Starting phenix.real_space_refine on Mon Aug 10 01:50:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iqi_35671/08_2026/8iqi_35671.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iqi_35671/08_2026/8iqi_35671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iqi_35671/08_2026/8iqi_35671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iqi_35671/08_2026/8iqi_35671.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iqi_35671/08_2026/8iqi_35671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iqi_35671/08_2026/8iqi_35671.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8iqi_35671/08_2026/8iqi_35671.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iqi_35671/08_2026/8iqi_35671.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 P 25 5.49 5 Mg 4 5.21 5 S 139 5.16 5 C 25602 2.51 5 N 7134 2.21 5 O 7528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 174 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40432 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 6625 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 869} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 935 Unresolved non-hydrogen angles: 1194 Unresolved non-hydrogen dihedrals: 775 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'HIS:plan': 13, 'ASP:plan': 9, 'GLN:plan1': 14, 'ARG:plan': 12, 'TYR:plan': 13, 'GLU:plan': 23, 'PHE:plan': 10, 'ASN:plan1': 11} Unresolved non-hydrogen planarities: 484 Chain: "B" Number of atoms: 6699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 6699 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 870} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 857 Unresolved non-hydrogen angles: 1094 Unresolved non-hydrogen dihedrals: 713 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'HIS:plan': 12, 'ASP:plan': 9, 'GLN:plan1': 13, 'ARG:plan': 12, 'TYR:plan': 12, 'GLU:plan': 18, 'PHE:plan': 10, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 445 Chain: "C" Number of atoms: 6699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 6699 Classifications: {'peptide': 916} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 871} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 865 Unresolved non-hydrogen angles: 1106 Unresolved non-hydrogen dihedrals: 717 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'HIS:plan': 12, 'ASP:plan': 9, 'GLN:plan1': 13, 'ARG:plan': 12, 'TYR:plan': 12, 'GLU:plan': 18, 'PHE:plan': 10, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 445 Chain: "D" Number of atoms: 6720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 6720 Classifications: {'peptide': 916} Incomplete info: {'truncation_to_alanine': 240} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 871} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 844 Unresolved non-hydrogen angles: 1079 Unresolved non-hydrogen dihedrals: 702 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'HIS:plan': 12, 'ASP:plan': 9, 'GLN:plan1': 13, 'ARG:plan': 10, 'TYR:plan': 12, 'GLU:plan': 18, 'PHE:plan': 10, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 435 Chain: "E" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 6664 Classifications: {'peptide': 916} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 871} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 901 Unresolved non-hydrogen angles: 1153 Unresolved non-hydrogen dihedrals: 745 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'HIS:plan': 12, 'ASP:plan': 9, 'GLN:plan1': 13, 'ARG:plan': 12, 'TYR:plan': 13, 'GLU:plan': 20, 'PHE:plan': 10, 'ASN:plan1': 12} Unresolved non-hydrogen planarities: 466 Chain: "F" Number of atoms: 6647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6647 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 246} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 865} Chain breaks: 3 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 870 Unresolved non-hydrogen angles: 1111 Unresolved non-hydrogen dihedrals: 724 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'HIS:plan': 12, 'ASP:plan': 10, 'GLN:plan1': 13, 'ARG:plan': 11, 'TYR:plan': 12, 'GLU:plan': 19, 'PHE:plan': 11, 'ASN:plan1': 11} Unresolved non-hydrogen planarities: 456 Chain: "G" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ANP%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.09, per 1000 atoms: 0.25 Number of scatterers: 40432 At special positions: 0 Unit cell: (196.9, 190.3, 190.3, 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) S 139 16.00 P 25 15.00 Mg 4 11.99 O 7528 8.00 N 7134 7.00 C 25602 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: 3.64 Conformation dependent library (CDL) restraints added in 2.0 seconds 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10508 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 58 sheets defined 52.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 removed outlier: 3.908A pdb=" N GLN A 13 " --> pdb=" O HIS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 61 through 78 Processing helix chain 'A' and resid 111 through 130 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 180 through 191 Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.227A pdb=" N ALA A 204 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 285 through 297 removed outlier: 3.903A pdb=" N LEU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.671A pdb=" N ASN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.776A pdb=" N ILE A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 removed outlier: 3.636A pdb=" N GLU A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.651A pdb=" N SER A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.796A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 4.199A pdb=" N SER A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 520 through 535 removed outlier: 4.455A pdb=" N PHE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.506A pdb=" N THR A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 657 removed outlier: 3.618A pdb=" N MET A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP A 655 " --> pdb=" O MET A 651 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N HIS A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 701 through 710 removed outlier: 3.564A pdb=" N ASN A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 787 through 810 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 818 through 831 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 850 removed outlier: 4.031A pdb=" N GLU A 850 " --> pdb=" O PRO A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 870 Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 886 through 892 removed outlier: 6.783A pdb=" N LEU A 889 " --> pdb=" O ASN A 886 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 890 " --> pdb=" O SER A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 945 Processing helix chain 'B' and resid 10 through 21 removed outlier: 4.163A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 61 through 78 Processing helix chain 'B' and resid 111 through 130 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 200 through 205 removed outlier: 4.410A pdb=" N ALA B 204 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 288 through 297 removed outlier: 3.539A pdb=" N HIS B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.561A pdb=" N ASN B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 317 through 332 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.569A pdb=" N SER B 366 " --> pdb=" O TRP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.855A pdb=" N ILE B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 409 Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.711A pdb=" N SER B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 494 removed outlier: 4.134A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 removed outlier: 4.193A pdb=" N SER B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 520 through 535 removed outlier: 4.568A pdb=" N PHE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.565A pdb=" N THR B 620 " --> pdb=" O PHE B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 654 removed outlier: 3.753A pdb=" N LEU B 645 " --> pdb=" O GLY B 641 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 650 " --> pdb=" O MET B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 701 through 709 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.524A pdb=" N TRP B 750 " --> pdb=" O ASP B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 783 Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 787 through 810 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 818 through 833 Processing helix chain 'B' and resid 833 through 842 Processing helix chain 'B' and resid 855 through 870 Processing helix chain 'B' and resid 876 through 885 Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 61 through 78 removed outlier: 3.538A pdb=" N GLN C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 130 Processing helix chain 'C' and resid 167 through 179 Processing helix chain 'C' and resid 180 through 190 removed outlier: 3.873A pdb=" N GLN C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 removed outlier: 3.514A pdb=" N ALA C 204 " --> pdb=" O PRO C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.548A pdb=" N LYS C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 317 through 332 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 353 through 366 removed outlier: 3.871A pdb=" N SER C 366 " --> pdb=" O TRP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 386 removed outlier: 3.847A pdb=" N ILE C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 410 Processing helix chain 'C' and resid 414 through 427 Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.617A pdb=" N SER C 474 " --> pdb=" O HIS C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 494 removed outlier: 4.232A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 516 removed outlier: 4.264A pdb=" N SER C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 520 through 535 removed outlier: 4.300A pdb=" N PHE C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 605 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.610A pdb=" N THR C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 657 removed outlier: 3.877A pdb=" N MET C 646 " --> pdb=" O LYS C 642 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 650 " --> pdb=" O MET C 646 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP C 655 " --> pdb=" O MET C 651 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N HIS C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 677 through 682 Processing helix chain 'C' and resid 701 through 709 removed outlier: 3.520A pdb=" N GLU C 707 " --> pdb=" O SER C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 787 through 810 Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 818 through 833 Processing helix chain 'C' and resid 833 through 842 Processing helix chain 'C' and resid 855 through 870 Processing helix chain 'C' and resid 876 through 886 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.222A pdb=" N LYS C 891 " --> pdb=" O VAL C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 945 Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 34 through 37 removed outlier: 4.274A pdb=" N VAL D 37 " --> pdb=" O GLU D 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 34 through 37' Processing helix chain 'D' and resid 61 through 78 removed outlier: 3.868A pdb=" N GLN D 78 " --> pdb=" O GLN D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 Processing helix chain 'D' and resid 166 through 180 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 200 through 205 removed outlier: 4.439A pdb=" N ALA D 204 " --> pdb=" O PRO D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.557A pdb=" N TYR D 250 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 317 through 332 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 374 through 386 removed outlier: 3.762A pdb=" N ILE D 378 " --> pdb=" O THR D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 409 Processing helix chain 'D' and resid 414 through 427 removed outlier: 3.723A pdb=" N VAL D 421 " --> pdb=" O MET D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 476 removed outlier: 3.601A pdb=" N SER D 474 " --> pdb=" O HIS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 494 removed outlier: 3.564A pdb=" N MET D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 removed outlier: 4.158A pdb=" N SER D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 520 through 535 removed outlier: 4.442A pdb=" N PHE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 605 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.596A pdb=" N THR D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 657 removed outlier: 3.562A pdb=" N VAL D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 650 " --> pdb=" O MET D 646 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP D 655 " --> pdb=" O MET D 651 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N HIS D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 667 Processing helix chain 'D' and resid 677 through 682 Processing helix chain 'D' and resid 701 through 709 Processing helix chain 'D' and resid 746 through 751 Processing helix chain 'D' and resid 778 through 783 Processing helix chain 'D' and resid 787 through 810 Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 818 through 833 Processing helix chain 'D' and resid 833 through 842 Processing helix chain 'D' and resid 855 through 870 Processing helix chain 'D' and resid 876 through 885 removed outlier: 3.699A pdb=" N GLN D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 891 No H-bonds generated for 'chain 'D' and resid 889 through 891' Processing helix chain 'D' and resid 941 through 945 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 21 through 34 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 61 through 78 removed outlier: 3.757A pdb=" N GLN E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 130 Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'E' and resid 201 through 205 removed outlier: 3.615A pdb=" N ALA E 204 " --> pdb=" O PRO E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 250 removed outlier: 3.587A pdb=" N SER E 249 " --> pdb=" O ASN E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.325A pdb=" N SER E 291 " --> pdb=" O ASP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 308 Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 317 through 332 Processing helix chain 'E' and resid 335 through 344 Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 353 through 366 removed outlier: 4.162A pdb=" N SER E 366 " --> pdb=" O TRP E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 386 removed outlier: 3.699A pdb=" N ILE E 378 " --> pdb=" O THR E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 409 removed outlier: 3.580A pdb=" N TYR E 405 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 427 Processing helix chain 'E' and resid 466 through 476 removed outlier: 3.586A pdb=" N SER E 474 " --> pdb=" O HIS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 removed outlier: 3.782A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 516 removed outlier: 4.095A pdb=" N SER E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 532 Processing helix chain 'E' and resid 591 through 605 Processing helix chain 'E' and resid 607 through 620 removed outlier: 3.634A pdb=" N THR E 620 " --> pdb=" O PHE E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 657 removed outlier: 5.721A pdb=" N ASP E 655 " --> pdb=" O MET E 651 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N HIS E 656 " --> pdb=" O VAL E 652 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR E 657 " --> pdb=" O LEU E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 668 removed outlier: 3.552A pdb=" N THR E 667 " --> pdb=" O ILE E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 682 Processing helix chain 'E' and resid 701 through 709 removed outlier: 3.504A pdb=" N VAL E 709 " --> pdb=" O LEU E 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 751 Processing helix chain 'E' and resid 778 through 783 Processing helix chain 'E' and resid 787 through 810 Processing helix chain 'E' and resid 812 through 816 Processing helix chain 'E' and resid 818 through 832 removed outlier: 3.560A pdb=" N GLU E 822 " --> pdb=" O CYS E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 842 Processing helix chain 'E' and resid 855 through 870 Processing helix chain 'E' and resid 876 through 886 removed outlier: 3.649A pdb=" N LEU E 880 " --> pdb=" O ILE E 876 " (cutoff:3.500A) Processing helix chain 'E' and resid 887 through 891 removed outlier: 4.243A pdb=" N LYS E 891 " --> pdb=" O VAL E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 941 through 945 Processing helix chain 'F' and resid 10 through 21 removed outlier: 3.525A pdb=" N ARG F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS F 19 " --> pdb=" O THR F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 34 Processing helix chain 'F' and resid 35 through 39 Processing helix chain 'F' and resid 61 through 78 Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 180 through 190 removed outlier: 3.745A pdb=" N GLN F 184 " --> pdb=" O ASP F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 205 removed outlier: 3.852A pdb=" N ALA F 204 " --> pdb=" O PRO F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 287 through 297 removed outlier: 4.068A pdb=" N SER F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 308 removed outlier: 3.509A pdb=" N ARG F 301 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 312 through 317 Processing helix chain 'F' and resid 317 through 332 Processing helix chain 'F' and resid 335 through 344 Processing helix chain 'F' and resid 346 through 352 Processing helix chain 'F' and resid 353 through 366 removed outlier: 3.728A pdb=" N SER F 366 " --> pdb=" O TRP F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 386 removed outlier: 3.866A pdb=" N ILE F 378 " --> pdb=" O THR F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 409 removed outlier: 3.613A pdb=" N TYR F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 removed outlier: 3.516A pdb=" N ILE F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 476 removed outlier: 3.708A pdb=" N SER F 474 " --> pdb=" O HIS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 494 removed outlier: 3.829A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 516 removed outlier: 4.146A pdb=" N SER F 516 " --> pdb=" O GLU F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 519 No H-bonds generated for 'chain 'F' and resid 517 through 519' Processing helix chain 'F' and resid 520 through 535 removed outlier: 4.478A pdb=" N PHE F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 544 Processing helix chain 'F' and resid 591 through 605 Processing helix chain 'F' and resid 607 through 620 removed outlier: 3.651A pdb=" N THR F 620 " --> pdb=" O PHE F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 654 removed outlier: 3.747A pdb=" N MET F 646 " --> pdb=" O LYS F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 668 Processing helix chain 'F' and resid 679 through 683 Processing helix chain 'F' and resid 701 through 707 Processing helix chain 'F' and resid 746 through 751 Processing helix chain 'F' and resid 777 through 783 removed outlier: 4.344A pdb=" N ILE F 781 " --> pdb=" O ASP F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 784 through 786 No H-bonds generated for 'chain 'F' and resid 784 through 786' Processing helix chain 'F' and resid 787 through 810 Processing helix chain 'F' and resid 818 through 831 Processing helix chain 'F' and resid 833 through 842 Processing helix chain 'F' and resid 855 through 870 Processing helix chain 'F' and resid 876 through 885 Processing helix chain 'F' and resid 888 through 892 removed outlier: 3.968A pdb=" N TYR F 892 " --> pdb=" O VAL F 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 888 through 892' Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 4.199A pdb=" N THR A 57 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 101 removed outlier: 8.832A pdb=" N SER A 92 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY A 162 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 94 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N HIS A 140 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 163 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 11.646A pdb=" N LYS A 138 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 15.901A pdb=" N MET A 165 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 19.560A pdb=" N SER A 136 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 225 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 145 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A 223 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 226 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 101 removed outlier: 8.832A pdb=" N SER A 92 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY A 162 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 94 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL A 269 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY A 162 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.818A pdb=" N TRP A 442 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.626A pdb=" N GLY A 556 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.501A pdb=" N SER A 659 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 690 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 632 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER A 736 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP A 634 " --> pdb=" O SER A 736 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 713 through 717 removed outlier: 3.637A pdb=" N GLU A 724 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 761 through 763 Processing sheet with id=AA9, first strand: chain 'A' and resid 843 through 844 Processing sheet with id=AB1, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AB2, first strand: chain 'B' and resid 39 through 40 removed outlier: 4.221A pdb=" N THR B 57 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 101 removed outlier: 8.656A pdb=" N SER B 92 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLY B 162 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N HIS B 140 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 163 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N LYS B 138 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 17.317A pdb=" N MET B 165 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 20.533A pdb=" N SER B 136 " --> pdb=" O MET B 165 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B 225 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 145 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 223 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY B 226 " --> pdb=" O ILE B 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 101 removed outlier: 8.656A pdb=" N SER B 92 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLY B 162 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.737A pdb=" N TRP B 442 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 550 through 553 removed outlier: 3.638A pdb=" N GLY B 556 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 557 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 658 through 660 removed outlier: 3.612A pdb=" N TYR B 690 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY B 689 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ALA B 735 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE B 691 " --> pdb=" O ALA B 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 713 through 716 Processing sheet with id=AB9, first strand: chain 'B' and resid 761 through 763 Processing sheet with id=AC1, first strand: chain 'B' and resid 843 through 845 Processing sheet with id=AC2, first strand: chain 'B' and resid 853 through 854 Processing sheet with id=AC3, first strand: chain 'C' and resid 56 through 58 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 101 removed outlier: 6.360A pdb=" N LEU C 163 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N LEU C 96 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 11.710A pdb=" N TYR C 98 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N LEU C 159 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N LEU C 100 " --> pdb=" O HIS C 157 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N HIS C 157 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS C 140 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 163 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 11.827A pdb=" N LYS C 138 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 225 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 145 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU C 223 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 101 removed outlier: 6.360A pdb=" N LEU C 163 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N LEU C 96 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 11.710A pdb=" N TYR C 98 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N LEU C 159 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N LEU C 100 " --> pdb=" O HIS C 157 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N HIS C 157 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL C 269 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY C 162 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.810A pdb=" N TRP C 442 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 550 through 553 removed outlier: 3.635A pdb=" N GLY C 556 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 557 " --> pdb=" O ILE C 568 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 658 through 660 removed outlier: 3.528A pdb=" N TYR C 690 " --> pdb=" O SER C 659 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 713 through 716 Processing sheet with id=AD1, first strand: chain 'C' and resid 761 through 763 removed outlier: 6.223A pdb=" N LYS C 761 " --> pdb=" O LYS C 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 843 through 845 Processing sheet with id=AD3, first strand: chain 'C' and resid 853 through 854 Processing sheet with id=AD4, first strand: chain 'D' and resid 39 through 40 removed outlier: 4.699A pdb=" N THR D 57 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 92 through 101 removed outlier: 7.928A pdb=" N SER D 92 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY D 162 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 156 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N HIS D 140 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU D 163 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N LYS D 138 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 16.539A pdb=" N MET D 165 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 19.506A pdb=" N SER D 136 " --> pdb=" O MET D 165 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS D 137 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 231 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D 225 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU D 145 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU D 223 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 430 through 434 removed outlier: 3.784A pdb=" N TRP D 442 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 550 through 553 removed outlier: 3.640A pdb=" N GLY D 556 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 557 " --> pdb=" O ILE D 568 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 658 through 660 removed outlier: 3.786A pdb=" N TYR D 690 " --> pdb=" O SER D 659 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D 693 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 713 through 717 Processing sheet with id=AE1, first strand: chain 'D' and resid 761 through 763 Processing sheet with id=AE2, first strand: chain 'D' and resid 843 through 845 Processing sheet with id=AE3, first strand: chain 'D' and resid 853 through 854 removed outlier: 3.604A pdb=" N ILE D 902 " --> pdb=" O GLN D 894 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 39 through 40 removed outlier: 4.293A pdb=" N THR E 57 " --> pdb=" O THR E 40 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 199 through 200 removed outlier: 4.653A pdb=" N ASP E 97 " --> pdb=" O ASP E 200 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N SER E 92 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLY E 162 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 159 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS E 140 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU E 163 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 12.246A pdb=" N LYS E 138 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 17.072A pdb=" N MET E 165 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 20.459A pdb=" N SER E 136 " --> pdb=" O MET E 165 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU E 145 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU E 223 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS E 242 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 430 through 434 removed outlier: 3.748A pdb=" N TRP E 442 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 550 through 553 removed outlier: 3.518A pdb=" N GLY E 556 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 658 through 660 removed outlier: 3.759A pdb=" N TYR E 690 " --> pdb=" O SER E 659 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU E 632 " --> pdb=" O ALA E 734 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER E 736 " --> pdb=" O LEU E 632 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP E 634 " --> pdb=" O SER E 736 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 699 through 700 Processing sheet with id=AF1, first strand: chain 'E' and resid 713 through 717 Processing sheet with id=AF2, first strand: chain 'E' and resid 761 through 762 removed outlier: 6.349A pdb=" N LYS E 761 " --> pdb=" O LYS E 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 843 through 845 removed outlier: 3.536A pdb=" N VAL E 844 " --> pdb=" O ARG E 907 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 853 through 854 removed outlier: 3.592A pdb=" N GLN E 894 " --> pdb=" O ILE E 902 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AF6, first strand: chain 'F' and resid 91 through 101 removed outlier: 8.195A pdb=" N SER F 92 " --> pdb=" O GLY F 162 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY F 162 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE F 156 " --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS F 140 " --> pdb=" O PRO F 161 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU F 163 " --> pdb=" O LYS F 138 " (cutoff:3.500A) removed outlier: 12.412A pdb=" N LYS F 138 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 16.534A pdb=" N MET F 165 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 20.048A pdb=" N SER F 136 " --> pdb=" O MET F 165 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N HIS F 137 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL F 230 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE F 139 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU F 228 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE F 141 " --> pdb=" O GLY F 226 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY F 226 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE F 143 " --> pdb=" O LYS F 224 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 430 through 434 removed outlier: 3.646A pdb=" N TRP F 442 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 550 through 553 removed outlier: 3.592A pdb=" N VAL F 557 " --> pdb=" O ILE F 568 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 658 through 660 removed outlier: 6.167A pdb=" N LEU F 632 " --> pdb=" O ALA F 734 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER F 736 " --> pdb=" O LEU F 632 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP F 634 " --> pdb=" O SER F 736 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 699 through 700 Processing sheet with id=AG2, first strand: chain 'F' and resid 761 through 763 Processing sheet with id=AG3, first strand: chain 'F' and resid 843 through 845 Processing sheet with id=AG4, first strand: chain 'F' and resid 853 through 854 2173 hydrogen bonds defined for protein. 6240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.89 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10608 1.33 - 1.46: 9077 1.46 - 1.58: 21436 1.58 - 1.70: 33 1.70 - 1.83: 230 Bond restraints: 41384 Sorted by residual: bond pdb=" N3B ANP A1001 " pdb=" PG ANP A1001 " ideal model delta sigma weight residual 1.795 1.529 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" N3B ANP C1001 " pdb=" PG ANP C1001 " ideal model delta sigma weight residual 1.795 1.543 0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" N3B ANP B1001 " pdb=" PG ANP B1001 " ideal model delta sigma weight residual 1.795 1.592 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" N3B ANP D1001 " pdb=" PG ANP D1001 " ideal model delta sigma weight residual 1.795 1.595 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" N3B ANP F1001 " pdb=" PG ANP F1001 " ideal model delta sigma weight residual 1.795 1.597 0.198 2.00e-02 2.50e+03 9.85e+01 ... (remaining 41379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 55489 3.20 - 6.40: 944 6.40 - 9.60: 27 9.60 - 12.80: 8 12.80 - 16.00: 5 Bond angle restraints: 56473 Sorted by residual: angle pdb=" O5' DT G 4 " pdb=" C5' DT G 4 " pdb=" C4' DT G 4 " ideal model delta sigma weight residual 109.40 117.24 -7.84 8.00e-01 1.56e+00 9.61e+01 angle pdb=" O4' DT G 7 " pdb=" C1' DT G 7 " pdb=" N1 DT G 7 " ideal model delta sigma weight residual 108.00 113.90 -5.90 7.00e-01 2.04e+00 7.10e+01 angle pdb=" O2 DT G 10 " pdb=" C2 DT G 10 " pdb=" N3 DT G 10 " ideal model delta sigma weight residual 122.30 118.89 3.41 6.00e-01 2.78e+00 3.23e+01 angle pdb=" O4' DT G 4 " pdb=" C1' DT G 4 " pdb=" N1 DT G 4 " ideal model delta sigma weight residual 108.00 111.86 -3.86 7.00e-01 2.04e+00 3.05e+01 angle pdb=" O4' DT G 10 " pdb=" C1' DT G 10 " pdb=" N1 DT G 10 " ideal model delta sigma weight residual 108.00 111.85 -3.85 7.00e-01 2.04e+00 3.03e+01 ... (remaining 56468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 24086 35.56 - 71.12: 276 71.12 - 106.68: 32 106.68 - 142.24: 3 142.24 - 177.80: 2 Dihedral angle restraints: 24399 sinusoidal: 8202 harmonic: 16197 Sorted by residual: dihedral pdb=" O1A ANP B1001 " pdb=" O3A ANP B1001 " pdb=" PA ANP B1001 " pdb=" PB ANP B1001 " ideal model delta sinusoidal sigma weight residual 83.11 -94.69 177.80 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP A1001 " pdb=" O3A ANP A1001 " pdb=" PA ANP A1001 " pdb=" PB ANP A1001 " ideal model delta sinusoidal sigma weight residual 83.11 -111.20 -165.69 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1A ANP C1001 " pdb=" O3A ANP C1001 " pdb=" PA ANP C1001 " pdb=" PB ANP C1001 " ideal model delta sinusoidal sigma weight residual 83.11 -58.91 142.02 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 24396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 6041 0.131 - 0.262: 216 0.262 - 0.392: 8 0.392 - 0.523: 4 0.523 - 0.654: 2 Chirality restraints: 6271 Sorted by residual: chirality pdb=" P DT G 1 " pdb=" OP1 DT G 1 " pdb=" OP2 DT G 1 " pdb=" O5' DT G 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DT G 2 " pdb=" OP1 DT G 2 " pdb=" OP2 DT G 2 " pdb=" O5' DT G 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" P DT G 3 " pdb=" OP1 DT G 3 " pdb=" OP2 DT G 3 " pdb=" O5' DT G 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 6268 not shown) Planarity restraints: 7315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT G 6 " 0.092 2.00e-02 2.50e+03 6.56e-02 1.07e+02 pdb=" N1 DT G 6 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DT G 6 " -0.023 2.00e-02 2.50e+03 pdb=" O2 DT G 6 " -0.120 2.00e-02 2.50e+03 pdb=" N3 DT G 6 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DT G 6 " 0.035 2.00e-02 2.50e+03 pdb=" O4 DT G 6 " 0.084 2.00e-02 2.50e+03 pdb=" C5 DT G 6 " -0.015 2.00e-02 2.50e+03 pdb=" C7 DT G 6 " -0.099 2.00e-02 2.50e+03 pdb=" C6 DT G 6 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP C1001 " 0.139 2.00e-02 2.50e+03 6.12e-02 1.03e+02 pdb=" C2 ANP C1001 " -0.017 2.00e-02 2.50e+03 pdb=" C4 ANP C1001 " -0.054 2.00e-02 2.50e+03 pdb=" C5 ANP C1001 " -0.044 2.00e-02 2.50e+03 pdb=" C6 ANP C1001 " 0.004 2.00e-02 2.50e+03 pdb=" C8 ANP C1001 " -0.024 2.00e-02 2.50e+03 pdb=" N1 ANP C1001 " 0.054 2.00e-02 2.50e+03 pdb=" N3 ANP C1001 " -0.071 2.00e-02 2.50e+03 pdb=" N6 ANP C1001 " 0.077 2.00e-02 2.50e+03 pdb=" N7 ANP C1001 " -0.040 2.00e-02 2.50e+03 pdb=" N9 ANP C1001 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT G 7 " 0.087 2.00e-02 2.50e+03 5.79e-02 8.39e+01 pdb=" N1 DT G 7 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DT G 7 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DT G 7 " -0.110 2.00e-02 2.50e+03 pdb=" N3 DT G 7 " 0.028 2.00e-02 2.50e+03 pdb=" C4 DT G 7 " 0.028 2.00e-02 2.50e+03 pdb=" O4 DT G 7 " 0.069 2.00e-02 2.50e+03 pdb=" C5 DT G 7 " -0.015 2.00e-02 2.50e+03 pdb=" C7 DT G 7 " -0.083 2.00e-02 2.50e+03 pdb=" C6 DT G 7 " 0.001 2.00e-02 2.50e+03 ... (remaining 7312 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 16 2.27 - 2.93: 16617 2.93 - 3.59: 58581 3.59 - 4.24: 89004 4.24 - 4.90: 150836 Nonbonded interactions: 315054 Sorted by model distance: nonbonded pdb=" O2G ANP B1001 " pdb="MG MG B1002 " model vdw 1.618 2.170 nonbonded pdb=" O3G ANP C1001 " pdb="MG MG C1002 " model vdw 1.879 2.170 nonbonded pdb=" O2B ANP A1001 " pdb="MG MG A1002 " model vdw 1.886 2.170 nonbonded pdb=" O2B ANP C1001 " pdb="MG MG C1002 " model vdw 1.978 2.170 nonbonded pdb=" O2G ANP A1001 " pdb="MG MG A1002 " model vdw 1.979 2.170 ... (remaining 315049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 274 or resid 285 through 293 or (resid 294 and ( \ name N or name CA or name C or name O or name CB )) or resid 295 through 301 or \ (resid 302 and (name N or name CA or name C or name O or name CB )) or resid 303 \ through 315 or (resid 316 through 317 and (name N or name CA or name C or name \ O or name CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or \ name C or name O or name CB )) or resid 337 through 456 or (resid 457 and (name \ N or name CA or name C or name O or name CB )) or resid 458 through 550 or (res \ id 551 and (name N or name CA or name C or name O or name CB )) or resid 552 thr \ ough 600 or (resid 601 and (name N or name CA or name C or name O or name CB )) \ or resid 602 through 680 or (resid 681 and (name N or name CA or name C or name \ O or name CB )) or resid 682 or (resid 683 and (name N or name CA or name C or n \ ame O or name CB )) or resid 684 through 691 or (resid 692 through 693 and (name \ N or name CA or name C or name O or name CB )) or resid 694 through 698 or (res \ id 699 and (name N or name CA or name C or name O or name CB )) or resid 700 thr \ ough 704 or (resid 705 and (name N or name CA or name C or name O or name CB )) \ or resid 706 through 707 or (resid 708 and (name N or name CA or name C or name \ O or name CB )) or resid 709 or (resid 710 and (name N or name CA or name C or n \ ame O or name CB )) or resid 711 through 712 or (resid 713 and (name N or name C \ A or name C or name O or name CB )) or resid 714 through 716 or (resid 717 and ( \ name N or name CA or name C or name O or name CB )) or resid 718 or resid 723 th \ rough 725 or (resid 726 and (name N or name CA or name C or name O or name CB )) \ or resid 727 through 740 or (resid 741 and (name N or name CA or name C or name \ O or name CB )) or resid 742 through 769 or (resid 770 and (name N or name CA o \ r name C or name O or name CB )) or resid 771 through 772 or (resid 773 and (nam \ e N or name CA or name C or name O or name CB )) or resid 774 through 840 or (re \ sid 841 through 842 and (name N or name CA or name C or name O or name CB )) or \ resid 843 through 853 or (resid 854 and (name N or name CA or name C or name O o \ r name CB )) or resid 855 through 858 or (resid 859 and (name N or name CA or na \ me C or name O or name CB )) or resid 860 through 863 or (resid 864 and (name N \ or name CA or name C or name O or name CB )) or resid 865 through 877 or (resid \ 878 and (name N or name CA or name C or name O or name CB )) or resid 879 or (re \ sid 880 and (name N or name CA or name C or name O or name CB )) or resid 881 th \ rough 888 or (resid 889 and (name N or name CA or name C or name O or name CB )) \ or resid 890 or (resid 891 and (name N or name CA or name C or name O or name C \ B )) or resid 892 or (resid 893 through 894 and (name N or name CA or name C or \ name O or name CB )) or resid 895 through 900 or (resid 901 and (name N or name \ CA or name C or name O or name CB )) or resid 902 or (resid 903 through 904 and \ (name N or name CA or name C or name O or name CB )) or resid 905 through 906 or \ (resid 907 through 908 and (name N or name CA or name C or name O or name CB )) \ or resid 909 through 914 or (resid 915 and (name N or name CA or name C or name \ O or name CB )) or resid 916 through 949)) selection = (chain 'B' and (resid 9 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or name \ CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or name C o \ r name O or name CB )) or resid 337 through 358 or (resid 359 and (name N or nam \ e CA or name C or name O or name CB )) or resid 360 through 366 or (resid 367 th \ rough 368 and (name N or name CA or name C or name O or name CB )) or resid 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 413 or (resid 414 and (name N or name CA or name C or na \ me O or name CB )) or resid 415 through 456 or (resid 457 and (name N or name CA \ or name C or name O or name CB )) or resid 458 through 550 or (resid 551 and (n \ ame N or name CA or name C or name O or name CB )) or resid 552 through 600 or ( \ resid 601 and (name N or name CA or name C or name O or name CB )) or resid 602 \ through 666 or (resid 667 and (name N or name CA or name C or name O or name CB \ )) or resid 668 through 670 or (resid 671 through 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 680 or (resid 681 and (name \ N or name CA or name C or name O or name CB )) or resid 682 or (resid 683 and (n \ ame N or name CA or name C or name O or name CB )) or resid 684 through 691 or ( \ resid 692 through 693 and (name N or name CA or name C or name O or name CB )) o \ r resid 694 through 698 or (resid 699 and (name N or name CA or name C or name O \ or name CB )) or resid 700 through 704 or (resid 705 and (name N or name CA or \ name C or name O or name CB )) or resid 706 through 707 or (resid 708 and (name \ N or name CA or name C or name O or name CB )) or resid 709 or (resid 710 and (n \ ame N or name CA or name C or name O or name CB )) or resid 711 through 712 or ( \ resid 713 and (name N or name CA or name C or name O or name CB )) or resid 714 \ through 716 or (resid 717 and (name N or name CA or name C or name O or name CB \ )) or resid 718 or resid 723 through 725 or (resid 726 and (name N or name CA or \ name C or name O or name CB )) or resid 727 or (resid 728 and (name N or name C \ A or name C or name O or name CB )) or resid 729 through 740 or (resid 741 and ( \ name N or name CA or name C or name O or name CB )) or resid 742 through 769 or \ (resid 770 and (name N or name CA or name C or name O or name CB )) or resid 771 \ through 772 or (resid 773 and (name N or name CA or name C or name O or name CB \ )) or resid 774 through 780 or (resid 781 and (name N or name CA or name C or n \ ame O or name CB )) or resid 782 through 813 or (resid 814 and (name N or name C \ A or name C or name O or name CB )) or resid 815 through 834 or (resid 835 and ( \ name N or name CA or name C or name O or name CB )) or resid 836 through 840 or \ (resid 841 through 842 and (name N or name CA or name C or name O or name CB )) \ or resid 843 through 851 or (resid 852 and (name N or name CA or name C or name \ O or name CB )) or resid 853 or (resid 854 and (name N or name CA or name C or n \ ame O or name CB )) or resid 855 through 857 or (resid 858 through 859 and (name \ N or name CA or name C or name O or name CB )) or resid 860 through 863 or (res \ id 864 and (name N or name CA or name C or name O or name CB )) or resid 865 or \ (resid 866 and (name N or name CA or name C or name O or name CB )) or resid 867 \ through 877 or (resid 878 and (name N or name CA or name C or name O or name CB \ )) or resid 879 or (resid 880 and (name N or name CA or name C or name O or nam \ e CB )) or resid 881 through 883 or (resid 884 and (name N or name CA or name C \ or name O or name CB )) or resid 885 through 888 or (resid 889 and (name N or na \ me CA or name C or name O or name CB )) or resid 890 through 892 or (resid 893 t \ hrough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 \ through 900 or (resid 901 and (name N or name CA or name C or name O or name CB \ )) or resid 902 or (resid 903 through 904 and (name N or name CA or name C or n \ ame O or name CB )) or resid 905 through 907 or (resid 908 and (name N or name C \ A or name C or name O or name CB )) or resid 909 through 914 or (resid 915 and ( \ name N or name CA or name C or name O or name CB )) or resid 916 through 947 or \ (resid 948 through 949 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'C' and (resid 9 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or name \ CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or name C o \ r name O or name CB )) or resid 337 through 358 or (resid 359 and (name N or nam \ e CA or name C or name O or name CB )) or resid 360 through 366 or (resid 367 th \ rough 368 and (name N or name CA or name C or name O or name CB )) or resid 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 393 or (resid 394 and (name N or name CA or name C or na \ me O or name CB )) or resid 395 through 413 or (resid 414 and (name N or name CA \ or name C or name O or name CB )) or resid 415 through 456 or (resid 457 and (n \ ame N or name CA or name C or name O or name CB )) or resid 458 through 550 or ( \ resid 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 575 or (resid 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 600 or (resid 601 and (name N or name CA or name C or na \ me O or name CB )) or resid 602 through 666 or (resid 667 and (name N or name CA \ or name C or name O or name CB )) or resid 668 through 670 or (resid 671 throug \ h 674 and (name N or name CA or name C or name O or name CB )) or resid 675 thro \ ugh 680 or (resid 681 and (name N or name CA or name C or name O or name CB )) o \ r resid 682 or (resid 683 and (name N or name CA or name C or name O or name CB \ )) or resid 684 through 691 or (resid 692 through 693 and (name N or name CA or \ name C or name O or name CB )) or resid 694 through 698 or (resid 699 and (name \ N or name CA or name C or name O or name CB )) or resid 700 through 707 or (resi \ d 708 and (name N or name CA or name C or name O or name CB )) or resid 709 or ( \ resid 710 and (name N or name CA or name C or name O or name CB )) or resid 711 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 716 or (resid 717 and (name N or name CA or name C or na \ me O or name CB )) or resid 718 or resid 723 through 725 or (resid 726 and (name \ N or name CA or name C or name O or name CB )) or resid 727 or (resid 728 and ( \ name N or name CA or name C or name O or name CB )) or resid 729 through 740 or \ (resid 741 and (name N or name CA or name C or name O or name CB )) or resid 742 \ through 769 or (resid 770 and (name N or name CA or name C or name O or name CB \ )) or resid 771 through 772 or (resid 773 and (name N or name CA or name C or n \ ame O or name CB )) or resid 774 through 780 or (resid 781 and (name N or name C \ A or name C or name O or name CB )) or resid 782 through 813 or (resid 814 and ( \ name N or name CA or name C or name O or name CB )) or resid 815 through 834 or \ (resid 835 and (name N or name CA or name C or name O or name CB )) or resid 836 \ through 840 or (resid 841 through 842 and (name N or name CA or name C or name \ O or name CB )) or resid 843 through 851 or (resid 852 and (name N or name CA or \ name C or name O or name CB )) or resid 853 or (resid 854 and (name N or name C \ A or name C or name O or name CB )) or resid 855 through 858 or (resid 859 and ( \ name N or name CA or name C or name O or name CB )) or resid 860 through 863 or \ (resid 864 and (name N or name CA or name C or name O or name CB )) or resid 865 \ or (resid 866 and (name N or name CA or name C or name O or name CB )) or resid \ 867 through 877 or (resid 878 and (name N or name CA or name C or name O or nam \ e CB )) or resid 879 or (resid 880 and (name N or name CA or name C or name O or \ name CB )) or resid 881 through 890 or (resid 891 and (name N or name CA or nam \ e C or name O or name CB )) or resid 892 through 893 or (resid 894 and (name N o \ r name CA or name C or name O or name CB )) or resid 895 through 902 or (resid 9 \ 03 through 904 and (name N or name CA or name C or name O or name CB )) or resid \ 905 through 906 or (resid 907 through 908 and (name N or name CA or name C or n \ ame O or name CB )) or resid 909 through 918 or resid 936 through 947 or (resid \ 948 through 949 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 9 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or name \ CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or name C o \ r name O or name CB )) or resid 337 through 358 or (resid 359 and (name N or nam \ e CA or name C or name O or name CB )) or resid 360 through 366 or (resid 367 th \ rough 368 and (name N or name CA or name C or name O or name CB )) or resid 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 413 or (resid 414 and (name N or name CA or name C or na \ me O or name CB )) or resid 415 through 456 or (resid 457 and (name N or name CA \ or name C or name O or name CB )) or resid 458 through 550 or (resid 551 and (n \ ame N or name CA or name C or name O or name CB )) or resid 552 through 575 or ( \ resid 576 and (name N or name CA or name C or name O or name CB )) or resid 577 \ through 600 or (resid 601 and (name N or name CA or name C or name O or name CB \ )) or resid 602 through 666 or (resid 667 and (name N or name CA or name C or na \ me O or name CB )) or resid 668 through 670 or (resid 671 through 674 and (name \ N or name CA or name C or name O or name CB )) or resid 675 through 680 or (resi \ d 681 and (name N or name CA or name C or name O or name CB )) or resid 682 thro \ ugh 692 or (resid 693 and (name N or name CA or name C or name O or name CB )) o \ r resid 694 through 698 or (resid 699 and (name N or name CA or name C or name O \ or name CB )) or resid 700 through 704 or (resid 705 and (name N or name CA or \ name C or name O or name CB )) or resid 706 through 709 or (resid 710 and (name \ N or name CA or name C or name O or name CB )) or resid 711 through 712 or (resi \ d 713 and (name N or name CA or name C or name O or name CB )) or resid 714 thro \ ugh 716 or (resid 717 and (name N or name CA or name C or name O or name CB )) o \ r resid 718 or resid 723 through 725 or (resid 726 and (name N or name CA or nam \ e C or name O or name CB )) or resid 727 or (resid 728 and (name N or name CA or \ name C or name O or name CB )) or resid 729 through 740 or (resid 741 and (name \ N or name CA or name C or name O or name CB )) or resid 742 through 769 or (res \ id 770 and (name N or name CA or name C or name O or name CB )) or resid 771 thr \ ough 772 or (resid 773 and (name N or name CA or name C or name O or name CB )) \ or resid 774 through 780 or (resid 781 and (name N or name CA or name C or name \ O or name CB )) or resid 782 through 813 or (resid 814 and (name N or name CA or \ name C or name O or name CB )) or resid 815 through 834 or (resid 835 and (name \ N or name CA or name C or name O or name CB )) or resid 836 or (resid 837 and ( \ name N or name CA or name C or name O or name CB )) or resid 838 through 840 or \ (resid 841 through 842 and (name N or name CA or name C or name O or name CB )) \ or resid 843 through 851 or (resid 852 and (name N or name CA or name C or name \ O or name CB )) or resid 853 or (resid 854 and (name N or name CA or name C or n \ ame O or name CB )) or resid 855 through 857 or (resid 858 through 859 and (name \ N or name CA or name C or name O or name CB )) or resid 860 through 863 or (res \ id 864 and (name N or name CA or name C or name O or name CB )) or resid 865 or \ (resid 866 and (name N or name CA or name C or name O or name CB )) or resid 867 \ through 877 or (resid 878 and (name N or name CA or name C or name O or name CB \ )) or resid 879 or (resid 880 and (name N or name CA or name C or name O or nam \ e CB )) or resid 881 through 883 or (resid 884 and (name N or name CA or name C \ or name O or name CB )) or resid 885 through 888 or (resid 889 and (name N or na \ me CA or name C or name O or name CB )) or resid 890 or (resid 891 and (name N o \ r name CA or name C or name O or name CB )) or resid 892 or (resid 893 through 8 \ 94 and (name N or name CA or name C or name O or name CB )) or resid 895 through \ 900 or (resid 901 and (name N or name CA or name C or name O or name CB )) or r \ esid 902 or (resid 903 through 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 906 or (resid 907 through 908 and (name N or na \ me CA or name C or name O or name CB )) or resid 909 through 914 or (resid 915 a \ nd (name N or name CA or name C or name O or name CB )) or resid 916 through 918 \ or resid 936 through 947 or (resid 948 through 949 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'E' and (resid 9 through 358 or (resid 359 and (name N or name CA or name \ C or name O or name CB )) or resid 360 through 366 or (resid 367 through 368 an \ d (name N or name CA or name C or name O or name CB )) or resid 369 or (resid 37 \ 0 through 371 and (name N or name CA or name C or name O or name CB )) or resid \ 372 through 393 or (resid 394 and (name N or name CA or name C or name O or name \ CB )) or resid 395 through 413 or (resid 414 and (name N or name CA or name C o \ r name O or name CB )) or resid 415 through 575 or (resid 576 and (name N or nam \ e CA or name C or name O or name CB )) or resid 577 through 600 or (resid 601 an \ d (name N or name CA or name C or name O or name CB )) or resid 602 through 666 \ or (resid 667 and (name N or name CA or name C or name O or name CB )) or resid \ 668 through 670 or (resid 671 through 674 and (name N or name CA or name C or na \ me O or name CB )) or resid 675 through 680 or (resid 681 and (name N or name CA \ or name C or name O or name CB )) or resid 682 or (resid 683 and (name N or nam \ e CA or name C or name O or name CB )) or resid 684 through 691 or (resid 692 th \ rough 693 and (name N or name CA or name C or name O or name CB )) or resid 694 \ through 704 or (resid 705 and (name N or name CA or name C or name O or name CB \ )) or resid 706 through 707 or (resid 708 and (name N or name CA or name C or na \ me O or name CB )) or resid 709 through 712 or (resid 713 and (name N or name CA \ or name C or name O or name CB )) or resid 714 through 716 or (resid 717 and (n \ ame N or name CA or name C or name O or name CB )) or resid 718 or resid 723 thr \ ough 725 or (resid 726 and (name N or name CA or name C or name O or name CB )) \ or resid 727 or (resid 728 and (name N or name CA or name C or name O or name CB \ )) or resid 729 through 769 or (resid 770 and (name N or name CA or name C or n \ ame O or name CB )) or resid 771 through 772 or (resid 773 and (name N or name C \ A or name C or name O or name CB )) or resid 774 through 780 or (resid 781 and ( \ name N or name CA or name C or name O or name CB )) or resid 782 through 813 or \ (resid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 \ through 834 or (resid 835 and (name N or name CA or name C or name O or name CB \ )) or resid 836 or (resid 837 and (name N or name CA or name C or name O or nam \ e CB )) or resid 838 through 851 or (resid 852 and (name N or name CA or name C \ or name O or name CB )) or resid 853 through 857 or (resid 858 through 859 and ( \ name N or name CA or name C or name O or name CB )) or resid 860 through 865 or \ (resid 866 and (name N or name CA or name C or name O or name CB )) or resid 867 \ through 883 or (resid 884 and (name N or name CA or name C or name O or name CB \ )) or resid 885 through 888 or (resid 889 and (name N or name CA or name C or n \ ame O or name CB )) or resid 890 or (resid 891 and (name N or name CA or name C \ or name O or name CB )) or resid 892 or (resid 893 through 894 and (name N or na \ me CA or name C or name O or name CB )) or resid 895 through 900 or (resid 901 a \ nd (name N or name CA or name C or name O or name CB )) or resid 902 through 903 \ or (resid 904 and (name N or name CA or name C or name O or name CB )) or resid \ 905 through 906 or (resid 907 through 908 and (name N or name CA or name C or n \ ame O or name CB )) or resid 909 through 914 or (resid 915 and (name N or name C \ A or name C or name O or name CB )) or resid 916 through 918 or resid 936 throug \ h 947 or (resid 948 through 949 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'F' and (resid 9 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or name \ CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or name C o \ r name O or name CB )) or resid 337 through 358 or (resid 359 and (name N or nam \ e CA or name C or name O or name CB )) or resid 360 through 366 or (resid 367 th \ rough 368 and (name N or name CA or name C or name O or name CB )) or resid 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 393 or (resid 394 and (name N or name CA or name C or na \ me O or name CB )) or resid 395 through 413 or (resid 414 and (name N or name CA \ or name C or name O or name CB )) or resid 415 through 456 or (resid 457 and (n \ ame N or name CA or name C or name O or name CB )) or resid 458 through 550 or ( \ resid 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 575 or (resid 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 666 or (resid 667 and (name N or name CA or name C or na \ me O or name CB )) or resid 668 through 670 or (resid 671 through 674 and (name \ N or name CA or name C or name O or name CB )) or resid 675 through 682 or (resi \ d 683 and (name N or name CA or name C or name O or name CB )) or resid 684 thro \ ugh 691 or (resid 692 through 693 and (name N or name CA or name C or name O or \ name CB )) or resid 694 through 698 or (resid 699 and (name N or name CA or name \ C or name O or name CB )) or resid 700 through 704 or (resid 705 and (name N or \ name CA or name C or name O or name CB )) or resid 706 through 707 or (resid 70 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 709 or (resi \ d 710 and (name N or name CA or name C or name O or name CB )) or resid 711 thro \ ugh 740 or (resid 741 and (name N or name CA or name C or name O or name CB )) o \ r resid 742 through 780 or (resid 781 and (name N or name CA or name C or name O \ or name CB )) or resid 782 through 813 or (resid 814 and (name N or name CA or \ name C or name O or name CB )) or resid 815 through 834 or (resid 835 and (name \ N or name CA or name C or name O or name CB )) or resid 836 or (resid 837 and (n \ ame N or name CA or name C or name O or name CB )) or resid 838 through 840 or ( \ resid 841 through 842 and (name N or name CA or name C or name O or name CB )) o \ r resid 843 through 851 or (resid 852 and (name N or name CA or name C or name O \ or name CB )) or resid 853 or (resid 854 and (name N or name CA or name C or na \ me O or name CB )) or resid 855 through 857 or (resid 858 through 859 and (name \ N or name CA or name C or name O or name CB )) or resid 860 through 863 or (resi \ d 864 and (name N or name CA or name C or name O or name CB )) or resid 865 or ( \ resid 866 and (name N or name CA or name C or name O or name CB )) or resid 867 \ through 877 or (resid 878 and (name N or name CA or name C or name O or name CB \ )) or resid 879 or (resid 880 and (name N or name CA or name C or name O or name \ CB )) or resid 881 through 883 or (resid 884 and (name N or name CA or name C o \ r name O or name CB )) or resid 885 through 888 or (resid 889 and (name N or nam \ e CA or name C or name O or name CB )) or resid 890 or (resid 891 and (name N or \ name CA or name C or name O or name CB )) or resid 892 or (resid 893 through 89 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 895 through \ 900 or (resid 901 and (name N or name CA or name C or name O or name CB )) or re \ sid 902 or (resid 903 through 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 906 or (resid 907 through 908 and (name N or nam \ e CA or name C or name O or name CB )) or resid 909 through 914 or (resid 915 an \ d (name N or name CA or name C or name O or name CB )) or resid 916 through 947 \ or (resid 948 through 949 and (name N or name CA or name C or name O or name CB \ )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 42.490 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.100 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: 0.020 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.007 0.266 41384 Z= 0.387 Angle : 0.943 15.999 56473 Z= 0.605 Chirality : 0.058 0.654 6271 Planarity : 0.007 0.118 7315 Dihedral : 12.880 177.797 13891 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.64 % Allowed : 0.64 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.11), residues: 5450 helix: 1.67 (0.11), residues: 2498 sheet: 0.79 (0.22), residues: 552 loop : 0.12 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 538 TYR 0.110 0.005 TYR A 669 PHE 0.086 0.003 PHE E 680 TRP 0.102 0.006 TRP F 634 HIS 0.014 0.001 HIS F 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.39 (41384) covalent geometry : angle 0.94251 / 0.61 (56473) hydrogen bonds : bond 0.17253 / 12.55 ( 2155) hydrogen bonds : angle 6.51507 / 4.73 ( 6240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 462 time to evaluate : 1.400 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 288 HIS cc_start: 0.8849 (m90) cc_final: 0.8414 (m90) REVERT: A 426 MET cc_start: 0.7725 (mmm) cc_final: 0.7513 (mmm) REVERT: B 862 TYR cc_start: 0.8606 (t80) cc_final: 0.8318 (t80) REVERT: C 718 GLU cc_start: 0.6184 (tp30) cc_final: 0.5524 (tp30) REVERT: C 722 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8670 (mtmm) REVERT: D 335 TYR cc_start: 0.8497 (m-10) cc_final: 0.8225 (m-10) REVERT: E 395 GLU cc_start: 0.8298 (tp30) cc_final: 0.8034 (tp30) REVERT: E 948 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7850 (p0) REVERT: F 288 HIS cc_start: 0.8308 (m90) cc_final: 0.7584 (m-70) REVERT: F 551 LEU cc_start: 0.9011 (tp) cc_final: 0.8770 (tp) outliers start: 22 outliers final: 2 residues processed: 480 average time/residue: 0.2804 time to fit residues: 211.4246 Evaluate side-chains 281 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain E residue 948 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 394 optimal weight: 0.9990 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 0.0670 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 40.0000 chunk 223 optimal weight: 0.5980 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 HIS ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN B 720 ASN C 368 HIS C 727 GLN C 765 ASN D 494 GLN D 765 ASN D 782 HIS E 304 HIS E 389 GLN E 437 ASN E 542 GLN F 836 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.113733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.070535 restraints weight = 116737.914| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.59 r_work: 0.2843 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 41384 Z= 0.119 Angle : 0.498 7.627 56473 Z= 0.270 Chirality : 0.041 0.180 6271 Planarity : 0.004 0.082 7315 Dihedral : 7.559 172.084 5983 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.61 % Allowed : 4.54 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.12), residues: 5450 helix: 1.87 (0.10), residues: 2521 sheet: 0.46 (0.20), residues: 659 loop : 0.29 (0.14), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 376 TYR 0.020 0.001 TYR A 853 PHE 0.015 0.001 PHE A 801 TRP 0.048 0.001 TRP B 865 HIS 0.011 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (41384) covalent geometry : angle 0.49762 / 0.27 (56473) hydrogen bonds : bond 0.04213 / 3.07 ( 2155) hydrogen bonds : angle 4.87782 / 3.54 ( 6240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 296 time to evaluate : 1.540 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 288 HIS cc_start: 0.9113 (m90) cc_final: 0.8655 (m90) REVERT: A 439 LYS cc_start: 0.9019 (mtpp) cc_final: 0.8752 (mttm) REVERT: A 681 MET cc_start: 0.8978 (tpp) cc_final: 0.8751 (tpp) REVERT: A 721 GLN cc_start: 0.6863 (mp10) cc_final: 0.6444 (mp10) REVERT: A 878 LEU cc_start: 0.9255 (pp) cc_final: 0.8976 (tp) REVERT: B 299 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8927 (mm-30) REVERT: B 467 ASP cc_start: 0.8754 (m-30) cc_final: 0.8531 (m-30) REVERT: B 862 TYR cc_start: 0.8617 (t80) cc_final: 0.8245 (t80) REVERT: C 299 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8902 (mp0) REVERT: C 404 GLU cc_start: 0.9280 (tp30) cc_final: 0.8795 (tp30) REVERT: C 486 GLU cc_start: 0.9358 (tp30) cc_final: 0.9048 (tm-30) REVERT: C 665 LEU cc_start: 0.8880 (tp) cc_final: 0.8665 (mt) REVERT: C 718 GLU cc_start: 0.6430 (tp30) cc_final: 0.6032 (tp30) REVERT: C 830 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9020 (mtmm) REVERT: D 294 MET cc_start: 0.8850 (tpp) cc_final: 0.8591 (mmt) REVERT: D 722 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8868 (mmmm) REVERT: E 299 GLU cc_start: 0.9035 (mp0) cc_final: 0.8800 (mp0) REVERT: E 395 GLU cc_start: 0.9068 (tp30) cc_final: 0.8665 (tp30) REVERT: E 439 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8554 (ttmm) REVERT: E 452 MET cc_start: 0.9473 (ptt) cc_final: 0.9163 (ptp) REVERT: E 684 LYS cc_start: 0.9470 (ttpp) cc_final: 0.9238 (mtpp) REVERT: E 707 GLU cc_start: 0.8863 (pp20) cc_final: 0.8153 (pp20) REVERT: E 724 GLU cc_start: 0.8484 (tp30) cc_final: 0.8098 (tp30) REVERT: E 948 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.8123 (p0) REVERT: F 551 LEU cc_start: 0.9390 (tp) cc_final: 0.9045 (tp) outliers start: 21 outliers final: 11 residues processed: 311 average time/residue: 0.2407 time to fit residues: 124.2625 Evaluate side-chains 273 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 830 LYS Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 948 ASN Chi-restraints excluded: chain F residue 836 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 384 optimal weight: 50.0000 chunk 395 optimal weight: 0.9990 chunk 541 optimal weight: 7.9990 chunk 401 optimal weight: 0.9990 chunk 525 optimal weight: 20.0000 chunk 257 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 411 optimal weight: 4.9990 chunk 484 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN D 308 ASN E 304 HIS E 437 ASN F 288 HIS F 491 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.112733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069546 restraints weight = 117108.895| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.51 r_work: 0.2817 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41384 Z= 0.117 Angle : 0.457 11.374 56473 Z= 0.246 Chirality : 0.040 0.201 6271 Planarity : 0.004 0.082 7315 Dihedral : 7.449 170.681 5979 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.81 % Allowed : 5.90 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.12), residues: 5450 helix: 2.03 (0.10), residues: 2506 sheet: 0.50 (0.20), residues: 678 loop : 0.28 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 779 TYR 0.044 0.001 TYR F 853 PHE 0.013 0.001 PHE C 817 TRP 0.025 0.001 TRP B 865 HIS 0.030 0.001 HIS F 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (41384) covalent geometry : angle 0.45708 / 0.25 (56473) hydrogen bonds : bond 0.03595 / 2.62 ( 2155) hydrogen bonds : angle 4.42479 / 3.23 ( 6240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 HIS cc_start: 0.9123 (m90) cc_final: 0.8661 (m90) REVERT: A 294 MET cc_start: 0.7794 (mmm) cc_final: 0.6898 (mmt) REVERT: A 439 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8823 (mttm) REVERT: A 721 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6537 (mp10) REVERT: A 862 TYR cc_start: 0.8723 (t80) cc_final: 0.8497 (t80) REVERT: A 878 LEU cc_start: 0.9267 (pp) cc_final: 0.9012 (tp) REVERT: C 404 GLU cc_start: 0.9333 (tp30) cc_final: 0.8702 (tp30) REVERT: C 486 GLU cc_start: 0.9345 (tp30) cc_final: 0.9054 (tm-30) REVERT: C 665 LEU cc_start: 0.8922 (tp) cc_final: 0.8638 (mt) REVERT: C 830 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9097 (mtmm) REVERT: D 294 MET cc_start: 0.8824 (tpp) cc_final: 0.8579 (mmt) REVERT: D 395 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9012 (mt-10) REVERT: D 722 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8885 (mmmm) REVERT: E 299 GLU cc_start: 0.9095 (mp0) cc_final: 0.8849 (mp0) REVERT: E 395 GLU cc_start: 0.9158 (tp30) cc_final: 0.8634 (tp30) REVERT: E 439 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8634 (ttmm) REVERT: E 681 MET cc_start: 0.8806 (tpp) cc_final: 0.8163 (tpp) REVERT: E 707 GLU cc_start: 0.8697 (pp20) cc_final: 0.7999 (pp20) REVERT: E 724 GLU cc_start: 0.8485 (tp30) cc_final: 0.7603 (pm20) REVERT: F 371 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8133 (tttt) REVERT: F 404 GLU cc_start: 0.9275 (tp30) cc_final: 0.8942 (tp30) REVERT: F 786 MET cc_start: 0.9206 (mmm) cc_final: 0.8801 (tmm) REVERT: F 853 TYR cc_start: 0.5641 (m-80) cc_final: 0.4807 (m-10) outliers start: 28 outliers final: 13 residues processed: 301 average time/residue: 0.2306 time to fit residues: 116.5648 Evaluate side-chains 268 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 252 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 830 LYS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 371 LYS Chi-restraints excluded: chain F residue 836 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 129 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 369 optimal weight: 30.0000 chunk 522 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 12 optimal weight: 0.0060 chunk 96 optimal weight: 50.0000 chunk 20 optimal weight: 40.0000 chunk 272 optimal weight: 10.0000 chunk 99 optimal weight: 50.0000 chunk 45 optimal weight: 0.9980 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 HIS ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 HIS B 542 GLN D 389 GLN E 304 HIS F 288 HIS F 640 ASN F 836 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.111953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068233 restraints weight = 116117.882| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.57 r_work: 0.2792 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41384 Z= 0.130 Angle : 0.458 9.026 56473 Z= 0.243 Chirality : 0.040 0.208 6271 Planarity : 0.003 0.095 7315 Dihedral : 7.336 167.832 5977 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.90 % Allowed : 6.94 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.12), residues: 5450 helix: 2.12 (0.10), residues: 2512 sheet: 0.43 (0.19), residues: 702 loop : 0.29 (0.14), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 907 TYR 0.022 0.001 TYR F 853 PHE 0.014 0.001 PHE C 817 TRP 0.021 0.001 TRP B 865 HIS 0.011 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (41384) covalent geometry : angle 0.45777 / 0.24 (56473) hydrogen bonds : bond 0.03403 / 2.48 ( 2155) hydrogen bonds : angle 4.23348 / 3.10 ( 6240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 1.084 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 288 HIS cc_start: 0.9130 (m90) cc_final: 0.8662 (m90) REVERT: A 294 MET cc_start: 0.8070 (mmm) cc_final: 0.7825 (mmm) REVERT: A 439 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8869 (mttm) REVERT: A 721 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: A 878 LEU cc_start: 0.9283 (pp) cc_final: 0.8997 (tp) REVERT: C 404 GLU cc_start: 0.9332 (tp30) cc_final: 0.8717 (tp30) REVERT: C 486 GLU cc_start: 0.9342 (tp30) cc_final: 0.9139 (tm-30) REVERT: C 665 LEU cc_start: 0.8993 (tp) cc_final: 0.8738 (mt) REVERT: C 830 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9107 (mtmm) REVERT: E 299 GLU cc_start: 0.9112 (mp0) cc_final: 0.8849 (mp0) REVERT: E 439 LYS cc_start: 0.8991 (ttmm) cc_final: 0.8706 (ttmm) REVERT: E 707 GLU cc_start: 0.8546 (pp20) cc_final: 0.8219 (pp20) REVERT: E 724 GLU cc_start: 0.8523 (tp30) cc_final: 0.8269 (tp30) REVERT: F 371 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8229 (tttt) REVERT: F 417 MET cc_start: 0.9388 (mtt) cc_final: 0.8919 (mtm) REVERT: F 786 MET cc_start: 0.9208 (mmm) cc_final: 0.8797 (tmm) REVERT: F 853 TYR cc_start: 0.5519 (m-80) cc_final: 0.4514 (m-10) REVERT: F 866 TYR cc_start: 0.8458 (t80) cc_final: 0.8096 (t80) outliers start: 31 outliers final: 15 residues processed: 286 average time/residue: 0.2193 time to fit residues: 105.1844 Evaluate side-chains 261 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 830 LYS Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 371 LYS Chi-restraints excluded: chain F residue 642 LYS Chi-restraints excluded: chain F residue 836 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 77 optimal weight: 0.7980 chunk 412 optimal weight: 4.9990 chunk 309 optimal weight: 0.8980 chunk 10 optimal weight: 50.0000 chunk 506 optimal weight: 3.9990 chunk 350 optimal weight: 0.9980 chunk 397 optimal weight: 4.9990 chunk 106 optimal weight: 50.0000 chunk 411 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 281 optimal weight: 30.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN C 308 ASN F 288 HIS ** F 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.111876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.067829 restraints weight = 116770.089| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.57 r_work: 0.2791 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41384 Z= 0.123 Angle : 0.445 9.860 56473 Z= 0.236 Chirality : 0.040 0.185 6271 Planarity : 0.003 0.080 7315 Dihedral : 7.257 165.143 5977 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.67 % Allowed : 7.84 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.12), residues: 5450 helix: 2.17 (0.10), residues: 2519 sheet: 0.45 (0.20), residues: 695 loop : 0.28 (0.14), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 837 TYR 0.021 0.001 TYR F 853 PHE 0.013 0.001 PHE C 817 TRP 0.023 0.001 TRP B 865 HIS 0.005 0.001 HIS F 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (41384) covalent geometry : angle 0.44500 / 0.24 (56473) hydrogen bonds : bond 0.03291 / 2.40 ( 2155) hydrogen bonds : angle 4.12818 / 3.03 ( 6240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 1.470 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 288 HIS cc_start: 0.9166 (m90) cc_final: 0.8695 (m90) REVERT: A 294 MET cc_start: 0.8345 (mmm) cc_final: 0.8135 (mmm) REVERT: A 439 LYS cc_start: 0.9137 (mtpp) cc_final: 0.8870 (mttm) REVERT: A 721 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6676 (mp10) REVERT: A 878 LEU cc_start: 0.9230 (pp) cc_final: 0.8922 (tp) REVERT: B 299 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8909 (mm-30) REVERT: C 299 GLU cc_start: 0.9162 (mp0) cc_final: 0.8947 (mp0) REVERT: C 404 GLU cc_start: 0.9334 (tp30) cc_final: 0.8743 (tp30) REVERT: C 665 LEU cc_start: 0.9030 (tp) cc_final: 0.8784 (mt) REVERT: C 830 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9078 (mtmm) REVERT: D 883 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8775 (mm-30) REVERT: E 299 GLU cc_start: 0.9190 (mp0) cc_final: 0.8945 (mp0) REVERT: E 439 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8678 (ttmm) REVERT: E 707 GLU cc_start: 0.8460 (pp20) cc_final: 0.7957 (pp20) REVERT: E 724 GLU cc_start: 0.8526 (tp30) cc_final: 0.8156 (tp30) REVERT: F 371 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8236 (ttpt) REVERT: F 417 MET cc_start: 0.9394 (mtt) cc_final: 0.8991 (mtm) REVERT: F 786 MET cc_start: 0.9153 (mmm) cc_final: 0.8778 (tmm) REVERT: F 853 TYR cc_start: 0.6369 (m-80) cc_final: 0.5524 (m-10) REVERT: F 866 TYR cc_start: 0.8549 (t80) cc_final: 0.8213 (t80) outliers start: 23 outliers final: 14 residues processed: 272 average time/residue: 0.2113 time to fit residues: 96.4279 Evaluate side-chains 258 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 830 LYS Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 684 LYS Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 371 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 18 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 213 optimal weight: 0.0980 chunk 338 optimal weight: 20.0000 chunk 247 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 425 optimal weight: 10.0000 chunk 272 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 328 optimal weight: 0.7980 chunk 294 optimal weight: 40.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 HIS ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN C 476 ASN F 288 HIS F 389 GLN F 836 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.112432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.068494 restraints weight = 116279.190| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.57 r_work: 0.2798 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 41384 Z= 0.092 Angle : 0.430 10.265 56473 Z= 0.227 Chirality : 0.039 0.166 6271 Planarity : 0.003 0.078 7315 Dihedral : 7.152 162.296 5977 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.75 % Allowed : 8.33 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.12), residues: 5450 helix: 2.29 (0.10), residues: 2509 sheet: 0.48 (0.21), residues: 644 loop : 0.31 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 670 TYR 0.027 0.001 TYR A 302 PHE 0.013 0.001 PHE E 477 TRP 0.018 0.001 TRP B 865 HIS 0.006 0.001 HIS E 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (41384) covalent geometry : angle 0.43005 / 0.23 (56473) hydrogen bonds : bond 0.02984 / 2.18 ( 2155) hydrogen bonds : angle 3.97693 / 2.91 ( 6240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 253 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 HIS cc_start: 0.9144 (m90) cc_final: 0.8668 (m90) REVERT: A 439 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8885 (mttp) REVERT: A 721 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6626 (mp10) REVERT: A 878 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8922 (tp) REVERT: B 299 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8823 (mp0) REVERT: C 299 GLU cc_start: 0.9166 (mp0) cc_final: 0.8936 (mp0) REVERT: C 404 GLU cc_start: 0.9317 (tp30) cc_final: 0.8753 (tp30) REVERT: C 665 LEU cc_start: 0.9005 (tp) cc_final: 0.8769 (mt) REVERT: C 830 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9061 (mtmm) REVERT: C 906 CYS cc_start: 0.5266 (m) cc_final: 0.4504 (m) REVERT: D 395 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8988 (mt-10) REVERT: E 299 GLU cc_start: 0.9200 (mp0) cc_final: 0.8958 (mp0) REVERT: E 439 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8695 (ttmm) REVERT: E 707 GLU cc_start: 0.8351 (pp20) cc_final: 0.8072 (pp20) REVERT: E 724 GLU cc_start: 0.8535 (tp30) cc_final: 0.8136 (tp30) REVERT: F 371 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8261 (ttpt) REVERT: F 404 GLU cc_start: 0.9295 (tp30) cc_final: 0.8986 (tp30) REVERT: F 417 MET cc_start: 0.9374 (mtt) cc_final: 0.8880 (mtm) REVERT: F 786 MET cc_start: 0.9158 (mmm) cc_final: 0.8769 (tmm) REVERT: F 836 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7106 (t-170) REVERT: F 853 TYR cc_start: 0.6402 (m-80) cc_final: 0.5713 (m-10) REVERT: F 866 TYR cc_start: 0.8551 (t80) cc_final: 0.8210 (t80) outliers start: 26 outliers final: 13 residues processed: 271 average time/residue: 0.2040 time to fit residues: 93.4505 Evaluate side-chains 250 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 830 LYS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 371 LYS Chi-restraints excluded: chain F residue 642 LYS Chi-restraints excluded: chain F residue 836 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 273 optimal weight: 40.0000 chunk 306 optimal weight: 6.9990 chunk 456 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 531 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 294 optimal weight: 0.3980 chunk 505 optimal weight: 2.9990 chunk 480 optimal weight: 0.0020 chunk 173 optimal weight: 7.9990 chunk 276 optimal weight: 40.0000 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 HIS B 542 GLN D 695 ASN F 288 HIS F 487 HIS F 491 HIS F 836 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.112155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068292 restraints weight = 116078.339| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.55 r_work: 0.2794 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 41384 Z= 0.100 Angle : 0.432 8.980 56473 Z= 0.227 Chirality : 0.039 0.165 6271 Planarity : 0.003 0.076 7315 Dihedral : 7.116 160.698 5977 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.69 % Allowed : 8.74 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.12), residues: 5450 helix: 2.31 (0.10), residues: 2518 sheet: 0.48 (0.20), residues: 656 loop : 0.33 (0.14), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 829 TYR 0.033 0.001 TYR A 302 PHE 0.012 0.001 PHE C 817 TRP 0.026 0.001 TRP B 865 HIS 0.018 0.001 HIS F 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (41384) covalent geometry : angle 0.43193 / 0.23 (56473) hydrogen bonds : bond 0.02955 / 2.16 ( 2155) hydrogen bonds : angle 3.93678 / 2.88 ( 6240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 1.436 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 288 HIS cc_start: 0.9164 (m90) cc_final: 0.8691 (m90) REVERT: A 439 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8886 (mttp) REVERT: A 721 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: A 878 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8920 (tp) REVERT: B 299 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8852 (mp0) REVERT: C 299 GLU cc_start: 0.9168 (mp0) cc_final: 0.8934 (mp0) REVERT: C 404 GLU cc_start: 0.9299 (tp30) cc_final: 0.8742 (tp30) REVERT: C 665 LEU cc_start: 0.9013 (tp) cc_final: 0.8785 (mt) REVERT: C 830 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9054 (mtmm) REVERT: C 906 CYS cc_start: 0.5286 (m) cc_final: 0.4400 (m) REVERT: D 395 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8887 (mt-10) REVERT: E 299 GLU cc_start: 0.9231 (mp0) cc_final: 0.8990 (mp0) REVERT: E 439 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8698 (ttmm) REVERT: E 707 GLU cc_start: 0.8240 (pp20) cc_final: 0.8007 (pp20) REVERT: E 724 GLU cc_start: 0.8546 (tp30) cc_final: 0.8173 (tp30) REVERT: F 371 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8268 (ttpt) REVERT: F 372 LYS cc_start: 0.9288 (mmtp) cc_final: 0.8601 (tptt) REVERT: F 417 MET cc_start: 0.9404 (mtt) cc_final: 0.8934 (mtm) REVERT: F 745 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8072 (m) REVERT: F 786 MET cc_start: 0.9115 (mmm) cc_final: 0.8752 (tmm) REVERT: F 853 TYR cc_start: 0.6461 (m-80) cc_final: 0.5768 (m-10) REVERT: F 866 TYR cc_start: 0.8591 (t80) cc_final: 0.8251 (t80) outliers start: 24 outliers final: 13 residues processed: 252 average time/residue: 0.2266 time to fit residues: 96.8938 Evaluate side-chains 249 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 830 LYS Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 371 LYS Chi-restraints excluded: chain F residue 745 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 165 optimal weight: 0.4980 chunk 251 optimal weight: 0.9980 chunk 456 optimal weight: 0.8980 chunk 332 optimal weight: 0.9990 chunk 393 optimal weight: 0.0770 chunk 504 optimal weight: 0.9990 chunk 477 optimal weight: 50.0000 chunk 15 optimal weight: 0.0770 chunk 74 optimal weight: 0.1980 chunk 275 optimal weight: 50.0000 chunk 40 optimal weight: 0.9980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 542 GLN F 288 HIS F 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.112703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069486 restraints weight = 116237.555| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.53 r_work: 0.2824 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 41384 Z= 0.076 Angle : 0.418 7.940 56473 Z= 0.220 Chirality : 0.039 0.203 6271 Planarity : 0.003 0.073 7315 Dihedral : 7.031 159.008 5977 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.58 % Allowed : 9.00 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.12), residues: 5450 helix: 2.37 (0.10), residues: 2512 sheet: 0.47 (0.19), residues: 723 loop : 0.40 (0.14), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 513 TYR 0.021 0.001 TYR D 302 PHE 0.013 0.001 PHE D 817 TRP 0.022 0.001 TRP B 865 HIS 0.004 0.000 HIS D 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00154 / 0.08 (41384) covalent geometry : angle 0.41823 / 0.22 (56473) hydrogen bonds : bond 0.02679 / 1.96 ( 2155) hydrogen bonds : angle 3.82988 / 2.80 ( 6240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 1.511 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 288 HIS cc_start: 0.9145 (m90) cc_final: 0.8670 (m90) REVERT: A 439 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8893 (mttp) REVERT: A 721 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6675 (mp10) REVERT: A 878 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8911 (tp) REVERT: B 299 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8846 (mp0) REVERT: C 294 MET cc_start: 0.8211 (mmt) cc_final: 0.7989 (mmt) REVERT: C 299 GLU cc_start: 0.9153 (mp0) cc_final: 0.8918 (mp0) REVERT: C 404 GLU cc_start: 0.9263 (tp30) cc_final: 0.8705 (tp30) REVERT: C 665 LEU cc_start: 0.8974 (tp) cc_final: 0.8759 (mt) REVERT: C 830 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9057 (mtmm) REVERT: C 906 CYS cc_start: 0.5172 (m) cc_final: 0.4331 (m) REVERT: D 395 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8877 (mt-10) REVERT: D 866 TYR cc_start: 0.9290 (t80) cc_final: 0.9048 (t80) REVERT: E 299 GLU cc_start: 0.9231 (mp0) cc_final: 0.8994 (mp0) REVERT: E 439 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8685 (ttmm) REVERT: E 707 GLU cc_start: 0.8139 (pp20) cc_final: 0.7939 (pp20) REVERT: E 724 GLU cc_start: 0.8537 (tp30) cc_final: 0.8177 (tp30) REVERT: F 371 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8284 (ttpt) REVERT: F 372 LYS cc_start: 0.9270 (mmtp) cc_final: 0.8606 (tptt) REVERT: F 404 GLU cc_start: 0.9286 (tp30) cc_final: 0.8980 (tp30) REVERT: F 417 MET cc_start: 0.9388 (mtt) cc_final: 0.8904 (mtm) REVERT: F 745 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.7980 (m) REVERT: F 786 MET cc_start: 0.9098 (mmm) cc_final: 0.8716 (tmm) REVERT: F 853 TYR cc_start: 0.6464 (m-80) cc_final: 0.5790 (m-10) REVERT: F 866 TYR cc_start: 0.8580 (t80) cc_final: 0.8243 (t80) outliers start: 20 outliers final: 10 residues processed: 258 average time/residue: 0.2186 time to fit residues: 96.2122 Evaluate side-chains 253 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 830 LYS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 684 LYS Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 371 LYS Chi-restraints excluded: chain F residue 745 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 64 optimal weight: 4.9990 chunk 356 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 373 optimal weight: 7.9990 chunk 426 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 50 optimal weight: 0.9990 chunk 463 optimal weight: 50.0000 chunk 215 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 886 ASN B 542 GLN F 288 HIS F 491 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.111098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067288 restraints weight = 116674.532| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.52 r_work: 0.2772 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41384 Z= 0.132 Angle : 0.452 8.732 56473 Z= 0.236 Chirality : 0.040 0.146 6271 Planarity : 0.003 0.073 7315 Dihedral : 7.089 157.018 5977 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.58 % Allowed : 9.17 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 2.01 (0.12), residues: 5450 helix: 2.40 (0.10), residues: 2518 sheet: 0.48 (0.19), residues: 746 loop : 0.47 (0.14), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.021 0.001 TYR A 302 PHE 0.012 0.001 PHE C 817 TRP 0.034 0.001 TRP B 865 HIS 0.005 0.001 HIS E 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (41384) covalent geometry : angle 0.45197 / 0.24 (56473) hydrogen bonds : bond 0.03126 / 2.28 ( 2155) hydrogen bonds : angle 3.92023 / 2.87 ( 6240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 1.561 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 288 HIS cc_start: 0.9166 (m90) cc_final: 0.8673 (m-70) REVERT: A 439 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8910 (mttp) REVERT: A 721 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: A 878 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8926 (tp) REVERT: B 299 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8882 (mp0) REVERT: B 693 GLU cc_start: 0.7837 (mp0) cc_final: 0.7583 (mp0) REVERT: C 299 GLU cc_start: 0.9156 (mp0) cc_final: 0.8923 (mp0) REVERT: C 404 GLU cc_start: 0.9285 (tp30) cc_final: 0.8748 (tp30) REVERT: C 665 LEU cc_start: 0.9106 (tp) cc_final: 0.8874 (mt) REVERT: D 866 TYR cc_start: 0.9268 (t80) cc_final: 0.9000 (t80) REVERT: E 299 GLU cc_start: 0.9218 (mp0) cc_final: 0.8926 (mp0) REVERT: E 439 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8733 (ttmm) REVERT: E 707 GLU cc_start: 0.8181 (pp20) cc_final: 0.7850 (pp20) REVERT: E 724 GLU cc_start: 0.8563 (tp30) cc_final: 0.8224 (tp30) REVERT: E 769 ASN cc_start: 0.8618 (m-40) cc_final: 0.8399 (t0) REVERT: F 371 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8304 (ttpt) REVERT: F 372 LYS cc_start: 0.9269 (mmtp) cc_final: 0.8594 (tptt) REVERT: F 417 MET cc_start: 0.9428 (mtt) cc_final: 0.9027 (mtm) REVERT: F 461 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.7607 (ptp-170) REVERT: F 708 MET cc_start: 0.8661 (tpp) cc_final: 0.8402 (tpp) REVERT: F 745 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8153 (m) REVERT: F 786 MET cc_start: 0.9195 (mmm) cc_final: 0.8817 (tmm) REVERT: F 853 TYR cc_start: 0.6466 (m-80) cc_final: 0.5797 (m-10) REVERT: F 866 TYR cc_start: 0.8608 (t80) cc_final: 0.8267 (t80) outliers start: 20 outliers final: 10 residues processed: 255 average time/residue: 0.2316 time to fit residues: 100.7735 Evaluate side-chains 246 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 684 LYS Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 371 LYS Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 745 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 96 optimal weight: 40.0000 chunk 536 optimal weight: 8.9990 chunk 475 optimal weight: 50.0000 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 539 optimal weight: 10.0000 chunk 19 optimal weight: 40.0000 chunk 135 optimal weight: 0.7980 chunk 325 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 542 GLN B 577 HIS C 308 ASN D 487 HIS D 940 ASN E 487 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.109269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065695 restraints weight = 117194.847| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.47 r_work: 0.2740 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 41384 Z= 0.233 Angle : 0.527 12.911 56473 Z= 0.275 Chirality : 0.042 0.212 6271 Planarity : 0.004 0.085 7315 Dihedral : 7.250 152.160 5977 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.46 % Allowed : 9.35 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.12), residues: 5450 helix: 2.25 (0.10), residues: 2512 sheet: 0.43 (0.20), residues: 708 loop : 0.35 (0.14), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.024 0.001 TYR A 302 PHE 0.014 0.001 PHE C 817 TRP 0.036 0.001 TRP B 865 HIS 0.005 0.001 HIS E 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (41384) covalent geometry : angle 0.52701 / 0.27 (56473) hydrogen bonds : bond 0.03844 / 2.81 ( 2155) hydrogen bonds : angle 4.15964 / 3.05 ( 6240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 1.560 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 288 HIS cc_start: 0.9158 (m90) cc_final: 0.8658 (m-70) REVERT: A 439 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8924 (mttp) REVERT: A 721 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6713 (mp10) REVERT: A 878 LEU cc_start: 0.9242 (pp) cc_final: 0.8923 (tp) REVERT: B 299 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8955 (mp0) REVERT: B 693 GLU cc_start: 0.7974 (mp0) cc_final: 0.7759 (mp0) REVERT: B 696 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8931 (ttmm) REVERT: C 299 GLU cc_start: 0.9149 (mp0) cc_final: 0.8916 (mp0) REVERT: C 404 GLU cc_start: 0.9329 (tp30) cc_final: 0.8883 (tp30) REVERT: D 299 GLU cc_start: 0.9032 (mp0) cc_final: 0.8768 (mp0) REVERT: E 299 GLU cc_start: 0.9245 (mp0) cc_final: 0.8928 (mp0) REVERT: E 379 MET cc_start: 0.9490 (mtp) cc_final: 0.9192 (mtm) REVERT: E 724 GLU cc_start: 0.8599 (tp30) cc_final: 0.8302 (tp30) REVERT: E 769 ASN cc_start: 0.8698 (m-40) cc_final: 0.8489 (t0) REVERT: F 371 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8328 (tttt) REVERT: F 372 LYS cc_start: 0.9266 (mmtp) cc_final: 0.8641 (tptt) REVERT: F 417 MET cc_start: 0.9475 (mtt) cc_final: 0.9096 (mtm) REVERT: F 461 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.7745 (ptp-170) REVERT: F 853 TYR cc_start: 0.6197 (m-80) cc_final: 0.5506 (m-10) REVERT: F 866 TYR cc_start: 0.8660 (t80) cc_final: 0.8402 (t80) outliers start: 16 outliers final: 10 residues processed: 243 average time/residue: 0.2318 time to fit residues: 95.6186 Evaluate side-chains 240 residues out of total 4948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 684 LYS Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 371 LYS Chi-restraints excluded: chain F residue 461 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 190 optimal weight: 50.0000 chunk 199 optimal weight: 0.9990 chunk 386 optimal weight: 50.0000 chunk 52 optimal weight: 3.9990 chunk 347 optimal weight: 0.7980 chunk 421 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 2 optimal weight: 40.0000 chunk 324 optimal weight: 0.7980 chunk 273 optimal weight: 30.0000 chunk 159 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 487 HIS B 542 GLN E 487 HIS F 491 HIS ** F 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.110917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067168 restraints weight = 116416.817| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.56 r_work: 0.2774 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41384 Z= 0.121 Angle : 0.462 12.283 56473 Z= 0.242 Chirality : 0.040 0.151 6271 Planarity : 0.003 0.078 7315 Dihedral : 7.120 147.370 5977 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.43 % Allowed : 9.32 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.12), residues: 5450 helix: 2.35 (0.10), residues: 2502 sheet: 0.46 (0.20), residues: 687 loop : 0.38 (0.14), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.018 0.001 TYR A 302 PHE 0.013 0.001 PHE D 817 TRP 0.033 0.001 TRP B 865 HIS 0.017 0.001 HIS F 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (41384) covalent geometry : angle 0.46243 / 0.24 (56473) hydrogen bonds : bond 0.03258 / 2.38 ( 2155) hydrogen bonds : angle 3.97209 / 2.91 ( 6240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12540.25 seconds wall clock time: 214 minutes 26.16 seconds (12866.16 seconds total)