoff:3.500A) Proline residue: U 232 - end of helix Processing helix chain 'V' and resid 74 through 94 removed outlier: 3.657A pdb=" N ARG V 85 " --> pdb=" O ASN V 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS V 86 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG V 88 " --> pdb=" O ARG V 84 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL V 90 " --> pdb=" O LYS V 86 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER V 91 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR V 92 " --> pdb=" O ARG V 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 114 removed outlier: 3.833A pdb=" N THR V 101 " --> pdb=" O PRO V 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA V 103 " --> pdb=" O TYR V 99 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN V 106 " --> pdb=" O ASP V 102 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 137 removed outlier: 3.576A pdb=" N ILE V 126 " --> pdb=" O SER V 122 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS V 129 " --> pdb=" O VAL V 125 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR V 131 " --> pdb=" O ALA V 127 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL V 132 " --> pdb=" O SER V 128 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA V 133 " --> pdb=" O CYS V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 168 removed outlier: 3.995A pdb=" N ILE V 157 " --> pdb=" O SER V 153 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR V 160 " --> pdb=" O SER V 156 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE V 161 " --> pdb=" O ILE V 157 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU V 162 " --> pdb=" O GLY V 158 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS V 163 " --> pdb=" O ALA V 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 186 removed outlier: 3.745A pdb=" N ILE V 182 " --> pdb=" O PRO V 178 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN V 183 " --> pdb=" O SER V 179 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS V 184 " --> pdb=" O LEU V 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA V 186 " --> pdb=" O ILE V 182 " (cutoff:3.500A) Processing helix chain 'V' and resid 195 through 212 Processing helix chain 'V' and resid 219 through 224 Processing helix chain 'V' and resid 226 through 234 removed outlier: 3.705A pdb=" N MET V 234 " --> pdb=" O LEU V 230 " (cutoff:3.500A) Processing helix chain 'V' and resid 244 through 249 Processing helix chain 'V' and resid 251 through 262 removed outlier: 3.538A pdb=" N LEU V 255 " --> pdb=" O ALA V 251 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN V 256 " --> pdb=" O GLU V 252 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG V 258 " --> pdb=" O THR V 254 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE V 262 " --> pdb=" O ARG V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 265 No H-bonds generated for 'chain 'V' and resid 263 through 265' Processing helix chain 'V' and resid 267 through 272 removed outlier: 3.525A pdb=" N SER V 271 " --> pdb=" O ALA V 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 289 through 297 Processing helix chain 'V' and resid 448 through 453 Processing helix chain 'V' and resid 468 through 473 Processing helix chain 'V' and resid 479 through 490 removed outlier: 3.605A pdb=" N GLU V 484 " --> pdb=" O SER V 480 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE V 486 " --> pdb=" O LEU V 482 " (cutoff:3.500A) Processing helix chain 'V' and resid 492 through 510 removed outlier: 4.088A pdb=" N GLU V 499 " --> pdb=" O LEU V 495 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER V 500 " --> pdb=" O LEU V 496 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS V 501 " --> pdb=" O GLU V 497 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 319 removed outlier: 3.815A pdb=" N LEU W 304 " --> pdb=" O LYS W 300 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU W 305 " --> pdb=" O LYS W 301 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG W 307 " --> pdb=" O LYS W 303 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU W 310 " --> pdb=" O LYS W 306 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU W 312 " --> pdb=" O ARG W 308 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG W 314 " --> pdb=" O LEU W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 386 through 394 removed outlier: 4.056A pdb=" N GLU W 390 " --> pdb=" O ASN W 386 " (cutoff:3.500A) Processing helix chain 'W' and resid 421 through 435 removed outlier: 3.901A pdb=" N LYS W 427 " --> pdb=" O GLU W 423 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA W 431 " --> pdb=" O LYS W 427 " (cutoff:3.500A) Processing helix chain 'W' and resid 438 through 446 removed outlier: 4.159A pdb=" N ILE W 442 " --> pdb=" O ASP W 438 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN W 444 " --> pdb=" O ASN W 440 " (cutoff:3.500A) Processing helix chain 'W' and resid 450 through 465 removed outlier: 3.623A pdb=" N VAL W 454 " --> pdb=" O SER W 450 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS W 463 " --> pdb=" O VAL W 459 " (cutoff:3.500A) Processing helix chain 'W' and resid 467 through 475 Processing helix chain 'W' and resid 482 through 490 removed outlier: 3.909A pdb=" N CYS W 486 " --> pdb=" O ASP W 482 " (cutoff:3.500A) Processing helix chain 'W' and resid 500 through 516 removed outlier: 4.680A pdb=" N GLU W 504 " --> pdb=" O GLU W 500 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU W 505 " --> pdb=" O LYS W 501 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN W 506 " --> pdb=" O LEU W 502 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS W 512 " --> pdb=" O GLU W 508 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET W 513 " --> pdb=" O HIS W 509 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS W 514 " --> pdb=" O LYS W 510 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.882A pdb=" N VAL A 32 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA5, first strand: chain 'B' and resid 1037 through 1038 removed outlier: 3.568A pdb=" N ARG B1038 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 376 " --> pdb=" O ARG B1038 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 377 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 519 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 518 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 500 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.611A pdb=" N ARG A 464 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA8, first strand: chain 'A' and resid 625 through 628 Processing sheet with id=AA9, first strand: chain 'A' and resid 896 through 899 removed outlier: 3.504A pdb=" N SER A 897 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 903 " --> pdb=" O GLN A 899 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 912 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1140 through 1144 Processing sheet with id=AB2, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 4.098A pdb=" N LYS A1273 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1170 through 1176 removed outlier: 4.000A pdb=" N TYR A1172 " --> pdb=" O ARG A1187 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A1187 " --> pdb=" O TYR A1172 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1176 " --> pdb=" O PHE A1183 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A1183 " --> pdb=" O VAL A1176 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A1229 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A1225 " --> pdb=" O ARG A1229 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1231 " --> pdb=" O ASN A1223 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A1223 " --> pdb=" O ALA A1231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.657A pdb=" N LYS A1429 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY G 57 " --> pdb=" O LYS A1432 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.591A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU B 93 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR B 136 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 132 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE B 133 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ASP B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR B 135 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS B 144 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.360A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 512 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 205 through 207 removed outlier: 3.594A pdb=" N LYS B 243 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC1, first strand: chain 'B' and resid 560 through 561 removed outlier: 6.077A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 724 through 728 removed outlier: 6.471A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 724 through 728 removed outlier: 6.471A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU L 56 " --> pdb=" O MET B 886 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC5, first strand: chain 'B' and resid 753 through 759 removed outlier: 3.567A pdb=" N GLN B 753 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 911 through 912 removed outlier: 7.318A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 839 through 843 removed outlier: 6.822A pdb=" N ILE B 841 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR B 873 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 871 " --> pdb=" O ILE B 843 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AC9, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id=AD1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AD2, first strand: chain 'C' and resid 41 through 44 removed outlier: 4.240A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.458A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 132 " --> pdb=" O CYS C 208 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 204 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 141 through 142 removed outlier: 4.037A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 161 through 163 removed outlier: 4.152A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 256 through 259 removed outlier: 4.392A pdb=" N GLU C 264 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 2 through 3 removed outlier: 3.916A pdb=" N SER G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA G 74 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR G 47 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY G 43 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 9 through 10 removed outlier: 3.984A pdb=" N ALA D 9 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 4 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA G 74 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 62 removed outlier: 4.165A pdb=" N PHE E 60 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL E 80 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER E 77 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE E 109 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AE2, first strand: chain 'G' and resid 84 through 87 removed outlier: 6.169A pdb=" N ILE G 150 " --> pdb=" O SER G 199 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER G 199 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG G 152 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA G 195 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 95 through 96 removed outlier: 6.588A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU H 126 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP H 41 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 14 through 16 removed outlier: 3.686A pdb=" N THR I 23 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 60 through 66 Processing sheet with id=AE6, first strand: chain 'K' and resid 60 through 66 Processing sheet with id=AE7, first strand: chain 'M' and resid 152 through 154 removed outlier: 6.339A pdb=" N LEU M 85 " --> pdb=" O ARG M 175 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA M 177 " --> pdb=" O LEU M 85 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL M 87 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER M 84 " --> pdb=" O ILE N 399 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE N 395 " --> pdb=" O PHE M 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP N 393 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL N 394 " --> pdb=" O ARG N 411 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG N 411 " --> pdb=" O VAL N 394 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA N 396 " --> pdb=" O LEU N 409 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER N 398 " --> pdb=" O GLU N 407 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU N 407 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE N 304 " --> pdb=" O ASP N 413 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS N 415 " --> pdb=" O PHE N 304 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL N 306 " --> pdb=" O LYS N 415 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL N 417 " --> pdb=" O VAL N 306 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN N 308 " --> pdb=" O VAL N 417 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR N 419 " --> pdb=" O GLN N 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE M 162 " --> pdb=" O TYR M 169 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR M 169 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N VAL M 168 " --> pdb=" O GLU M 73 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LEU M 170 " --> pdb=" O PRO M 75 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 247 through 248 Processing sheet with id=AE9, first strand: chain 'M' and resid 110 through 112 removed outlier: 4.002A pdb=" N ALA M 110 " --> pdb=" O LEU M 245 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE M 243 " --> pdb=" O TYR M 112 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 120 through 121 removed outlier: 3.623A pdb=" N ILE M 121 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 104 through 106 removed outlier: 3.615A pdb=" N LYS O 105 " --> pdb=" O TYR O 121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 109 through 110 Processing sheet with id=AF4, first strand: chain 'O' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'O' and resid 264 through 265 removed outlier: 3.526A pdb=" N ILE O 273 " --> pdb=" O THR O 264 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 549 through 552 Processing sheet with id=AF7, first strand: chain 'P' and resid 253 through 256 Processing sheet with id=AF8, first strand: chain 'U' and resid 103 through 105 removed outlier: 3.817A pdb=" N MET U 121 " --> pdb=" O VAL U 74 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY U 125 " --> pdb=" O ILE U 70 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE U 70 " --> pdb=" O GLY U 125 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL U 161 " --> pdb=" O GLN U 68 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE U 70 " --> pdb=" O ASN U 159 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN U 159 " --> pdb=" O ILE U 70 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA U 72 " --> pdb=" O ILE U 157 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE U 157 " --> pdb=" O ALA U 72 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE U 160 " --> pdb=" O GLY U 216 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 193 through 197 Processing sheet with id=AG1, first strand: chain 'V' and resid 12 through 14 removed outlier: 6.844A pdb=" N LEU V 23 " --> pdb=" O SER V 32 " (cutoff:3.500A) 1226 hydrogen bonds defined for protein. 3462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 12.34 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14314 1.34 - 1.46: 6418 1.46 - 1.58: 24965 1.58 - 1.69: 174 1.69 - 1.81: 373 Bond restraints: 46244 Sorted by residual: bond pdb=" C3' DG Y 65 " pdb=" C2' DG Y 65 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT Y 60 " pdb=" C2' DT Y 60 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DA Y 55 " pdb=" C2' DA Y 55 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DA Y 59 " pdb=" C2' DA Y 59 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA X 26 " pdb=" C2' DA X 26 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.56e+00 ... (remaining 46239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 61749 2.14 - 4.28: 915 4.28 - 6.43: 104 6.43 - 8.57: 25 8.57 - 10.71: 5 Bond angle restraints: 62798 Sorted by residual: angle pdb=" N PRO M 202 " pdb=" CA PRO M 202 " pdb=" CB PRO M 202 " ideal model delta sigma weight residual 103.25 110.40 -7.15 1.05e+00 9.07e-01 4.64e+01 angle pdb=" N PRO M 204 " pdb=" CA PRO M 204 " pdb=" CB PRO M 204 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.56e+01 angle pdb=" O4' DA X 22 " pdb=" C4' DA X 22 " pdb=" C3' DA X 22 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.22e+01 angle pdb=" N3 DT X 8 " pdb=" C4 DT X 8 " pdb=" O4 DT X 8 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT Y 63 " pdb=" C4 DT Y 63 " pdb=" O4 DT Y 63 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 62793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 27100 31.01 - 62.02: 1050 62.02 - 93.04: 42 93.04 - 124.05: 1 124.05 - 155.06: 2 Dihedral angle restraints: 28195 sinusoidal: 12244 harmonic: 15951 Sorted by residual: dihedral pdb=" CA CYS A 70 " pdb=" C CYS A 70 " pdb=" N HIS A 71 " pdb=" CA HIS A 71 " ideal model delta harmonic sigma weight residual 180.00 140.44 39.56 0 5.00e+00 4.00e-02 6.26e+01 dihedral pdb=" CA PHE W 284 " pdb=" C PHE W 284 " pdb=" N PRO W 285 " pdb=" CA PRO W 285 " ideal model delta harmonic sigma weight residual 180.00 145.22 34.78 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" CA GLU P 234 " pdb=" C GLU P 234 " pdb=" N LEU P 235 " pdb=" CA LEU P 235 " ideal model delta harmonic sigma weight residual 180.00 147.38 32.62 0 5.00e+00 4.00e-02 4.26e+01 ... (remaining 28192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 5828 0.053 - 0.106: 1092 0.106 - 0.159: 163 0.159 - 0.212: 4 0.212 - 0.265: 2 Chirality restraints: 7089 Sorted by residual: chirality pdb=" CA PRO M 202 " pdb=" N PRO M 202 " pdb=" C PRO M 202 " pdb=" CB PRO M 202 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA PRO M 204 " pdb=" N PRO M 204 " pdb=" C PRO M 204 " pdb=" CB PRO M 204 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE E 127 " pdb=" CA ILE E 127 " pdb=" CG1 ILE E 127 " pdb=" CG2 ILE E 127 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 7086 not shown) Planarity restraints: 7763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE W 284 " -0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO W 285 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO W 285 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO W 285 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS U 199 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO U 200 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO U 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO U 200 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1351 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A1352 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1352 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1352 " 0.035 5.00e-02 4.00e+02 ... (remaining 7760 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 3 2.02 - 2.74: 3400 2.74 - 3.46: 65148 3.46 - 4.18: 104701 4.18 - 4.90: 176274 Nonbonded interactions: 349526 Sorted by model distance: nonbonded pdb=" N CYS V 28 " pdb="ZN ZN V1001 " model vdw 1.297 2.310 nonbonded pdb=" CA CYS A 107 " pdb="ZN ZN A1502 " model vdw 1.529 2.128 nonbonded pdb=" O LYS B1097 " pdb="ZN ZN B2000 " model vdw 1.784 2.230 nonbonded pdb=" N CYS A 107 " pdb="ZN ZN A1502 " model vdw 2.075 2.310 nonbonded pdb=" C CYS A 107 " pdb="ZN ZN A1502 " model vdw 2.108 2.460 ... (remaining 349521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 50.690 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.009 1.258 46256 Z= 0.344 Angle : 0.634 10.711 62798 Z= 0.394 Chirality : 0.042 0.265 7089 Planarity : 0.006 0.075 7763 Dihedral : 14.741 155.058 17855 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.50 % Favored : 90.46 % Rotamer: Outliers : 0.85 % Allowed : 9.47 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.10 % 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: -4.81 (0.09), residues: 5387 helix: -3.97 (0.07), residues: 1629 sheet: -2.70 (0.19), residues: 569 loop : -2.95 (0.09), residues: 3189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG U 171 TYR 0.017 0.001 TYR O 494 PHE 0.019 0.001 PHE V 215 TRP 0.017 0.001 TRP B 442 HIS 0.010 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.17 (46244) covalent geometry : angle 0.63393 / 0.39 (62798) hydrogen bonds : bond 0.31071 / 20.64 ( 1255) hydrogen bonds : angle 10.40335 / 7.10 ( 3576) metal coordination : bond 0.55297 / 35.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 619 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.9491 (mt) cc_final: 0.9000 (tt) REVERT: A 58 MET cc_start: 0.9075 (ttm) cc_final: 0.8812 (tpp) REVERT: A 128 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7458 (mtt90) REVERT: A 138 MET cc_start: 0.8403 (mtp) cc_final: 0.8109 (mtp) REVERT: A 242 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9255 (mm) REVERT: A 351 ARG cc_start: 0.8418 (mtp180) cc_final: 0.7775 (mmm160) REVERT: A 535 MET cc_start: 0.8565 (mtm) cc_final: 0.8353 (mtm) REVERT: A 545 LYS cc_start: 0.9247 (ttpt) cc_final: 0.8765 (mttp) REVERT: A 809 MET cc_start: 0.8498 (mtp) cc_final: 0.8181 (mtt) REVERT: A 869 ARG cc_start: 0.8675 (tpp80) cc_final: 0.8139 (tpp-160) REVERT: A 890 MET cc_start: 0.9208 (tpt) cc_final: 0.9007 (tpp) REVERT: A 907 SER cc_start: 0.8867 (p) cc_final: 0.8546 (m) REVERT: A 926 MET cc_start: 0.8269 (mtp) cc_final: 0.7821 (ttp) REVERT: A 940 ASP cc_start: 0.9272 (m-30) cc_final: 0.8375 (t0) REVERT: A 1165 LEU cc_start: 0.8342 (tp) cc_final: 0.8004 (pt) REVERT: A 1260 MET cc_start: 0.7977 (ptt) cc_final: 0.7631 (ppp) REVERT: A 1343 MET cc_start: 0.8575 (ttp) cc_final: 0.8078 (tpp) REVERT: B 152 MET cc_start: 0.9225 (tpp) cc_final: 0.8992 (tpp) REVERT: B 213 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.4694 (mmmm) REVERT: B 269 MET cc_start: 0.8568 (tpp) cc_final: 0.8344 (tpp) REVERT: B 312 MET cc_start: 0.6620 (tmm) cc_final: 0.6237 (ppp) REVERT: B 358 MET cc_start: 0.8860 (mtp) cc_final: 0.8538 (mtm) REVERT: B 398 ASP cc_start: 0.8974 (t0) cc_final: 0.8720 (t0) REVERT: B 401 LEU cc_start: 0.9326 (mt) cc_final: 0.9091 (tt) REVERT: B 655 ASN cc_start: 0.8398 (m110) cc_final: 0.8059 (m-40) REVERT: B 707 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8897 (mttp) REVERT: B 834 MET cc_start: 0.8347 (ptp) cc_final: 0.8058 (ptp) REVERT: B 885 MET cc_start: 0.9125 (pp-130) cc_final: 0.8596 (ppp) REVERT: B 892 ASP cc_start: 0.8589 (t70) cc_final: 0.7983 (t0) REVERT: B 931 MET cc_start: 0.9307 (mmm) cc_final: 0.8943 (mmm) REVERT: B 1136 ASN cc_start: 0.8215 (t160) cc_final: 0.7995 (m110) REVERT: C 107 LYS cc_start: 0.8438 (ttmm) cc_final: 0.7987 (tptm) REVERT: D 100 ASP cc_start: 0.8458 (p0) cc_final: 0.8184 (p0) REVERT: E 18 THR cc_start: 0.8946 (m) cc_final: 0.8701 (p) REVERT: E 58 MET cc_start: 0.5244 (pmt) cc_final: 0.5036 (pmm) REVERT: E 93 MET cc_start: 0.7997 (pmt) cc_final: 0.7613 (pmm) REVERT: E 116 ILE cc_start: 0.7833 (tp) cc_final: 0.7480 (tp) REVERT: F 115 THR cc_start: 0.8490 (m) cc_final: 0.7916 (t) REVERT: F 116 ASP cc_start: 0.8513 (t70) cc_final: 0.8223 (t70) REVERT: F 119 ARG cc_start: 0.9100 (ttm110) cc_final: 0.8872 (ttp-110) REVERT: G 31 ASN cc_start: 0.8543 (m-40) cc_final: 0.8285 (m110) REVERT: H 20 TYR cc_start: 0.8237 (m-80) cc_final: 0.7912 (m-80) REVERT: H 116 TYR cc_start: 0.9028 (m-80) cc_final: 0.8637 (m-80) REVERT: J 32 GLU cc_start: 0.9263 (mp0) cc_final: 0.8943 (mp0) REVERT: J 49 MET cc_start: 0.9624 (mmm) cc_final: 0.9347 (mmt) REVERT: K 47 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8958 (mp) REVERT: K 67 GLU cc_start: 0.8760 (tt0) cc_final: 0.8032 (tm-30) REVERT: K 76 LEU cc_start: 0.9449 (tp) cc_final: 0.9154 (tt) REVERT: K 81 MET cc_start: 0.8775 (tpp) cc_final: 0.8473 (tpt) REVERT: K 98 GLU cc_start: 0.9144 (pt0) cc_final: 0.8638 (pm20) REVERT: N 281 GLU cc_start: 0.8504 (pp20) cc_final: 0.7948 (pm20) REVERT: N 395 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6603 (mm) REVERT: O 541 ILE cc_start: 0.8967 (mp) cc_final: 0.8582 (tp) REVERT: P 271 MET cc_start: 0.8131 (pp-130) cc_final: 0.7885 (ppp) REVERT: P 306 ASP cc_start: 0.7743 (t0) cc_final: 0.7351 (p0) REVERT: U 106 ILE cc_start: 0.5682 (OUTLIER) cc_final: 0.5463 (pp) REVERT: V 22 ASP cc_start: 0.6758 (m-30) cc_final: 0.6404 (m-30) REVERT: V 102 ASP cc_start: 0.9100 (m-30) cc_final: 0.8747 (p0) REVERT: V 106 GLN cc_start: 0.8798 (mp10) cc_final: 0.8441 (mp10) REVERT: V 144 ILE cc_start: 0.9367 (pt) cc_final: 0.9094 (pt) REVERT: V 188 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8259 (mmmm) REVERT: W 425 MET cc_start: 0.8088 (mmp) cc_final: 0.7867 (mmm) outliers start: 41 outliers final: 8 residues processed: 655 average time/residue: 0.2811 time to fit residues: 301.8796 Evaluate side-chains 348 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 335 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 30.0000 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS A 208 ASN A 367 ASN A 386 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A 533 ASN A 578 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN A 692 ASN A 805 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS A 864 HIS A 964 ASN A1040 GLN A1058 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 HIS A1419 GLN B 116 HIS B 203 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN B 434 ASN B 519 HIS B 558 ASN B 574 GLN B 577 HIS B 596 GLN B 600 HIS B 655 ASN B 693 HIS B 803 GLN B 821 HIS ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 175 GLN C 234 ASN ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 174 GLN G 31 ASN G 143 ASN H 21 ASN J 26 GLN ** K 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN M 117 HIS M 178 GLN M 190 ASN O 56 HIS O 147 ASN O 207 HIS O 244 ASN O 332 GLN O 575 ASN O 584 ASN P 258 HIS P 305 HIS ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 ASN U 144 GLN V 6 ASN ** V 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 391 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.067093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049597 restraints weight = 291910.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050806 restraints weight = 164163.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051579 restraints weight = 112229.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.052073 restraints weight = 88086.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.052325 restraints weight = 75811.817| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 46256 Z= 0.220 Angle : 0.774 9.669 62798 Z= 0.406 Chirality : 0.048 0.333 7089 Planarity : 0.006 0.061 7763 Dihedral : 15.396 154.469 6924 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.37 % Favored : 91.61 % Rotamer: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -3.80 (0.10), residues: 5387 helix: -2.50 (0.10), residues: 1750 sheet: -2.35 (0.19), residues: 615 loop : -2.63 (0.10), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG V 502 TYR 0.028 0.002 TYR E 211 PHE 0.025 0.002 PHE A 557 TRP 0.019 0.002 TRP B 442 HIS 0.018 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 (46244) covalent geometry : angle 0.77389 / 0.41 (62798) hydrogen bonds : bond 0.06407 / 4.34 ( 1255) hydrogen bonds : angle 6.65443 / 4.51 ( 3576) metal coordination : bond 0.03764 / 2.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 441 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.9542 (mt) cc_final: 0.9157 (tt) REVERT: A 58 MET cc_start: 0.9003 (ttm) cc_final: 0.8801 (tpp) REVERT: A 193 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7531 (pm20) REVERT: A 217 ARG cc_start: 0.8201 (tpm170) cc_final: 0.7673 (tmm-80) REVERT: A 325 MET cc_start: 0.9150 (tpp) cc_final: 0.8771 (tpp) REVERT: A 351 ARG cc_start: 0.8421 (mtp180) cc_final: 0.7840 (mmm160) REVERT: A 525 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 545 LYS cc_start: 0.9289 (ttpt) cc_final: 0.8758 (mttp) REVERT: A 869 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8356 (tpt170) REVERT: A 926 MET cc_start: 0.8026 (mtp) cc_final: 0.7826 (ttp) REVERT: A 929 ASN cc_start: 0.8952 (t0) cc_final: 0.8455 (t0) REVERT: A 940 ASP cc_start: 0.9273 (m-30) cc_final: 0.8558 (t0) REVERT: A 1165 LEU cc_start: 0.8396 (tp) cc_final: 0.8034 (pt) REVERT: A 1304 MET cc_start: 0.8580 (mmp) cc_final: 0.8292 (mmt) REVERT: A 1343 MET cc_start: 0.8584 (ttp) cc_final: 0.8287 (tpp) REVERT: B 312 MET cc_start: 0.7481 (tmm) cc_final: 0.6486 (ppp) REVERT: B 358 MET cc_start: 0.8949 (mtp) cc_final: 0.8693 (mtm) REVERT: B 476 GLN cc_start: 0.7638 (pm20) cc_final: 0.7127 (pp30) REVERT: B 834 MET cc_start: 0.8302 (ptp) cc_final: 0.8066 (ptp) REVERT: B 892 ASP cc_start: 0.8465 (t70) cc_final: 0.7990 (t0) REVERT: B 953 MET cc_start: 0.8867 (mtt) cc_final: 0.8563 (mtt) REVERT: B 1035 MET cc_start: 0.7991 (ttp) cc_final: 0.7769 (ttp) REVERT: E 22 MET cc_start: 0.9335 (tmm) cc_final: 0.9000 (tmm) REVERT: E 93 MET cc_start: 0.8318 (ptt) cc_final: 0.8019 (ptt) REVERT: F 85 MET cc_start: 0.8201 (tmm) cc_final: 0.7986 (tmm) REVERT: F 115 THR cc_start: 0.8426 (m) cc_final: 0.7914 (t) REVERT: F 116 ASP cc_start: 0.8082 (t70) cc_final: 0.7684 (t70) REVERT: G 205 MET cc_start: 0.3705 (mmm) cc_final: 0.3011 (tpp) REVERT: H 20 TYR cc_start: 0.7999 (m-80) cc_final: 0.7757 (m-80) REVERT: J 32 GLU cc_start: 0.9140 (mp0) cc_final: 0.8911 (mp0) REVERT: K 121 LEU cc_start: 0.9419 (pp) cc_final: 0.9152 (tp) REVERT: N 279 GLU cc_start: 0.8803 (pp20) cc_final: 0.8430 (pm20) REVERT: N 281 GLU cc_start: 0.8227 (pp20) cc_final: 0.7672 (pm20) REVERT: N 380 MET cc_start: 0.8543 (tpt) cc_final: 0.8272 (mmm) REVERT: O 37 LEU cc_start: 0.9091 (tt) cc_final: 0.8796 (pp) REVERT: O 330 LEU cc_start: 0.8172 (tt) cc_final: 0.7752 (pp) REVERT: P 251 ASP cc_start: 0.7996 (t70) cc_final: 0.7705 (t70) REVERT: P 305 HIS cc_start: 0.7615 (m90) cc_final: 0.7376 (m-70) REVERT: P 306 ASP cc_start: 0.8062 (t0) cc_final: 0.7425 (p0) REVERT: U 206 ILE cc_start: 0.9466 (pt) cc_final: 0.9173 (mp) REVERT: V 234 MET cc_start: 0.8574 (ppp) cc_final: 0.8109 (ppp) REVERT: V 259 LEU cc_start: 0.8071 (tt) cc_final: 0.7809 (mt) REVERT: W 425 MET cc_start: 0.8433 (mmp) cc_final: 0.8181 (mmm) outliers start: 9 outliers final: 2 residues processed: 448 average time/residue: 0.2566 time to fit residues: 195.5015 Evaluate side-chains 311 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 502 optimal weight: 9.9990 chunk 318 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 528 optimal weight: 1.9990 chunk 534 optimal weight: 9.9990 chunk 521 optimal weight: 0.0970 chunk 286 optimal weight: 4.9990 chunk 397 optimal weight: 6.9990 chunk 524 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS B 225 HIS B 382 GLN B 596 GLN B 753 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 175 GLN ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 174 GLN G 143 ASN H 21 ASN K 70 HIS O 43 ASN O 321 GLN P 258 HIS ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 219 GLN V 20 ASN V 140 HIS V 184 HIS ** V 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.067158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.049693 restraints weight = 290493.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050879 restraints weight = 163820.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051642 restraints weight = 111924.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.052133 restraints weight = 87859.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052380 restraints weight = 75677.013| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 46256 Z= 0.168 Angle : 0.687 10.676 62798 Z= 0.359 Chirality : 0.046 0.262 7089 Planarity : 0.005 0.060 7763 Dihedral : 15.270 151.255 6924 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.32 % Favored : 91.67 % Rotamer: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -3.32 (0.10), residues: 5387 helix: -1.90 (0.11), residues: 1777 sheet: -2.04 (0.19), residues: 633 loop : -2.47 (0.10), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG M 111 TYR 0.018 0.001 TYR B 658 PHE 0.017 0.001 PHE U 168 TRP 0.018 0.001 TRP A 201 HIS 0.015 0.001 HIS P 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (46244) covalent geometry : angle 0.68674 / 0.36 (62798) hydrogen bonds : bond 0.05500 / 3.71 ( 1255) hydrogen bonds : angle 6.03268 / 4.10 ( 3576) metal coordination : bond 0.00634 / 0.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 403 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8879 (ttm) cc_final: 0.8671 (tpp) REVERT: A 193 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7213 (tm-30) REVERT: A 217 ARG cc_start: 0.8183 (tpm170) cc_final: 0.7679 (tmm-80) REVERT: A 325 MET cc_start: 0.9188 (tpp) cc_final: 0.8830 (tpp) REVERT: A 351 ARG cc_start: 0.8387 (mtp180) cc_final: 0.7789 (mmm160) REVERT: A 525 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 545 LYS cc_start: 0.9317 (ttpt) cc_final: 0.8811 (mttp) REVERT: A 869 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8213 (tpt170) REVERT: A 940 ASP cc_start: 0.9164 (m-30) cc_final: 0.8569 (t0) REVERT: A 1165 LEU cc_start: 0.8378 (tp) cc_final: 0.8066 (pt) REVERT: A 1304 MET cc_start: 0.8631 (mmp) cc_final: 0.8331 (mmm) REVERT: A 1343 MET cc_start: 0.8588 (ttp) cc_final: 0.8242 (tpp) REVERT: B 358 MET cc_start: 0.9029 (mtp) cc_final: 0.8775 (mtm) REVERT: B 760 MET cc_start: 0.8916 (ptm) cc_final: 0.8312 (ppp) REVERT: B 834 MET cc_start: 0.8243 (ptp) cc_final: 0.8041 (ptp) REVERT: B 892 ASP cc_start: 0.8443 (t70) cc_final: 0.8005 (t0) REVERT: B 953 MET cc_start: 0.8841 (mtt) cc_final: 0.8591 (mtt) REVERT: E 22 MET cc_start: 0.9393 (tmm) cc_final: 0.9115 (tmm) REVERT: E 93 MET cc_start: 0.8600 (ptt) cc_final: 0.8332 (ptt) REVERT: G 29 GLN cc_start: 0.9439 (tm-30) cc_final: 0.9111 (tm-30) REVERT: G 205 MET cc_start: 0.3400 (mmm) cc_final: 0.2940 (tpp) REVERT: H 123 MET cc_start: 0.8949 (ppp) cc_final: 0.8636 (ppp) REVERT: J 32 GLU cc_start: 0.9198 (mp0) cc_final: 0.8979 (mp0) REVERT: K 121 LEU cc_start: 0.9484 (pp) cc_final: 0.8959 (tp) REVERT: M 178 GLN cc_start: 0.8408 (mt0) cc_final: 0.8111 (mt0) REVERT: N 279 GLU cc_start: 0.8787 (pp20) cc_final: 0.8546 (pp20) REVERT: N 380 MET cc_start: 0.8487 (tpt) cc_final: 0.8220 (mmm) REVERT: O 330 LEU cc_start: 0.8226 (tt) cc_final: 0.7788 (pp) REVERT: P 251 ASP cc_start: 0.8170 (t70) cc_final: 0.7807 (t70) REVERT: P 305 HIS cc_start: 0.7748 (m90) cc_final: 0.7438 (m-70) REVERT: P 306 ASP cc_start: 0.7983 (t0) cc_final: 0.7375 (p0) REVERT: U 206 ILE cc_start: 0.9460 (pt) cc_final: 0.9195 (mp) REVERT: V 234 MET cc_start: 0.8672 (ppp) cc_final: 0.8235 (ppp) outliers start: 2 outliers final: 0 residues processed: 405 average time/residue: 0.2410 time to fit residues: 168.4101 Evaluate side-chains 308 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 70 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 146 optimal weight: 0.0980 chunk 437 optimal weight: 0.0270 chunk 10 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 423 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 overall best weight: 4.8244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN B 596 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 175 GLN ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN G 143 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 GLN O 310 GLN ** O 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 607 ASN ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 ASN V 118 GLN ** V 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.065722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.048227 restraints weight = 293936.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.049390 restraints weight = 165056.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.050100 restraints weight = 113313.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.050610 restraints weight = 89560.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050913 restraints weight = 77393.945| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 46256 Z= 0.214 Angle : 0.712 11.254 62798 Z= 0.370 Chirality : 0.047 0.301 7089 Planarity : 0.005 0.052 7763 Dihedral : 15.218 152.898 6924 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.13 % Favored : 90.85 % Rotamer: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -3.05 (0.10), residues: 5387 helix: -1.57 (0.11), residues: 1786 sheet: -1.94 (0.19), residues: 649 loop : -2.37 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 95 TYR 0.027 0.002 TYR E 211 PHE 0.040 0.002 PHE O 249 TRP 0.022 0.002 TRP O 215 HIS 0.008 0.001 HIS O 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (46244) covalent geometry : angle 0.71173 / 0.37 (62798) hydrogen bonds : bond 0.04805 / 3.25 ( 1255) hydrogen bonds : angle 5.80946 / 3.96 ( 3576) metal coordination : bond 0.00289 / 0.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8889 (ttm) cc_final: 0.8649 (tpp) REVERT: A 193 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7331 (pm20) REVERT: A 217 ARG cc_start: 0.8213 (tpm170) cc_final: 0.7606 (tmm-80) REVERT: A 325 MET cc_start: 0.9245 (tpp) cc_final: 0.8598 (tpp) REVERT: A 351 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7656 (mmm160) REVERT: A 525 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 545 LYS cc_start: 0.9341 (ttpt) cc_final: 0.8939 (mttp) REVERT: A 869 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8209 (tpt170) REVERT: A 940 ASP cc_start: 0.9168 (m-30) cc_final: 0.8542 (t0) REVERT: A 960 MET cc_start: 0.9263 (mmm) cc_final: 0.9013 (mmm) REVERT: A 1165 LEU cc_start: 0.8398 (tp) cc_final: 0.8109 (pt) REVERT: A 1304 MET cc_start: 0.8765 (mmp) cc_final: 0.8497 (mmm) REVERT: A 1343 MET cc_start: 0.8606 (ttp) cc_final: 0.8202 (tpp) REVERT: A 1403 MET cc_start: 0.8989 (mmt) cc_final: 0.8780 (mmt) REVERT: B 358 MET cc_start: 0.9150 (mtp) cc_final: 0.8847 (mtm) REVERT: B 496 MET cc_start: 0.9071 (mmm) cc_final: 0.8862 (mmm) REVERT: G 29 GLN cc_start: 0.9496 (tm-30) cc_final: 0.9137 (tm-30) REVERT: I 11 MET cc_start: 0.7485 (tpp) cc_final: 0.7118 (tpp) REVERT: J 32 GLU cc_start: 0.9251 (mp0) cc_final: 0.9039 (mp0) REVERT: K 121 LEU cc_start: 0.9521 (pp) cc_final: 0.8981 (tp) REVERT: M 178 GLN cc_start: 0.8475 (mt0) cc_final: 0.8176 (mt0) REVERT: N 380 MET cc_start: 0.8523 (tpt) cc_final: 0.8264 (mmm) REVERT: O 326 ILE cc_start: 0.3832 (OUTLIER) cc_final: 0.3140 (mt) REVERT: O 585 MET cc_start: 0.9283 (mmp) cc_final: 0.9032 (mmt) REVERT: P 251 ASP cc_start: 0.8200 (t70) cc_final: 0.7816 (t70) REVERT: P 305 HIS cc_start: 0.7692 (m90) cc_final: 0.7391 (m-70) REVERT: P 306 ASP cc_start: 0.8105 (t0) cc_final: 0.7449 (p0) REVERT: U 206 ILE cc_start: 0.9473 (pt) cc_final: 0.9260 (mp) outliers start: 2 outliers final: 0 residues processed: 387 average time/residue: 0.2535 time to fit residues: 169.6383 Evaluate side-chains 293 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 331 optimal weight: 30.0000 chunk 386 optimal weight: 20.0000 chunk 212 optimal weight: 0.9980 chunk 466 optimal weight: 3.9990 chunk 355 optimal weight: 6.9990 chunk 462 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN A 931 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 382 GLN B 596 GLN B 753 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 GLN C 65 ASN C 175 GLN C 297 HIS ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 174 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 GLN ** O 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 258 HIS ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 509 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.066235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048746 restraints weight = 291092.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.049910 restraints weight = 163545.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050667 restraints weight = 112215.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.051139 restraints weight = 88337.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.051437 restraints weight = 76525.857| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 46256 Z= 0.151 Angle : 0.673 11.273 62798 Z= 0.347 Chirality : 0.046 0.303 7089 Planarity : 0.004 0.053 7763 Dihedral : 15.129 151.151 6924 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.26 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.83 (0.11), residues: 5387 helix: -1.37 (0.11), residues: 1783 sheet: -1.78 (0.20), residues: 621 loop : -2.27 (0.11), residues: 2983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 314 TYR 0.022 0.001 TYR A1402 PHE 0.028 0.001 PHE V 215 TRP 0.033 0.002 TRP M 140 HIS 0.018 0.001 HIS P 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (46244) covalent geometry : angle 0.67294 / 0.35 (62798) hydrogen bonds : bond 0.04382 / 2.95 ( 1255) hydrogen bonds : angle 5.55781 / 3.79 ( 3576) metal coordination : bond 0.00362 / 0.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8872 (ttm) cc_final: 0.8574 (tpp) REVERT: A 193 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7224 (pm20) REVERT: A 217 ARG cc_start: 0.8188 (tpm170) cc_final: 0.7537 (tmm-80) REVERT: A 325 MET cc_start: 0.9259 (tpp) cc_final: 0.8552 (tpp) REVERT: A 351 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7601 (mmm160) REVERT: A 545 LYS cc_start: 0.9335 (ttpt) cc_final: 0.8902 (mttp) REVERT: A 929 ASN cc_start: 0.8728 (t0) cc_final: 0.8142 (t0) REVERT: A 960 MET cc_start: 0.9256 (mmm) cc_final: 0.8951 (mmm) REVERT: A 1165 LEU cc_start: 0.8315 (tp) cc_final: 0.8044 (pt) REVERT: A 1304 MET cc_start: 0.8782 (mmp) cc_final: 0.8501 (mmm) REVERT: A 1343 MET cc_start: 0.8605 (ttp) cc_final: 0.8244 (tpp) REVERT: A 1403 MET cc_start: 0.8914 (mmt) cc_final: 0.8697 (mmt) REVERT: B 312 MET cc_start: 0.7235 (tmm) cc_final: 0.7022 (tmm) REVERT: B 352 MET cc_start: 0.9473 (ttm) cc_final: 0.9151 (ttm) REVERT: B 358 MET cc_start: 0.9132 (mtp) cc_final: 0.8839 (mtm) REVERT: B 670 MET cc_start: 0.7780 (tpp) cc_final: 0.7452 (tpt) REVERT: B 760 MET cc_start: 0.9052 (ptm) cc_final: 0.8155 (ppp) REVERT: B 953 MET cc_start: 0.8684 (mtt) cc_final: 0.8397 (mtt) REVERT: B 1035 MET cc_start: 0.8031 (ttp) cc_final: 0.7696 (ttm) REVERT: D 98 MET cc_start: 0.2630 (mtt) cc_final: 0.2168 (mtm) REVERT: G 29 GLN cc_start: 0.9518 (tm-30) cc_final: 0.9133 (tm-30) REVERT: I 11 MET cc_start: 0.7556 (tpp) cc_final: 0.7241 (tpp) REVERT: J 32 GLU cc_start: 0.9225 (mp0) cc_final: 0.9019 (mp0) REVERT: K 121 LEU cc_start: 0.9552 (pp) cc_final: 0.8939 (tp) REVERT: M 178 GLN cc_start: 0.8112 (mt0) cc_final: 0.7842 (mt0) REVERT: N 380 MET cc_start: 0.8516 (tpt) cc_final: 0.8246 (mmm) REVERT: O 86 MET cc_start: 0.2856 (mmt) cc_final: 0.2618 (mmt) REVERT: O 585 MET cc_start: 0.9252 (mmp) cc_final: 0.8953 (mmt) REVERT: P 251 ASP cc_start: 0.8234 (t70) cc_final: 0.7822 (t70) REVERT: P 305 HIS cc_start: 0.7665 (m90) cc_final: 0.7326 (m-70) REVERT: P 306 ASP cc_start: 0.8020 (t0) cc_final: 0.7383 (p0) REVERT: U 206 ILE cc_start: 0.9466 (pt) cc_final: 0.9258 (mp) REVERT: W 484 TYR cc_start: 0.8773 (t80) cc_final: 0.8364 (t80) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2506 time to fit residues: 165.2404 Evaluate side-chains 290 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 503 optimal weight: 9.9990 chunk 529 optimal weight: 6.9990 chunk 428 optimal weight: 0.0170 chunk 207 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 467 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 51 optimal weight: 0.1980 chunk 202 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 828 GLN A 934 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN B 596 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 175 GLN D 27 HIS E 174 GLN O 108 GLN ** O 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.067449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049927 restraints weight = 292853.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.051135 restraints weight = 162762.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051930 restraints weight = 110905.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.052432 restraints weight = 86782.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052647 restraints weight = 74704.284| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 46256 Z= 0.116 Angle : 0.665 10.718 62798 Z= 0.336 Chirality : 0.046 0.287 7089 Planarity : 0.004 0.046 7763 Dihedral : 14.951 147.960 6924 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.70 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.69 (0.11), residues: 5387 helix: -1.21 (0.12), residues: 1799 sheet: -1.68 (0.20), residues: 629 loop : -2.22 (0.11), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 111 TYR 0.020 0.001 TYR W 411 PHE 0.019 0.001 PHE V 215 TRP 0.018 0.001 TRP M 140 HIS 0.008 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (46244) covalent geometry : angle 0.66548 / 0.34 (62798) hydrogen bonds : bond 0.04019 / 2.68 ( 1255) hydrogen bonds : angle 5.23284 / 3.56 ( 3576) metal coordination : bond 0.01023 / 0.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8863 (ttm) cc_final: 0.8506 (tpp) REVERT: A 193 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7164 (pm20) REVERT: A 217 ARG cc_start: 0.8263 (tpm170) cc_final: 0.7804 (ttp-170) REVERT: A 325 MET cc_start: 0.9289 (tpp) cc_final: 0.8833 (mmp) REVERT: A 351 ARG cc_start: 0.8229 (mtp180) cc_final: 0.7635 (mmm160) REVERT: A 809 MET cc_start: 0.7911 (mtp) cc_final: 0.7555 (mtp) REVERT: A 929 ASN cc_start: 0.8823 (t0) cc_final: 0.8283 (t0) REVERT: A 960 MET cc_start: 0.9290 (mmm) cc_final: 0.8990 (mmm) REVERT: A 1165 LEU cc_start: 0.8253 (tp) cc_final: 0.8013 (pt) REVERT: A 1304 MET cc_start: 0.8786 (mmp) cc_final: 0.8549 (mmm) REVERT: A 1343 MET cc_start: 0.8653 (ttp) cc_final: 0.8289 (tpp) REVERT: A 1403 MET cc_start: 0.8861 (mmt) cc_final: 0.8612 (mmt) REVERT: B 269 MET cc_start: 0.8184 (mmm) cc_final: 0.7852 (tpt) REVERT: B 358 MET cc_start: 0.9077 (mtp) cc_final: 0.8783 (mtm) REVERT: B 370 ASP cc_start: 0.8238 (m-30) cc_final: 0.7483 (t0) REVERT: B 578 LEU cc_start: 0.9238 (tt) cc_final: 0.8983 (pp) REVERT: B 670 MET cc_start: 0.7814 (tpp) cc_final: 0.7494 (tpt) REVERT: B 705 MET cc_start: 0.8639 (mtt) cc_final: 0.8435 (mtp) REVERT: B 760 MET cc_start: 0.8972 (ptm) cc_final: 0.8070 (ppp) REVERT: B 939 VAL cc_start: 0.9403 (t) cc_final: 0.9137 (p) REVERT: B 953 MET cc_start: 0.8625 (mtt) cc_final: 0.8247 (mtt) REVERT: B 1035 MET cc_start: 0.8017 (ttp) cc_final: 0.7675 (ttm) REVERT: D 98 MET cc_start: 0.2934 (mtt) cc_final: 0.2322 (mtm) REVERT: E 50 MET cc_start: -0.0004 (mtm) cc_final: -0.0208 (ppp) REVERT: E 211 TYR cc_start: 0.8299 (m-10) cc_final: 0.8062 (m-10) REVERT: G 29 GLN cc_start: 0.9531 (tm-30) cc_final: 0.9117 (tm-30) REVERT: G 205 MET cc_start: 0.4621 (mmm) cc_final: 0.3865 (tpp) REVERT: H 106 GLU cc_start: 0.8042 (pp20) cc_final: 0.7836 (pp20) REVERT: I 11 MET cc_start: 0.7530 (tpp) cc_final: 0.7249 (tpp) REVERT: J 49 MET cc_start: 0.9237 (mmt) cc_final: 0.8855 (mtp) REVERT: K 121 LEU cc_start: 0.9515 (pp) cc_final: 0.8996 (tp) REVERT: M 144 ASN cc_start: 0.8742 (t0) cc_final: 0.7991 (m110) REVERT: M 178 GLN cc_start: 0.8151 (mt0) cc_final: 0.7889 (mt0) REVERT: N 380 MET cc_start: 0.8584 (tpt) cc_final: 0.8341 (mmm) REVERT: P 251 ASP cc_start: 0.8376 (t70) cc_final: 0.7985 (t70) REVERT: P 305 HIS cc_start: 0.7795 (m90) cc_final: 0.7437 (m-70) REVERT: P 306 ASP cc_start: 0.8120 (t0) cc_final: 0.7373 (p0) REVERT: U 206 ILE cc_start: 0.9443 (pt) cc_final: 0.9238 (mp) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.2507 time to fit residues: 177.9295 Evaluate side-chains 308 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 446 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 405 optimal weight: 4.9990 chunk 466 optimal weight: 6.9990 chunk 500 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 288 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 520 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 828 GLN A 834 HIS ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 175 GLN E 174 GLN G 31 ASN O 108 GLN O 321 GLN ** O 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 258 HIS ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.065798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048240 restraints weight = 293087.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049409 restraints weight = 164363.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050154 restraints weight = 112735.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050616 restraints weight = 88963.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050919 restraints weight = 77097.799| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 46256 Z= 0.183 Angle : 0.686 10.725 62798 Z= 0.353 Chirality : 0.046 0.285 7089 Planarity : 0.004 0.048 7763 Dihedral : 14.931 150.024 6924 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.72 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.57 (0.11), residues: 5387 helix: -1.04 (0.12), residues: 1799 sheet: -1.69 (0.20), residues: 636 loop : -2.17 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 610 TYR 0.018 0.001 TYR E 211 PHE 0.027 0.001 PHE V 215 TRP 0.021 0.002 TRP C 31 HIS 0.010 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (46244) covalent geometry : angle 0.68634 / 0.35 (62798) hydrogen bonds : bond 0.04199 / 2.84 ( 1255) hydrogen bonds : angle 5.26863 / 3.59 ( 3576) metal coordination : bond 0.00253 / 0.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8921 (ttm) cc_final: 0.8590 (tpp) REVERT: A 193 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7237 (pm20) REVERT: A 217 ARG cc_start: 0.8232 (tpm170) cc_final: 0.7613 (tmm-80) REVERT: A 309 ILE cc_start: 0.8003 (tt) cc_final: 0.7742 (tp) REVERT: A 321 LEU cc_start: 0.9231 (tt) cc_final: 0.9007 (pp) REVERT: A 325 MET cc_start: 0.9174 (tpp) cc_final: 0.8747 (mmp) REVERT: A 351 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7571 (mmm160) REVERT: A 809 MET cc_start: 0.7990 (mtp) cc_final: 0.7654 (mtp) REVERT: A 940 ASP cc_start: 0.9120 (m-30) cc_final: 0.8529 (t0) REVERT: A 960 MET cc_start: 0.9276 (mmm) cc_final: 0.8939 (tmm) REVERT: A 1028 MET cc_start: 0.7887 (tpt) cc_final: 0.7657 (tpt) REVERT: A 1092 ILE cc_start: 0.9533 (pt) cc_final: 0.9262 (mm) REVERT: A 1165 LEU cc_start: 0.8286 (tp) cc_final: 0.8024 (pt) REVERT: A 1304 MET cc_start: 0.8820 (mmp) cc_final: 0.8535 (mmm) REVERT: A 1343 MET cc_start: 0.8619 (ttp) cc_final: 0.8260 (tpp) REVERT: A 1403 MET cc_start: 0.8921 (mmt) cc_final: 0.8667 (mmt) REVERT: B 312 MET cc_start: 0.7430 (tmm) cc_final: 0.6877 (tmm) REVERT: B 358 MET cc_start: 0.9135 (mtp) cc_final: 0.8855 (mtm) REVERT: B 370 ASP cc_start: 0.8214 (m-30) cc_final: 0.7417 (t0) REVERT: B 760 MET cc_start: 0.9064 (ptm) cc_final: 0.8188 (ppp) REVERT: B 953 MET cc_start: 0.8666 (mtt) cc_final: 0.8347 (mtt) REVERT: B 1035 MET cc_start: 0.8234 (ttp) cc_final: 0.7861 (ttm) REVERT: D 7 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7731 (mmm-85) REVERT: G 29 GLN cc_start: 0.9507 (tm-30) cc_final: 0.9105 (tm-30) REVERT: K 121 LEU cc_start: 0.9519 (pp) cc_final: 0.9075 (tp) REVERT: M 144 ASN cc_start: 0.8685 (t0) cc_final: 0.7958 (m110) REVERT: M 178 GLN cc_start: 0.8117 (mt0) cc_final: 0.7854 (mt0) REVERT: O 653 MET cc_start: 0.9172 (tpp) cc_final: 0.8874 (tpp) REVERT: P 251 ASP cc_start: 0.8449 (t70) cc_final: 0.8099 (t70) REVERT: P 305 HIS cc_start: 0.7808 (m90) cc_final: 0.7439 (m-70) REVERT: P 306 ASP cc_start: 0.8092 (t0) cc_final: 0.7338 (p0) REVERT: U 206 ILE cc_start: 0.9458 (pt) cc_final: 0.9219 (mp) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2493 time to fit residues: 160.4538 Evaluate side-chains 289 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 304 optimal weight: 10.0000 chunk 360 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 233 optimal weight: 8.9990 chunk 353 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 230 optimal weight: 0.1980 chunk 116 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 416 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 828 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 175 GLN E 174 GLN O 108 GLN ** O 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 258 HIS ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 235 ASN ** V 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.066517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.049082 restraints weight = 293615.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050588 restraints weight = 171401.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051114 restraints weight = 104305.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.051224 restraints weight = 84502.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051324 restraints weight = 85448.606| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46256 Z= 0.129 Angle : 0.665 11.429 62798 Z= 0.338 Chirality : 0.045 0.322 7089 Planarity : 0.004 0.089 7763 Dihedral : 14.866 148.589 6924 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.00 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.43 (0.11), residues: 5387 helix: -0.91 (0.12), residues: 1787 sheet: -1.60 (0.20), residues: 616 loop : -2.11 (0.11), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1265 TYR 0.017 0.001 TYR E 28 PHE 0.028 0.001 PHE G 77 TRP 0.022 0.001 TRP E 79 HIS 0.008 0.001 HIS P 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (46244) covalent geometry : angle 0.66528 / 0.34 (62798) hydrogen bonds : bond 0.03829 / 2.56 ( 1255) hydrogen bonds : angle 5.15045 / 3.52 ( 3576) metal coordination : bond 0.00175 / 0.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.784 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8876 (ttm) cc_final: 0.8557 (tpp) REVERT: A 193 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7201 (pm20) REVERT: A 217 ARG cc_start: 0.8226 (tpm170) cc_final: 0.7644 (tmm-80) REVERT: A 273 MET cc_start: 0.4756 (mmp) cc_final: 0.4408 (mmp) REVERT: A 309 ILE cc_start: 0.7981 (tt) cc_final: 0.7731 (tp) REVERT: A 321 LEU cc_start: 0.9217 (tt) cc_final: 0.8997 (pp) REVERT: A 325 MET cc_start: 0.9196 (tpp) cc_final: 0.8761 (mmp) REVERT: A 351 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7663 (mmm160) REVERT: A 694 MET cc_start: 0.8223 (tmm) cc_final: 0.7987 (tmm) REVERT: A 940 ASP cc_start: 0.9055 (m-30) cc_final: 0.8563 (t0) REVERT: A 960 MET cc_start: 0.9343 (mmm) cc_final: 0.9042 (tmm) REVERT: A 1028 MET cc_start: 0.7800 (tpt) cc_final: 0.7540 (tpt) REVERT: A 1165 LEU cc_start: 0.8274 (tp) cc_final: 0.8060 (pt) REVERT: A 1304 MET cc_start: 0.8816 (mmp) cc_final: 0.8545 (mmm) REVERT: A 1343 MET cc_start: 0.8665 (ttp) cc_final: 0.8300 (tpp) REVERT: A 1403 MET cc_start: 0.8840 (mmt) cc_final: 0.8571 (mmt) REVERT: B 269 MET cc_start: 0.8194 (mmm) cc_final: 0.7731 (tpt) REVERT: B 358 MET cc_start: 0.9106 (mtp) cc_final: 0.8847 (mtm) REVERT: B 370 ASP cc_start: 0.8268 (m-30) cc_final: 0.7428 (t0) REVERT: B 578 LEU cc_start: 0.9202 (tt) cc_final: 0.8934 (pp) REVERT: B 670 MET cc_start: 0.7825 (tpp) cc_final: 0.7500 (tpt) REVERT: B 760 MET cc_start: 0.9055 (ptm) cc_final: 0.8119 (ppp) REVERT: B 953 MET cc_start: 0.8626 (mtt) cc_final: 0.8294 (mtt) REVERT: D 7 ARG cc_start: 0.8058 (tpp80) cc_final: 0.7747 (mmm-85) REVERT: D 98 MET cc_start: 0.3065 (mtt) cc_final: 0.2532 (mtm) REVERT: E 50 MET cc_start: 0.2564 (ppp) cc_final: 0.2218 (ptp) REVERT: G 205 MET cc_start: 0.4733 (mmm) cc_final: 0.3675 (tpp) REVERT: K 121 LEU cc_start: 0.9474 (pp) cc_final: 0.9002 (tp) REVERT: M 144 ASN cc_start: 0.8704 (t0) cc_final: 0.7891 (m110) REVERT: M 178 GLN cc_start: 0.8159 (mt0) cc_final: 0.7885 (mt0) REVERT: P 251 ASP cc_start: 0.8431 (t70) cc_final: 0.8080 (t70) REVERT: P 305 HIS cc_start: 0.7808 (m90) cc_final: 0.7462 (m-70) REVERT: P 306 ASP cc_start: 0.8082 (t0) cc_final: 0.7244 (p0) REVERT: U 206 ILE cc_start: 0.9447 (pt) cc_final: 0.9211 (mp) REVERT: W 484 TYR cc_start: 0.8756 (t80) cc_final: 0.8359 (t80) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2482 time to fit residues: 164.7387 Evaluate side-chains 292 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 321 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 518 optimal weight: 20.0000 chunk 503 optimal weight: 9.9990 chunk 378 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 431 optimal weight: 7.9990 chunk 402 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 GLN C 65 ASN C 175 GLN E 174 GLN H 11 GLN M 104 HIS O 108 GLN O 147 ASN ** O 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 523 ASN O 652 GLN P 258 HIS ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 506 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.063942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046710 restraints weight = 302274.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048205 restraints weight = 179414.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048428 restraints weight = 109596.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048802 restraints weight = 91867.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048784 restraints weight = 101945.240| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 46256 Z= 0.290 Angle : 0.795 10.832 62798 Z= 0.411 Chirality : 0.048 0.348 7089 Planarity : 0.005 0.075 7763 Dihedral : 14.988 152.627 6924 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.15 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.58 (0.11), residues: 5387 helix: -1.04 (0.12), residues: 1805 sheet: -1.75 (0.20), residues: 586 loop : -2.18 (0.11), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 245 TYR 0.030 0.002 TYR B1024 PHE 0.034 0.002 PHE W 498 TRP 0.032 0.003 TRP E 79 HIS 0.015 0.002 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.29 (46244) covalent geometry : angle 0.79474 / 0.41 (62798) hydrogen bonds : bond 0.04699 / 3.18 ( 1255) hydrogen bonds : angle 5.48015 / 3.75 ( 3576) metal coordination : bond 0.00372 / 0.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.824 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 193 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7173 (pm20) REVERT: A 217 ARG cc_start: 0.8101 (tpm170) cc_final: 0.7403 (tmm-80) REVERT: A 273 MET cc_start: 0.5299 (mmp) cc_final: 0.5035 (mmp) REVERT: A 274 MET cc_start: 0.4715 (ptt) cc_final: 0.4500 (ptt) REVERT: A 309 ILE cc_start: 0.8122 (tt) cc_final: 0.7879 (tp) REVERT: A 321 LEU cc_start: 0.9251 (tt) cc_final: 0.9031 (pp) REVERT: A 325 MET cc_start: 0.9349 (tpp) cc_final: 0.8930 (mmp) REVERT: A 351 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7702 (mmm160) REVERT: A 525 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 1028 MET cc_start: 0.7951 (tpt) cc_final: 0.7604 (tpt) REVERT: A 1092 ILE cc_start: 0.9582 (pt) cc_final: 0.9337 (mm) REVERT: A 1165 LEU cc_start: 0.8315 (tp) cc_final: 0.8069 (pt) REVERT: A 1304 MET cc_start: 0.8749 (mmp) cc_final: 0.8473 (mmm) REVERT: A 1343 MET cc_start: 0.8730 (ttp) cc_final: 0.8176 (tpp) REVERT: A 1403 MET cc_start: 0.8944 (mmt) cc_final: 0.8685 (mmt) REVERT: B 143 MET cc_start: 0.8232 (tmm) cc_final: 0.7927 (tmm) REVERT: B 312 MET cc_start: 0.7626 (tmm) cc_final: 0.7031 (tmm) REVERT: B 358 MET cc_start: 0.9223 (mtp) cc_final: 0.8924 (mtm) REVERT: B 370 ASP cc_start: 0.8456 (m-30) cc_final: 0.7513 (t0) REVERT: B 494 PHE cc_start: 0.9019 (t80) cc_final: 0.8757 (t80) REVERT: B 760 MET cc_start: 0.9170 (ptm) cc_final: 0.8168 (ppp) REVERT: B 809 MET cc_start: 0.8524 (mtm) cc_final: 0.8146 (mtt) REVERT: B 931 MET cc_start: 0.9038 (mmm) cc_final: 0.8705 (mmm) REVERT: B 953 MET cc_start: 0.8736 (mtt) cc_final: 0.8419 (mtt) REVERT: C 71 MET cc_start: 0.8116 (mtm) cc_final: 0.7889 (mtm) REVERT: D 98 MET cc_start: 0.2975 (mtt) cc_final: 0.2594 (mtt) REVERT: E 2 ASP cc_start: 0.9134 (p0) cc_final: 0.8000 (t0) REVERT: E 50 MET cc_start: 0.2453 (ppp) cc_final: 0.2096 (ptp) REVERT: G 205 MET cc_start: 0.4995 (mmm) cc_final: 0.4064 (tpp) REVERT: K 121 LEU cc_start: 0.9595 (pp) cc_final: 0.8900 (tp) REVERT: M 159 TYR cc_start: 0.9172 (m-10) cc_final: 0.8879 (m-10) REVERT: P 251 ASP cc_start: 0.8435 (t70) cc_final: 0.8110 (t70) REVERT: P 305 HIS cc_start: 0.7708 (m90) cc_final: 0.7452 (m-70) REVERT: P 306 ASP cc_start: 0.8334 (t0) cc_final: 0.7342 (p0) REVERT: U 114 LEU cc_start: 0.9304 (tp) cc_final: 0.9098 (tp) REVERT: U 206 ILE cc_start: 0.9459 (pt) cc_final: 0.9230 (mp) REVERT: W 484 TYR cc_start: 0.8616 (t80) cc_final: 0.8173 (t80) REVERT: W 500 GLU cc_start: 0.8535 (pp20) cc_final: 0.8265 (tp30) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2460 time to fit residues: 145.6065 Evaluate side-chains 266 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 419 optimal weight: 9.9990 chunk 523 optimal weight: 10.0000 chunk 331 optimal weight: 40.0000 chunk 412 optimal weight: 20.0000 chunk 502 optimal weight: 0.7980 chunk 396 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 368 optimal weight: 2.9990 chunk 462 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 450 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 828 GLN ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 HIS ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 175 GLN E 174 GLN O 108 GLN ** O 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.047752 restraints weight = 298208.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049207 restraints weight = 176225.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.049772 restraints weight = 108638.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049850 restraints weight = 88526.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.049928 restraints weight = 89609.997| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 46256 Z= 0.168 Angle : 0.712 11.442 62798 Z= 0.364 Chirality : 0.047 0.301 7089 Planarity : 0.004 0.073 7763 Dihedral : 14.925 150.868 6924 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.56 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.46 (0.11), residues: 5387 helix: -0.95 (0.12), residues: 1819 sheet: -1.72 (0.21), residues: 569 loop : -2.09 (0.11), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1265 TYR 0.023 0.001 TYR A1402 PHE 0.032 0.002 PHE A 123 TRP 0.024 0.002 TRP B 819 HIS 0.007 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (46244) covalent geometry : angle 0.71241 / 0.36 (62798) hydrogen bonds : bond 0.04012 / 2.68 ( 1255) hydrogen bonds : angle 5.27779 / 3.61 ( 3576) metal coordination : bond 0.00128 / 0.07 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10774 Ramachandran restraints generated. 5387 Oldfield, 0 Emsley, 5387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.733 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 193 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7214 (pm20) REVERT: A 217 ARG cc_start: 0.8057 (tpm170) cc_final: 0.7297 (tmm-80) REVERT: A 273 MET cc_start: 0.5187 (mmp) cc_final: 0.4722 (mmt) REVERT: A 274 MET cc_start: 0.4555 (ptt) cc_final: 0.4343 (ptt) REVERT: A 309 ILE cc_start: 0.8128 (tt) cc_final: 0.7904 (tp) REVERT: A 321 LEU cc_start: 0.9242 (tt) cc_final: 0.9009 (pp) REVERT: A 325 MET cc_start: 0.9266 (tpp) cc_final: 0.8843 (mmp) REVERT: A 351 ARG cc_start: 0.8240 (mtp180) cc_final: 0.7672 (mmm160) REVERT: A 694 MET cc_start: 0.8385 (tmm) cc_final: 0.8030 (tmm) REVERT: A 794 MET cc_start: 0.8923 (ptp) cc_final: 0.8679 (ptm) REVERT: A 809 MET cc_start: 0.7962 (mtp) cc_final: 0.7670 (mtp) REVERT: A 1028 MET cc_start: 0.7817 (tpt) cc_final: 0.7473 (tpt) REVERT: A 1092 ILE cc_start: 0.9548 (pt) cc_final: 0.9310 (mm) REVERT: A 1165 LEU cc_start: 0.8591 (tp) cc_final: 0.8256 (pt) REVERT: A 1304 MET cc_start: 0.8733 (mmp) cc_final: 0.8450 (mmm) REVERT: A 1343 MET cc_start: 0.8645 (ttp) cc_final: 0.8213 (tpp) REVERT: A 1403 MET cc_start: 0.8897 (mmt) cc_final: 0.8636 (mmt) REVERT: B 143 MET cc_start: 0.8403 (tmm) cc_final: 0.8115 (tmm) REVERT: B 226 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7251 (mm-30) REVERT: B 358 MET cc_start: 0.9152 (mtp) cc_final: 0.8857 (mtm) REVERT: B 370 ASP cc_start: 0.8458 (m-30) cc_final: 0.7488 (t0) REVERT: B 494 PHE cc_start: 0.9016 (t80) cc_final: 0.8701 (t80) REVERT: B 578 LEU cc_start: 0.9272 (tt) cc_final: 0.8984 (pp) REVERT: B 705 MET cc_start: 0.8456 (mtt) cc_final: 0.8118 (mtp) REVERT: B 760 MET cc_start: 0.9112 (ptm) cc_final: 0.8133 (ppp) REVERT: B 809 MET cc_start: 0.8515 (mtm) cc_final: 0.8050 (mtt) REVERT: B 931 MET cc_start: 0.9054 (mmm) cc_final: 0.8725 (mmm) REVERT: B 953 MET cc_start: 0.8666 (mtt) cc_final: 0.8401 (mtt) REVERT: D 98 MET cc_start: 0.2747 (mtt) cc_final: 0.2453 (mtt) REVERT: E 2 ASP cc_start: 0.9122 (p0) cc_final: 0.7962 (t0) REVERT: F 85 MET cc_start: 0.8528 (tmm) cc_final: 0.8089 (tmm) REVERT: G 31 ASN cc_start: 0.9271 (m-40) cc_final: 0.8955 (m-40) REVERT: G 205 MET cc_start: 0.4929 (mmm) cc_final: 0.4023 (tpp) REVERT: J 55 ASP cc_start: 0.7729 (t70) cc_final: 0.7149 (t0) REVERT: K 121 LEU cc_start: 0.9554 (pp) cc_final: 0.8952 (tp) REVERT: M 144 ASN cc_start: 0.8766 (t0) cc_final: 0.8301 (m110) REVERT: M 159 TYR cc_start: 0.9140 (m-10) cc_final: 0.8857 (m-10) REVERT: N 380 MET cc_start: 0.8570 (tpt) cc_final: 0.8320 (tpp) REVERT: P 251 ASP cc_start: 0.8420 (t70) cc_final: 0.8085 (t70) REVERT: P 268 ILE cc_start: 0.8185 (pt) cc_final: 0.7938 (pt) REVERT: P 269 LEU cc_start: 0.7913 (mp) cc_final: 0.7373 (tt) REVERT: P 305 HIS cc_start: 0.7721 (m90) cc_final: 0.7429 (m-70) REVERT: P 306 ASP cc_start: 0.8284 (t0) cc_final: 0.7325 (p0) REVERT: U 114 LEU cc_start: 0.9254 (tp) cc_final: 0.9019 (tp) REVERT: U 206 ILE cc_start: 0.9459 (pt) cc_final: 0.9253 (mp) REVERT: V 234 MET cc_start: 0.9117 (ppp) cc_final: 0.8419 (ppp) REVERT: W 484 TYR cc_start: 0.8609 (t80) cc_final: 0.8153 (t80) REVERT: W 500 GLU cc_start: 0.8586 (pp20) cc_final: 0.8348 (tp30) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2435 time to fit residues: 150.2811 Evaluate side-chains 272 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 289 optimal weight: 0.4980 chunk 219 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 457 optimal weight: 9.9990 chunk 319 optimal weight: 0.9990 chunk 428 optimal weight: 0.2980 chunk 522 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 306 optimal weight: 0.5980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 828 GLN ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 175 GLN E 174 GLN H 11 GLN O 108 GLN ** O 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 258 HIS ** U 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.066640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049142 restraints weight = 292415.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.050340 restraints weight = 163251.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.051101 restraints weight = 111392.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051590 restraints weight = 87597.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051850 restraints weight = 75675.568| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 46256 Z= 0.120 Angle : 0.697 13.646 62798 Z= 0.349 Chirality : 0.046 0.341 7089 Planarity : 0.004 0.073 7763 Dihedral : 14.712 147.080 6924 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.96 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: -2.26 (0.11), residues: 5387 helix: -0.80 (0.12), residues: 1814 sheet: -1.54 (0.21), residues: 578 loop : -1.98 (0.11), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG V 440 TYR 0.019 0.001 TYR E 46 PHE 0.025 0.001 PHE A 123 TRP 0.022 0.001 TRP E 79 HIS 0.011 0.001 HIS P 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (46244) covalent geometry : angle 0.69676 / 0.35 (62798) hydrogen bonds : bond 0.03774 / 2.49 ( 1255) hydrogen bonds : angle 5.02598 / 3.42 ( 3576) metal coordination : bond 0.00107 / 0.06 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7696.85 seconds wall clock time: 134 minutes 9.69 seconds (8049.69 seconds total)